In order to characterize the structural elements that might play a role in non-covalent DNA binding by the antitumor antibiotic leinamycin, we have solved the crystal structures of the two leinamycin analogs, methyl (R)-5-{2-[1-(tert-butoxycarbonylamino)ethyl]thiazol-4-yl}penta-(E,E)-2,4-dienoate, C16H22N2O4S, (II), and 2-methyl-8-oxa-16-thia-3,17-diazabicyclo[12.2.1]heptadeca-(Z,E)-1(17),10,12,14-tetraene-4,9-dione, C14H16N2O3S, (III). The penta-2,4-dienone moiety in both of these analogs adopts a conformation close to planarity, with the thiazole ring twisted out of the plane by 12.9 (2)° in (II) and by 21.4 (4)° in (III).
Supporting information
CCDC references: 193413; 193414
Compounds (II) and (III) were prepared from (R)—N-Boc alanine, and
their synthesis will be described separately. Racemization of compound (III)
occurred in the course of the synthesis. Crystals suitable for X-ray
diffraction analysis were obtained by slow evaporation of dichloromethane
solutions of the compounds.
H atoms were placed at calculated positions and were updated with each cycle of
refinement, but not refined. The C—H distances were fixed in the range
0.95–1.00 Å and N—H distances were fixed at 0.88 Å. The displacement
parameters were fixed at 1.2 times the equivalent isotropic factor for the
parent atom.
For both compounds, data collection: SMART (Bruker, 1998); cell refinement: SAINT (Bruker, 1998); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: ORTEPIII (Burnett & Johnson, 1996); software used to prepare material for publication: CIFTAB (Sheldrick, 1997).
(II) Methyl
(
R)-5-{2-[1-(
tert-butoxycarbonylamino)ethyl]-thiazol-4-yl}-penta- (E,
E)-2,4-dienoate
top
Crystal data top
C16H22N2O4S | Z = 1 |
Mr = 338.42 | F(000) = 180 |
Triclinic, P1 | Dx = 1.278 Mg m−3 |
a = 5.207 (2) Å | Mo Kα radiation, λ = 0.71070 Å |
b = 5.876 (3) Å | Cell parameters from 2894 reflections |
c = 15.339 (7) Å | θ = 2.7–27.1° |
α = 82.21 (1)° | µ = 0.20 mm−1 |
β = 81.43 (1)° | T = 173 K |
γ = 72.17 (1)° | Prism, yellow |
V = 439.8 (3) Å3 | 0.45 × 0.35 × 0.35 mm |
Data collection top
Bruker SMART CCD area-detector diffractometer | 2820 independent reflections |
Radiation source: fine-focus sealed tube | 2702 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.019 |
ω scans | θmax = 27.1°, θmin = 1.4° |
Absorption correction: multi-scan (SADABS; Blessing, 1995) | h = −6→6 |
Tmin = 0.89, Tmax = 0.94 | k = −7→7 |
3484 measured reflections | l = −19→16 |
Refinement top
Refinement on F2 | Secondary atom site location: difference Fourier map |
Least-squares matrix: full | Hydrogen site location: inferred from neighbouring sites |
R[F2 > 2σ(F2)] = 0.035 | H-atom parameters constrained |
wR(F2) = 0.100 | w = 1/[σ2(Fo2) + (0.0665P)2 + 0.0536P] where P = (Fo2 + 2Fc2)/3 |
S = 1.12 | (Δ/σ)max < 0.001 |
2820 reflections | Δρmax = 0.25 e Å−3 |
213 parameters | Δρmin = −0.26 e Å−3 |
3 restraints | Absolute structure: Flack (1983); 908 Friedel pairs |
Primary atom site location: structure-invariant direct methods | Absolute structure parameter: 0.07 (7) |
Crystal data top
C16H22N2O4S | γ = 72.17 (1)° |
Mr = 338.42 | V = 439.8 (3) Å3 |
Triclinic, P1 | Z = 1 |
a = 5.207 (2) Å | Mo Kα radiation |
b = 5.876 (3) Å | µ = 0.20 mm−1 |
c = 15.339 (7) Å | T = 173 K |
α = 82.21 (1)° | 0.45 × 0.35 × 0.35 mm |
β = 81.43 (1)° | |
Data collection top
Bruker SMART CCD area-detector diffractometer | 2820 independent reflections |
Absorption correction: multi-scan (SADABS; Blessing, 1995) | 2702 reflections with I > 2σ(I) |
Tmin = 0.89, Tmax = 0.94 | Rint = 0.019 |
3484 measured reflections | |
Refinement top
R[F2 > 2σ(F2)] = 0.035 | H-atom parameters constrained |
wR(F2) = 0.100 | Δρmax = 0.25 e Å−3 |
S = 1.12 | Δρmin = −0.26 e Å−3 |
2820 reflections | Absolute structure: Flack (1983); 908 Friedel pairs |
213 parameters | Absolute structure parameter: 0.07 (7) |
3 restraints | |
Special details top
Geometry. All e.s.d.'s (except the e.s.d. in the dihedral angle between two l.s. planes)
are estimated using the full covariance matrix. The cell e.s.d.'s are taken
into account individually in the estimation of e.s.d.'s in distances, angles
and torsion angles; correlations between e.s.d.'s in cell parameters are only
used when they are defined by crystal symmetry. An approximate (isotropic)
treatment of cell e.s.d.'s is used for estimating e.s.d.'s involving l.s.
planes. |
Refinement. Refinement of F2 against ALL reflections. The weighted R-factor
wR and goodness of fit S are based on F2, conventional
R-factors R are based on F, with F set to zero for
negative F2. The threshold expression of F2 >
2σ(F2) is used only for calculating R-factors(gt) etc.
and is not relevant to the choice of reflections for refinement.
R-factors based on F2 are statistically about twice as large
as those based on F, and R- factors based on ALL data will be
even larger. |
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top | x | y | z | Uiso*/Ueq | |
S1 | 0.87448 (9) | 0.75876 (8) | 0.47934 (5) | 0.03525 (16) | |
O1 | 0.6765 (3) | 0.6049 (3) | 0.77640 (12) | 0.0341 (4) | |
N1 | 0.6938 (4) | 0.4313 (3) | 0.43791 (13) | 0.0266 (4) | |
C1 | 0.8123 (4) | 0.4810 (4) | 0.49867 (16) | 0.0253 (4) | |
O2 | 0.4359 (3) | 0.4865 (3) | 0.68712 (13) | 0.0372 (4) | |
N2 | 0.8903 (4) | 0.4308 (3) | 0.65545 (14) | 0.0304 (4) | |
H2 | 1.0354 | 0.4565 | 0.6701 | 0.037* | |
C2 | 0.6438 (5) | 0.6189 (4) | 0.37076 (16) | 0.0282 (5) | |
O3 | −0.0892 (4) | 0.0388 (3) | 0.15064 (14) | 0.0439 (5) | |
C3 | 0.7319 (5) | 0.8076 (4) | 0.38194 (19) | 0.0341 (5) | |
H3 | 0.7166 | 0.9472 | 0.3414 | 0.041* | |
O4 | −0.0580 (5) | 0.3922 (4) | 0.08202 (15) | 0.0538 (6) | |
C4 | 0.9104 (4) | 0.3065 (4) | 0.57729 (16) | 0.0272 (4) | |
H4 | 0.7934 | 0.1964 | 0.5915 | 0.033* | |
C5 | 0.6475 (4) | 0.5067 (4) | 0.70538 (16) | 0.0281 (5) | |
C6 | 0.4403 (5) | 0.6928 (4) | 0.84305 (16) | 0.0305 (5) | |
C7 | 1.2047 (5) | 0.1543 (4) | 0.55458 (17) | 0.0313 (5) | |
H7A | 1.3239 | 0.2583 | 0.5435 | 0.047* | |
H7B | 1.2176 | 0.0736 | 0.5015 | 0.047* | |
H7C | 1.2605 | 0.0338 | 0.6043 | 0.047* | |
C8 | 0.2299 (5) | 0.9053 (4) | 0.79992 (19) | 0.0373 (5) | |
H8A | 0.3203 | 1.0204 | 0.7675 | 0.056* | |
H8B | 0.0923 | 0.9842 | 0.8459 | 0.056* | |
H8C | 0.1427 | 0.8472 | 0.7588 | 0.056* | |
C9 | 0.5663 (6) | 0.7775 (5) | 0.9114 (2) | 0.0436 (6) | |
H9A | 0.6966 | 0.6395 | 0.9396 | 0.065* | |
H9B | 0.4231 | 0.8539 | 0.9565 | 0.065* | |
H9C | 0.6600 | 0.8934 | 0.8821 | 0.065* | |
C10 | 0.3274 (6) | 0.4908 (5) | 0.8847 (2) | 0.0416 (6) | |
H10A | 0.2356 | 0.4454 | 0.8415 | 0.062* | |
H10B | 0.1972 | 0.5436 | 0.9363 | 0.062* | |
H10C | 0.4759 | 0.3522 | 0.9034 | 0.062* | |
C11 | 0.5037 (5) | 0.6039 (4) | 0.29702 (17) | 0.0314 (5) | |
H11 | 0.5043 | 0.7176 | 0.2467 | 0.038* | |
C12 | 0.3743 (5) | 0.4392 (4) | 0.29608 (18) | 0.0303 (5) | |
H12 | 0.3715 | 0.3272 | 0.3468 | 0.036* | |
C13 | 0.2394 (5) | 0.4215 (4) | 0.22320 (17) | 0.0316 (5) | |
H13 | 0.2354 | 0.5379 | 0.1736 | 0.038* | |
C14 | 0.1191 (5) | 0.2518 (4) | 0.22068 (17) | 0.0325 (5) | |
H14 | 0.1203 | 0.1346 | 0.2699 | 0.039* | |
C15 | −0.0152 (5) | 0.2409 (4) | 0.14385 (18) | 0.0334 (5) | |
C16 | −0.2147 (7) | 0.0087 (5) | 0.0766 (2) | 0.0479 (7) | |
H16A | −0.3802 | 0.1423 | 0.0696 | 0.072* | |
H16B | −0.2609 | −0.1431 | 0.0876 | 0.072* | |
H16C | −0.0879 | 0.0065 | 0.0224 | 0.072* | |
Atomic displacement parameters (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
S1 | 0.0336 (3) | 0.0298 (3) | 0.0470 (4) | −0.0127 (2) | −0.0057 (3) | −0.0106 (2) |
O1 | 0.0238 (8) | 0.0504 (9) | 0.0312 (9) | −0.0110 (7) | 0.0002 (7) | −0.0184 (7) |
N1 | 0.0256 (9) | 0.0277 (8) | 0.0280 (10) | −0.0085 (7) | −0.0043 (8) | −0.0052 (7) |
C1 | 0.0201 (10) | 0.0262 (9) | 0.0305 (12) | −0.0081 (7) | 0.0028 (9) | −0.0094 (8) |
O2 | 0.0230 (8) | 0.0555 (10) | 0.0378 (10) | −0.0137 (7) | −0.0012 (7) | −0.0186 (8) |
N2 | 0.0228 (9) | 0.0446 (10) | 0.0287 (11) | −0.0124 (8) | −0.0016 (8) | −0.0151 (8) |
C2 | 0.0241 (11) | 0.0276 (9) | 0.0303 (12) | −0.0042 (8) | −0.0002 (9) | −0.0050 (9) |
O3 | 0.0563 (12) | 0.0407 (9) | 0.0398 (11) | −0.0155 (8) | −0.0178 (9) | −0.0046 (8) |
C3 | 0.0287 (12) | 0.0275 (10) | 0.0444 (15) | −0.0059 (9) | −0.0021 (10) | −0.0053 (10) |
O4 | 0.0709 (15) | 0.0630 (12) | 0.0378 (11) | −0.0326 (11) | −0.0230 (11) | 0.0088 (10) |
C4 | 0.0247 (11) | 0.0344 (10) | 0.0268 (11) | −0.0118 (8) | −0.0025 (9) | −0.0102 (9) |
C5 | 0.0246 (11) | 0.0351 (10) | 0.0272 (12) | −0.0097 (8) | −0.0041 (9) | −0.0076 (9) |
C6 | 0.0269 (11) | 0.0395 (11) | 0.0253 (12) | −0.0077 (9) | 0.0002 (9) | −0.0112 (9) |
C7 | 0.0270 (11) | 0.0357 (11) | 0.0307 (13) | −0.0066 (9) | −0.0024 (9) | −0.0090 (9) |
C8 | 0.0365 (13) | 0.0383 (11) | 0.0361 (14) | −0.0077 (10) | −0.0057 (11) | −0.0056 (10) |
C9 | 0.0333 (14) | 0.0640 (16) | 0.0358 (14) | −0.0098 (12) | −0.0037 (11) | −0.0236 (13) |
C10 | 0.0409 (14) | 0.0437 (13) | 0.0375 (15) | −0.0115 (11) | −0.0003 (11) | −0.0009 (11) |
C11 | 0.0269 (11) | 0.0323 (11) | 0.0313 (12) | −0.0038 (8) | −0.0043 (9) | −0.0013 (9) |
C12 | 0.0243 (11) | 0.0342 (11) | 0.0294 (13) | −0.0031 (8) | −0.0041 (9) | −0.0038 (9) |
C13 | 0.0256 (11) | 0.0384 (11) | 0.0276 (12) | −0.0035 (9) | −0.0036 (9) | −0.0055 (9) |
C14 | 0.0305 (12) | 0.0358 (11) | 0.0275 (12) | −0.0035 (9) | −0.0047 (9) | −0.0031 (9) |
C15 | 0.0287 (12) | 0.0418 (12) | 0.0297 (12) | −0.0079 (9) | −0.0019 (10) | −0.0100 (10) |
C16 | 0.0531 (18) | 0.0556 (15) | 0.0423 (16) | −0.0177 (13) | −0.0128 (14) | −0.0170 (13) |
Geometric parameters (Å, º) top
S1—C3 | 1.717 (3) | C7—H7B | 0.9800 |
S1—C1 | 1.738 (2) | C7—H7C | 0.9800 |
O1—C5 | 1.347 (3) | C8—H8A | 0.9800 |
O1—C6 | 1.484 (3) | C8—H8B | 0.9800 |
N1—C1 | 1.300 (3) | C8—H8C | 0.9800 |
N1—C2 | 1.393 (3) | C9—H9A | 0.9800 |
C1—C4 | 1.515 (3) | C9—H9B | 0.9800 |
O2—C5 | 1.220 (3) | C9—H9C | 0.9800 |
N2—C5 | 1.357 (3) | C10—H10A | 0.9800 |
N2—C4 | 1.461 (3) | C10—H10B | 0.9800 |
N2—H2 | 0.8800 | C10—H10C | 0.9800 |
C2—C3 | 1.363 (3) | C11—C12 | 1.340 (3) |
C2—C11 | 1.460 (3) | C11—H11 | 0.9500 |
O3—C15 | 1.343 (3) | C12—C13 | 1.437 (4) |
O3—C16 | 1.447 (3) | C12—H12 | 0.9500 |
C3—H3 | 0.9500 | C13—C14 | 1.338 (4) |
O4—C15 | 1.205 (3) | C13—H13 | 0.9500 |
C4—C7 | 1.534 (3) | C14—C15 | 1.475 (4) |
C4—H4 | 1.0000 | C14—H14 | 0.9500 |
C6—C10 | 1.508 (4) | C16—H16A | 0.9800 |
C6—C9 | 1.524 (3) | C16—H16B | 0.9800 |
C6—C8 | 1.533 (3) | C16—H16C | 0.9800 |
C7—H7A | 0.9800 | | |
| | | |
C3—S1—C1 | 88.99 (11) | C6—C8—H8B | 109.5 |
C5—O1—C6 | 120.41 (18) | H8A—C8—H8B | 109.5 |
C1—N1—C2 | 110.92 (18) | C6—C8—H8C | 109.5 |
N1—C1—C4 | 123.65 (18) | H8A—C8—H8C | 109.5 |
N1—C1—S1 | 114.85 (17) | H8B—C8—H8C | 109.5 |
C4—C1—S1 | 121.34 (16) | C6—C9—H9A | 109.5 |
C5—N2—C4 | 119.94 (18) | C6—C9—H9B | 109.5 |
C5—N2—H2 | 120.0 | H9A—C9—H9B | 109.5 |
C4—N2—H2 | 120.0 | C6—C9—H9C | 109.5 |
C3—C2—N1 | 114.5 (2) | H9A—C9—H9C | 109.5 |
C3—C2—C11 | 125.5 (2) | H9B—C9—H9C | 109.5 |
N1—C2—C11 | 120.0 (2) | C6—C10—H10A | 109.5 |
C15—O3—C16 | 115.5 (2) | C6—C10—H10B | 109.5 |
C2—C3—S1 | 110.8 (2) | H10A—C10—H10B | 109.5 |
C2—C3—H3 | 124.6 | C6—C10—H10C | 109.5 |
S1—C3—H3 | 124.6 | H10A—C10—H10C | 109.5 |
N2—C4—C1 | 111.60 (18) | H10B—C10—H10C | 109.5 |
N2—C4—C7 | 109.83 (18) | C12—C11—C2 | 123.9 (2) |
C1—C4—C7 | 110.38 (19) | C12—C11—H11 | 118.1 |
N2—C4—H4 | 108.3 | C2—C11—H11 | 118.1 |
C1—C4—H4 | 108.3 | C11—C12—C13 | 124.1 (2) |
C7—C4—H4 | 108.3 | C11—C12—H12 | 117.9 |
O2—C5—O1 | 125.9 (2) | C13—C12—H12 | 117.9 |
O2—C5—N2 | 123.7 (2) | C14—C13—C12 | 124.2 (2) |
O1—C5—N2 | 110.34 (18) | C14—C13—H13 | 117.9 |
O1—C6—C10 | 110.7 (2) | C12—C13—H13 | 117.9 |
O1—C6—C9 | 102.49 (19) | C13—C14—C15 | 122.1 (2) |
C10—C6—C9 | 110.1 (2) | C13—C14—H14 | 119.0 |
O1—C6—C8 | 109.3 (2) | C15—C14—H14 | 119.0 |
C10—C6—C8 | 113.4 (2) | O4—C15—O3 | 122.8 (2) |
C9—C6—C8 | 110.3 (2) | O4—C15—C14 | 125.6 (2) |
C4—C7—H7A | 109.5 | O3—C15—C14 | 111.6 (2) |
C4—C7—H7B | 109.5 | O3—C16—H16A | 109.5 |
H7A—C7—H7B | 109.5 | O3—C16—H16B | 109.5 |
C4—C7—H7C | 109.5 | H16A—C16—H16B | 109.5 |
H7A—C7—H7C | 109.5 | O3—C16—H16C | 109.5 |
H7B—C7—H7C | 109.5 | H16A—C16—H16C | 109.5 |
C6—C8—H8A | 109.5 | H16B—C16—H16C | 109.5 |
| | | |
C2—N1—C1—C4 | −175.7 (2) | C6—O1—C5—N2 | −177.63 (19) |
C2—N1—C1—S1 | −0.3 (2) | C4—N2—C5—O2 | −3.2 (4) |
C3—S1—C1—N1 | −0.47 (18) | C4—N2—C5—O1 | 176.76 (18) |
C3—S1—C1—C4 | 175.11 (19) | C5—O1—C6—C10 | 60.5 (3) |
C1—N1—C2—C3 | 1.1 (3) | C5—O1—C6—C9 | 177.9 (2) |
C1—N1—C2—C11 | −178.0 (2) | C5—O1—C6—C8 | −65.1 (3) |
N1—C2—C3—S1 | −1.5 (3) | C3—C2—C11—C12 | −166.7 (2) |
C11—C2—C3—S1 | 177.62 (18) | N1—C2—C11—C12 | 12.4 (3) |
C1—S1—C3—C2 | 1.07 (19) | C2—C11—C12—C13 | −179.1 (2) |
C5—N2—C4—C1 | 79.8 (3) | C11—C12—C13—C14 | 177.3 (2) |
C5—N2—C4—C7 | −157.4 (2) | C12—C13—C14—C15 | −179.6 (2) |
N1—C1—C4—N2 | −147.7 (2) | C16—O3—C15—O4 | 2.5 (4) |
S1—C1—C4—N2 | 37.1 (2) | C16—O3—C15—C14 | −178.0 (2) |
N1—C1—C4—C7 | 89.9 (3) | C13—C14—C15—O4 | −8.9 (4) |
S1—C1—C4—C7 | −85.3 (2) | C13—C14—C15—O3 | 171.6 (2) |
C6—O1—C5—O2 | 2.3 (3) | | |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
N2—H2···O2i | 0.88 | 2.20 | 3.072 (3) | 170 |
Symmetry code: (i) x+1, y, z. |
(III) 2-methyl-8-oxa-16-thia-3,17-diazabicyclo[12.2.1]heptadeca-(
Z,
E)-
1(17),10,12,14-tetraene-4,9-dione
top
Crystal data top
C14H16N2O3S | F(000) = 308 |
Mr = 292.35 | Dx = 1.355 Mg m−3 |
Monoclinic, Pc | Mo Kα radiation, λ = 0.71073 Å |
a = 10.078 (1) Å | Cell parameters from 2334 reflections |
b = 8.882 (1) Å | θ = 2.3–27.0° |
c = 8.512 (1) Å | µ = 0.23 mm−1 |
β = 109.89 (1)° | T = 173 K |
V = 716.5 (1) Å3 | Plate, colorless |
Z = 2 | 0.4 × 0.3 × 0.1 mm |
Data collection top
Bruker SMART CCD area-detector diffractometer | 2391 independent reflections |
Radiation source: fine-focus sealed tube | 2177 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.023 |
ω scans | θmax = 27.1°, θmin = 2.2° |
Absorption correction: multi-scan (SADABS; Blessing, 1995) | h = −12→12 |
Tmin = 0.77, Tmax = 0.98 | k = −10→11 |
4350 measured reflections | l = −10→8 |
Refinement top
Refinement on F2 | Secondary atom site location: difference Fourier map |
Least-squares matrix: full | Hydrogen site location: inferred from neighbouring sites |
R[F2 > 2σ(F2)] = 0.030 | H-atom parameters constrained |
wR(F2) = 0.070 | w = 1/[σ2(Fo2) + (0.0425P)2] where P = (Fo2 + 2Fc2)/3 |
S = 1.00 | (Δ/σ)max = 0.001 |
2391 reflections | Δρmax = 0.24 e Å−3 |
182 parameters | Δρmin = −0.17 e Å−3 |
2 restraints | Absolute structure: Flack (1983); 812 Friedel pairs |
Primary atom site location: structure-invariant direct methods | Absolute structure parameter: 0.05 (7) |
Crystal data top
C14H16N2O3S | V = 716.5 (1) Å3 |
Mr = 292.35 | Z = 2 |
Monoclinic, Pc | Mo Kα radiation |
a = 10.078 (1) Å | µ = 0.23 mm−1 |
b = 8.882 (1) Å | T = 173 K |
c = 8.512 (1) Å | 0.4 × 0.3 × 0.1 mm |
β = 109.89 (1)° | |
Data collection top
Bruker SMART CCD area-detector diffractometer | 2391 independent reflections |
Absorption correction: multi-scan (SADABS; Blessing, 1995) | 2177 reflections with I > 2σ(I) |
Tmin = 0.77, Tmax = 0.98 | Rint = 0.023 |
4350 measured reflections | |
Refinement top
R[F2 > 2σ(F2)] = 0.030 | H-atom parameters constrained |
wR(F2) = 0.070 | Δρmax = 0.24 e Å−3 |
S = 1.00 | Δρmin = −0.17 e Å−3 |
2391 reflections | Absolute structure: Flack (1983); 812 Friedel pairs |
182 parameters | Absolute structure parameter: 0.05 (7) |
2 restraints | |
Special details top
Geometry. All e.s.d.'s (except the e.s.d. in the dihedral angle between two l.s. planes)
are estimated using the full covariance matrix. The cell e.s.d.'s are taken
into account individually in the estimation of e.s.d.'s in distances, angles
and torsion angles; correlations between e.s.d.'s in cell parameters are only
used when they are defined by crystal symmetry. An approximate (isotropic)
treatment of cell e.s.d.'s is used for estimating e.s.d.'s involving l.s.
planes. |
Refinement. Refinement of F2 against ALL reflections. The weighted R-factor
wR and goodness of fit S are based on F2, conventional
R-factors R are based on F, with F set to zero for
negative F2. The threshold expression of F2 >
σ(F2) is used only for calculating R-factors(gt) etc.
and is not relevant to the choice of reflections for refinement.
R-factors based on F2 are statistically about twice as large
as those based on F, and R- factors based on ALL data will be
even larger. |
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top | x | y | z | Uiso*/Ueq | |
S1 | 0.51970 (6) | 0.85254 (6) | 1.15002 (7) | 0.04036 (15) | |
O1 | 0.04934 (15) | 0.86575 (15) | 1.08613 (18) | 0.0329 (3) | |
O2 | −0.13676 (15) | 0.68768 (17) | 0.67895 (19) | 0.0363 (4) | |
O3 | −0.25950 (17) | 0.5626 (2) | 0.4443 (2) | 0.0533 (5) | |
N1 | 0.30161 (17) | 0.78224 (18) | 0.9008 (2) | 0.0267 (4) | |
N2 | 0.12174 (17) | 1.01991 (17) | 0.9200 (2) | 0.0271 (4) | |
H2 | 0.0982 | 1.0674 | 0.8237 | 0.033* | |
C1 | 0.3492 (2) | 0.8850 (2) | 1.0134 (2) | 0.0263 (4) | |
C2 | 0.5246 (2) | 0.6898 (2) | 1.0447 (3) | 0.0347 (5) | |
H2A | 0.6031 | 0.6235 | 1.0716 | 0.042* | |
C3 | 0.4009 (2) | 0.6681 (2) | 0.9173 (3) | 0.0272 (4) | |
C4 | 0.2678 (2) | 1.0248 (2) | 1.0305 (3) | 0.0287 (4) | |
H4 | 0.2682 | 1.0290 | 1.1480 | 0.034* | |
C5 | 0.0214 (2) | 0.9456 (2) | 0.9595 (3) | 0.0263 (4) | |
C6 | −0.1287 (2) | 0.9748 (2) | 0.8473 (3) | 0.0310 (5) | |
H6A | −0.1289 | 0.9950 | 0.7328 | 0.037* | |
H6B | −0.1633 | 1.0666 | 0.8868 | 0.037* | |
C7 | −0.2317 (2) | 0.8452 (2) | 0.8399 (3) | 0.0327 (5) | |
H7A | −0.1898 | 0.7791 | 0.9380 | 0.039* | |
H7B | −0.3199 | 0.8878 | 0.8479 | 0.039* | |
C8 | −0.2675 (2) | 0.7514 (3) | 0.6841 (3) | 0.0373 (5) | |
H8A | −0.3341 | 0.6703 | 0.6864 | 0.045* | |
H8B | −0.3119 | 0.8146 | 0.5841 | 0.045* | |
C9 | −0.1486 (2) | 0.5900 (2) | 0.5522 (3) | 0.0376 (5) | |
C10 | −0.0128 (2) | 0.5205 (2) | 0.5669 (3) | 0.0366 (5) | |
H10 | −0.0114 | 0.4432 | 0.4903 | 0.044* | |
C11 | 0.1091 (2) | 0.5608 (2) | 0.6829 (3) | 0.0303 (4) | |
H11 | 0.1073 | 0.6405 | 0.7565 | 0.036* | |
C12 | 0.2439 (2) | 0.4907 (2) | 0.7037 (3) | 0.0328 (5) | |
H12 | 0.2430 | 0.4047 | 0.6370 | 0.039* | |
C13 | 0.3699 (2) | 0.5361 (2) | 0.8085 (3) | 0.0317 (5) | |
H13 | 0.4484 | 0.4751 | 0.8124 | 0.038* | |
C14 | 0.3365 (2) | 1.1680 (2) | 0.9974 (3) | 0.0379 (5) | |
H14A | 0.2834 | 1.2556 | 1.0137 | 0.057* | |
H14B | 0.3365 | 1.1671 | 0.8823 | 0.057* | |
H14C | 0.4338 | 1.1737 | 1.0750 | 0.057* | |
Atomic displacement parameters (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
S1 | 0.0263 (3) | 0.0413 (3) | 0.0438 (3) | 0.0004 (2) | −0.0008 (2) | −0.0080 (3) |
O1 | 0.0383 (8) | 0.0337 (8) | 0.0250 (8) | −0.0008 (6) | 0.0085 (7) | 0.0017 (6) |
O2 | 0.0263 (8) | 0.0388 (8) | 0.0397 (9) | 0.0023 (6) | 0.0057 (7) | −0.0088 (7) |
O3 | 0.0357 (9) | 0.0624 (11) | 0.0535 (12) | −0.0078 (8) | 0.0044 (8) | −0.0188 (9) |
N1 | 0.0275 (8) | 0.0237 (8) | 0.0280 (9) | 0.0004 (6) | 0.0083 (7) | 0.0011 (6) |
N2 | 0.0306 (9) | 0.0260 (8) | 0.0242 (9) | 0.0018 (7) | 0.0084 (8) | 0.0009 (7) |
C1 | 0.0270 (10) | 0.0274 (10) | 0.0236 (11) | −0.0022 (8) | 0.0071 (8) | 0.0022 (8) |
C2 | 0.0262 (11) | 0.0330 (11) | 0.0443 (14) | 0.0037 (8) | 0.0113 (10) | 0.0011 (9) |
C3 | 0.0262 (10) | 0.0257 (9) | 0.0326 (11) | 0.0018 (7) | 0.0139 (9) | 0.0035 (8) |
C4 | 0.0305 (10) | 0.0299 (10) | 0.0247 (11) | −0.0001 (8) | 0.0081 (9) | −0.0022 (8) |
C5 | 0.0314 (11) | 0.0234 (9) | 0.0251 (11) | 0.0037 (8) | 0.0107 (9) | −0.0029 (8) |
C6 | 0.0311 (11) | 0.0294 (10) | 0.0336 (12) | 0.0064 (8) | 0.0125 (10) | 0.0043 (9) |
C7 | 0.0255 (10) | 0.0351 (11) | 0.0395 (13) | 0.0061 (8) | 0.0136 (10) | 0.0057 (9) |
C8 | 0.0224 (10) | 0.0387 (12) | 0.0472 (14) | 0.0015 (8) | 0.0071 (10) | −0.0002 (10) |
C9 | 0.0362 (12) | 0.0328 (11) | 0.0408 (14) | −0.0078 (9) | 0.0092 (11) | −0.0055 (10) |
C10 | 0.0401 (12) | 0.0308 (11) | 0.0392 (12) | −0.0037 (9) | 0.0140 (10) | −0.0085 (9) |
C11 | 0.0352 (11) | 0.0240 (9) | 0.0337 (11) | −0.0003 (8) | 0.0142 (10) | −0.0035 (8) |
C12 | 0.0414 (12) | 0.0237 (10) | 0.0364 (12) | 0.0014 (9) | 0.0170 (10) | −0.0044 (9) |
C13 | 0.0335 (11) | 0.0254 (10) | 0.0397 (13) | 0.0059 (8) | 0.0170 (10) | 0.0009 (9) |
C14 | 0.0369 (13) | 0.0289 (11) | 0.0475 (14) | −0.0050 (9) | 0.0138 (11) | −0.0073 (10) |
Geometric parameters (Å, º) top
S1—C2 | 1.711 (2) | C6—H6A | 0.9900 |
S1—C1 | 1.740 (2) | C6—H6B | 0.9900 |
O1—C5 | 1.240 (2) | C7—C8 | 1.503 (3) |
O2—C9 | 1.358 (3) | C7—H7A | 0.9900 |
O2—C8 | 1.448 (3) | C7—H7B | 0.9900 |
O3—C9 | 1.205 (3) | C8—H8A | 0.9900 |
N1—C1 | 1.292 (3) | C8—H8B | 0.9900 |
N1—C3 | 1.397 (2) | C9—C10 | 1.467 (3) |
N2—C5 | 1.342 (2) | C10—C11 | 1.337 (3) |
N2—C4 | 1.453 (2) | C10—H10 | 0.9500 |
N2—H2 | 0.8800 | C11—C12 | 1.449 (3) |
C1—C4 | 1.522 (3) | C11—H11 | 0.9500 |
C2—C3 | 1.359 (3) | C12—C13 | 1.342 (3) |
C2—H2A | 0.9500 | C12—H12 | 0.9500 |
C3—C13 | 1.460 (3) | C13—H13 | 0.9500 |
C4—C14 | 1.520 (3) | C14—H14A | 0.9800 |
C4—H4 | 1.0000 | C14—H14B | 0.9800 |
C5—C6 | 1.511 (3) | C14—H14C | 0.9800 |
C6—C7 | 1.537 (3) | | |
| | | |
C2—S1—C1 | 89.30 (10) | C6—C7—H7A | 108.7 |
C9—O2—C8 | 116.02 (17) | C8—C7—H7B | 108.7 |
C1—N1—C3 | 111.45 (17) | C6—C7—H7B | 108.7 |
C5—N2—C4 | 122.42 (16) | H7A—C7—H7B | 107.6 |
C5—N2—H2 | 118.8 | O2—C8—C7 | 107.20 (17) |
C4—N2—H2 | 118.8 | O2—C8—H8A | 110.3 |
N1—C1—C4 | 124.82 (18) | C7—C8—H8A | 110.3 |
N1—C1—S1 | 114.30 (15) | O2—C8—H8B | 110.3 |
C4—C1—S1 | 120.88 (14) | C7—C8—H8B | 110.3 |
C3—C2—S1 | 110.85 (15) | H8A—C8—H8B | 108.5 |
C3—C2—H2A | 124.6 | O3—C9—O2 | 122.8 (2) |
S1—C2—H2A | 124.6 | O3—C9—C10 | 125.2 (2) |
C2—C3—N1 | 114.10 (17) | O2—C9—C10 | 111.95 (19) |
C2—C3—C13 | 124.04 (18) | C11—C10—C9 | 123.1 (2) |
N1—C3—C13 | 121.84 (18) | C11—C10—H10 | 118.4 |
N2—C4—C14 | 109.28 (17) | C9—C10—H10 | 118.4 |
N2—C4—C1 | 111.98 (15) | C10—C11—C12 | 124.28 (19) |
C14—C4—C1 | 111.77 (17) | C10—C11—H11 | 117.9 |
N2—C4—H4 | 107.9 | C12—C11—H11 | 117.9 |
C14—C4—H4 | 107.9 | C13—C12—C11 | 126.01 (18) |
C1—C4—H4 | 107.9 | C13—C12—H12 | 117.0 |
O1—C5—N2 | 122.09 (18) | C11—C12—H12 | 117.0 |
O1—C5—C6 | 121.98 (18) | C12—C13—C3 | 127.78 (18) |
N2—C5—C6 | 115.78 (17) | C12—C13—H13 | 116.1 |
C5—C6—C7 | 114.49 (16) | C3—C13—H13 | 116.1 |
C5—C6—H6A | 108.6 | C4—C14—H14A | 109.5 |
C7—C6—H6A | 108.6 | C4—C14—H14B | 109.5 |
C5—C6—H6B | 108.6 | H14A—C14—H14B | 109.5 |
C7—C6—H6B | 108.6 | C4—C14—H14C | 109.5 |
H6A—C6—H6B | 107.6 | H14A—C14—H14C | 109.5 |
C8—C7—C6 | 114.05 (18) | H14B—C14—H14C | 109.5 |
C8—C7—H7A | 108.7 | | |
| | | |
C3—N1—C1—C4 | 179.99 (18) | C4—N2—C5—C6 | 169.12 (16) |
C3—N1—C1—S1 | 0.1 (2) | O1—C5—C6—C7 | −31.0 (3) |
C2—S1—C1—N1 | 0.31 (16) | N2—C5—C6—C7 | 153.50 (18) |
C2—S1—C1—C4 | −179.54 (17) | C5—C6—C7—C8 | −102.6 (2) |
C1—S1—C2—C3 | −0.68 (17) | C9—O2—C8—C7 | 175.52 (18) |
S1—C2—C3—N1 | 0.9 (2) | C6—C7—C8—O2 | 60.1 (2) |
S1—C2—C3—C13 | −177.35 (17) | C8—O2—C9—O3 | 3.8 (3) |
C1—N1—C3—C2 | −0.7 (2) | C8—O2—C9—C10 | −174.46 (19) |
C1—N1—C3—C13 | 177.62 (19) | O3—C9—C10—C11 | 175.9 (2) |
C5—N2—C4—C14 | −153.05 (18) | O2—C9—C10—C11 | −6.0 (3) |
C5—N2—C4—C1 | 82.6 (2) | C9—C10—C11—C12 | 177.9 (2) |
N1—C1—C4—N2 | 8.2 (3) | C10—C11—C12—C13 | 173.8 (2) |
S1—C1—C4—N2 | −171.97 (14) | C11—C12—C13—C3 | −3.3 (4) |
N1—C1—C4—C14 | −114.8 (2) | C2—C3—C13—C12 | 165.4 (2) |
S1—C1—C4—C14 | 65.0 (2) | N1—C3—C13—C12 | −12.7 (3) |
C4—N2—C5—O1 | −6.4 (3) | | |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
N2—H2···O1i | 0.88 | 2.00 | 2.869 (2) | 168 |
Symmetry code: (i) x, −y+2, z−1/2. |
Experimental details
| (II) | (III) |
Crystal data |
Chemical formula | C16H22N2O4S | C14H16N2O3S |
Mr | 338.42 | 292.35 |
Crystal system, space group | Triclinic, P1 | Monoclinic, Pc |
Temperature (K) | 173 | 173 |
a, b, c (Å) | 5.207 (2), 5.876 (3), 15.339 (7) | 10.078 (1), 8.882 (1), 8.512 (1) |
α, β, γ (°) | 82.21 (1), 81.43 (1), 72.17 (1) | 90, 109.89 (1), 90 |
V (Å3) | 439.8 (3) | 716.5 (1) |
Z | 1 | 2 |
Radiation type | Mo Kα | Mo Kα |
µ (mm−1) | 0.20 | 0.23 |
Crystal size (mm) | 0.45 × 0.35 × 0.35 | 0.4 × 0.3 × 0.1 |
|
Data collection |
Diffractometer | Bruker SMART CCD area-detector diffractometer | Bruker SMART CCD area-detector diffractometer |
Absorption correction | Multi-scan (SADABS; Blessing, 1995) | Multi-scan (SADABS; Blessing, 1995) |
Tmin, Tmax | 0.89, 0.94 | 0.77, 0.98 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 3484, 2820, 2702 | 4350, 2391, 2177 |
Rint | 0.019 | 0.023 |
(sin θ/λ)max (Å−1) | 0.641 | 0.641 |
|
Refinement |
R[F2 > 2σ(F2)], wR(F2), S | 0.035, 0.100, 1.12 | 0.030, 0.070, 1.00 |
No. of reflections | 2820 | 2391 |
No. of parameters | 213 | 182 |
No. of restraints | 3 | 2 |
H-atom treatment | H-atom parameters constrained | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 0.25, −0.26 | 0.24, −0.17 |
Absolute structure | Flack (1983); 908 Friedel pairs | Flack (1983); 812 Friedel pairs |
Absolute structure parameter | 0.07 (7) | 0.05 (7) |
Selected geometric parameters (Å, º) for (II) topC2—C3 | 1.363 (3) | C12—C13 | 1.437 (4) |
C2—C11 | 1.460 (3) | C13—C14 | 1.338 (4) |
O4—C15 | 1.205 (3) | C14—C15 | 1.475 (4) |
C11—C12 | 1.340 (3) | | |
| | | |
C3—C2—N1 | 114.5 (2) | C14—C13—C12 | 124.2 (2) |
C3—C2—C11 | 125.5 (2) | C13—C14—C15 | 122.1 (2) |
C12—C11—C2 | 123.9 (2) | O4—C15—C14 | 125.6 (2) |
C11—C12—C13 | 124.1 (2) | | |
| | | |
C1—N1—C2—C11 | −178.0 (2) | C2—C11—C12—C13 | −179.1 (2) |
C11—C2—C3—S1 | 177.62 (18) | C11—C12—C13—C14 | 177.3 (2) |
C3—C2—C11—C12 | −166.7 (2) | C12—C13—C14—C15 | −179.6 (2) |
N1—C2—C11—C12 | 12.4 (3) | C13—C14—C15—O4 | −8.9 (4) |
Hydrogen-bond geometry (Å, º) for (II) top
D—H···A | D—H | H···A | D···A | D—H···A |
N2—H2···O2i | 0.88 | 2.20 | 3.072 (3) | 170.1 |
Symmetry code: (i) x+1, y, z. |
Selected geometric parameters (Å, º) for (III) topO3—C9 | 1.205 (3) | C9—C10 | 1.467 (3) |
N1—C1 | 1.292 (3) | C10—C11 | 1.337 (3) |
C1—C4 | 1.522 (3) | C11—C12 | 1.449 (3) |
C2—C3 | 1.359 (3) | C12—C13 | 1.342 (3) |
| | | |
C1—N1—C3 | 111.45 (17) | O3—C9—C10 | 125.2 (2) |
C4—C1—S1 | 120.88 (14) | C11—C10—C9 | 123.1 (2) |
C3—C2—S1 | 110.85 (15) | C10—C11—C12 | 124.28 (19) |
C2—C3—C13 | 124.04 (18) | C13—C12—C11 | 126.01 (18) |
N1—C3—C13 | 121.84 (18) | C12—C13—C3 | 127.78 (18) |
| | | |
C1—S1—C2—C3 | −0.68 (17) | C10—C11—C12—C13 | 173.8 (2) |
S1—C2—C3—C13 | −177.35 (17) | C11—C12—C13—C3 | −3.3 (4) |
O3—C9—C10—C11 | 175.9 (2) | C2—C3—C13—C12 | 165.4 (2) |
C9—C10—C11—C12 | 177.9 (2) | N1—C3—C13—C12 | −12.7 (3) |
Hydrogen-bond geometry (Å, º) for (III) top
D—H···A | D—H | H···A | D···A | D—H···A |
N2—H2···O1i | 0.88 | 2.00 | 2.869 (2) | 168.3 |
Symmetry code: (i) x, −y+2, z−1/2. |
Leinamycin, (I), is a natural product with promising antitumor activity (Hara et al., 1989, 1990). This activity is believed to result from the ability of the compound to damage cellular DNA (Hara et al., 1990; Asai et al., 1996; Mitra et al., 1997; Breydo et al., 2001). Leinamycin has a unique structure, with an unusual 1,2-dithiolan-3-one 1-oxide moiety connected by a spiro linkage to an 18-membered macrocycle. This antibiotic is capable of both DNA alkylation and oxidative DNA damage (Gates, 2000). \sch
Recent studies showing that leinamycin does not efficiently alkylate single-stranded DNA suggest that non-covalent association of leinamycin with the double helix facilitates DNA alkylation by the antibiotic (Asai et al., 1996; Breydo et al., 2002). It seems likely that the macrocycle of leinamycin plays a major role in non-covalent binding of the compound to DNA. Thus, in order to understand better the nature of the interaction between leinamycin and DNA, it is important to characterize the three-dimensional structure of the thiazol-5-yl-penta-2,4-dienone fragment of the antibiotic. Although crystal structures of leinamycin and several of its derivatives have been solved previously (Hirayama & Matsuzawa, 1993; Kanda et al., 1999), the coordinates for these structures have not been published.
As a part of an investigation of non-covalent DNA binding by leinamycin, we prepared several E,E- and Z,E-thiazol-5-yl-penta-2,4-dienones. Here, we present the crystal structures of methyl (R)-5-{2-[1-(tert-butoxycarbonylamino)ethyl]thiazol-4-yl}-penta-(E,E)- 2,4-dienoate, (II), and 2-methyl-8-oxa-16-thia-3,17-diazabicyclo[12.2.1]heptadeca(Z,E)- 1(17),10,12,14-tetraene-4,9-dione, (III). Our results provide the first detailed structural information regarding leinamycin analogs containing the thiazol-5-yl-penta-2,4-dienone moiety.
The structures of (II) and (III) reveal that the penta-2,4-dienone fragment is nearly planar [to within 0.02 Å for (II) and 0.05 Å for (III)], similar to the known structures of compounds containing an α,β,γ,δ-conjugated carbonyl group (Cox, 1994; Rabinovich & Schmidt, 1967). The bond lengths in the penta-2,4-dienone system indicate conjugation (Ladd & Palmer, 1993; Wiberg et al., 1991) between the double bonds and with the thiazole ring. The thiazole ring is twisted out of plane relative to the penta-2,4-dienone moiety, by 12.9 (2)° in (II) and by 21.4 (4)° in (III) (PLATON; Spek, 2001). Presumably, this twist serves to minimize steric repulsion between the lone pair on the thiazole N atom and an adjacent H atom [H12 in (II) or H11 in (III)]. This assumption is supported by a comparison with the known structure of epothilone B, (IV) (Hoefle et al., 1996). Epothilone B contains an alkene moiety in the C4 position of the thiazole ring that is also slightly twisted out of plane. Although coordinates for the crystal structure of leinamycin are not available, the graphical representations that have been published (Hirayama & Matsuzawa, 1993) indicate that the antibiotic also adopts a conformation with a nearly planar penta-2,4-dienone moiety and the thiazole ring twisted slightly out of plane.
The 18-membered macrocycle of leinamycin clearly presents a large hydrophobic surface that may drive association of the natural product with the hydrophobic major groove of duplex DNA (Jadhav et al., 1999). In addition, it is possible that the conjugated thiazol-5-yl-penta-2,4-dienone moiety found in leinamycin may represent a novel type of DNA intercalator where, individual double bonds are a part of the intercalating system. Several examples of such small intercalators are known and include esperamycin A1 (Yu et al., 1994), C-1027 (Yu et al., 1995), and amiloride (Bailly et al., 1993). The results reported here may provide important structural information that will ultimately help us understand the detailed nature of the non-covalent interactions between leinamycin and DNA.