Kynostatin {KNI-272; systematic name: 3-[3-benzyl-2-hydroxy-9-(isoquinolin-5-yloxy)-6-methylsulfanylmethyl-5,8-dioxo-4,7-diazanonanoyl]-N-tert-butyl-1,3-thiazolane-4-carboxamide}, a highly selective and potent HIV protease inhibitor containing allophenylnorstatin [(2S,3S)-3-amino-2-hydroxy-4-phenylbutyric acid], has been crystallized as the hydrate, C33H41N5O6S2·0.803H2O, from aqueous hexylene glycol. The observed disorder of the phenyl group in the structure is related to the mode of hydration. The backbone conformation of the molecule is twisted and the overall conformation of the free inhibitor is similar to that observed in its complex with HIV protease.
Supporting information
CCDC reference: 175102
Compound (I) was synthesized according to the method published by Mimoto et
al. (1991). Compound (I) (20 mg) was dissolved in hexylene glycol (0.3 ml), and water was added to this solution in several small portions of ?ml.
The addition of water was stopped before the solution became opaque. The
solution was then sealed in a vial and crystals were grown for 2–5 d at room
temperature. A crystal of (I) was mounted on a nylon loop with mother liquor
solution (aqueous hexylene glycol) and frozen in a nitrogen stream at 100 K.
Intensity data were collected by the oscillation method using synchrotron
radiation (SPring-8/BL24XU—A). A total of 60 images covered 180° rotation
on the ϕ axis. Image data were processed using MOSFLM (Leslie, 1990)
(Query year - 1999 given in tables above) and the CCP4 program suite
(Collaborative Computational Project, Number 4, 1994). The high background
regions were observed at approximately 3.0 Å resolution and these regions
were excluded from the processing. A total of 15444 reflections were observed
from the image data, and these were averaged to 6157 reflections by the
CCP4 program suite, with Rmerge = 0.092. The H atoms of the
peptide were placed in calculated positions and constrained during the
refinement, with C—H = ?Å and Uiso(H) = ?Ueq(C). Please
provide details of constraints used. Please also provide CIF-format details of
the bond distances and angles involving H atoms. The H atoms of the water
molecules were positioned by considering the hydrogen-bonding networks and
were fixed during the refinement. Constraints? The absolute stereochemistry is
known from the known chirality of the starting materials in the synthesis, but
it could not be determined from the present data.
Data collection: PROCESS (Rigaku, 1996); cell refinement: MOSFLM (Leslie, 1999); data reduction: MOSFLM; program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: PLATON (Spek, 1998); software used to prepare material for publication: PARST (Nardelli, 1983).
3-[3-benzyl-2-hydroxy-9-(isoquinolin-5-yloxy)-6-methylsulfanylmethyl-5,8-dioxo-
4,7-diazanonanoyl]-
N-
tert-butyl-1,3-thiazolane-4-carboxamide
top
Crystal data top
C33H41N5O6S2·0.803H2O | Z = 2 |
Mr = 682.33 | F(000) = 724 |
Monoclinic, P21 | Dx = 1.281 Mg m−3 |
a = 10.7631 (4) Å | Synchrotron radiation, λ = 0.83600 Å |
b = 13.1751 (4) Å | µ = 0.20 mm−1 |
c = 12.5623 (5) Å | T = 100 K |
β = 96.887 (2)° | Plate, colourless |
V = 1768.54 (11) Å3 | 0.25 × 0.10 × 0.02 mm |
Data collection top
Rigaku RAXIS-IV image-plate detector diffractometer | 3321 reflections with I > 2σ(I) |
Radiation source: double monochromated beam | Rint = 0.070 |
Diamond monochromator | θmax = 31.5°, θmin = 8.1° |
Detector resolution: 10 pixels mm-1 | h = −13→13 |
oscillation scans | k = −16→16 |
5965 measured reflections | l = 0→15 |
3571 independent reflections | |
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)] = 0.067 | H-atom parameters constrained |
wR(F2) = 0.191 | w = 1/[σ2(Fo2) + (0.1047P)2 + 2.2778P] where P = (Fo2 + 2Fc2)/3 |
S = 0.99 | (Δ/σ)max = 0.020 |
3571 reflections | Δρmax = 0.81 e Å−3 |
504 parameters | Δρmin = −0.61 e Å−3 |
1 restraint | Extinction correction: SHELXL97 (Sheldrick, 1997), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4 |
Primary atom site location: structure-invariant direct methods | Extinction coefficient: 0.30 (3) |
Crystal data top
C33H41N5O6S2·0.803H2O | V = 1768.54 (11) Å3 |
Mr = 682.33 | Z = 2 |
Monoclinic, P21 | Synchrotron radiation, λ = 0.83600 Å |
a = 10.7631 (4) Å | µ = 0.20 mm−1 |
b = 13.1751 (4) Å | T = 100 K |
c = 12.5623 (5) Å | 0.25 × 0.10 × 0.02 mm |
β = 96.887 (2)° | |
Data collection top
Rigaku RAXIS-IV image-plate detector diffractometer | 3321 reflections with I > 2σ(I) |
5965 measured reflections | Rint = 0.070 |
3571 independent reflections | |
Refinement top
R[F2 > 2σ(F2)] = 0.067 | 1 restraint |
wR(F2) = 0.191 | H-atom parameters constrained |
S = 0.99 | Δρmax = 0.81 e Å−3 |
3571 reflections | Δρmin = −0.61 e Å−3 |
504 parameters | |
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 | Occ. (<1) |
N1 | 0.7262 (5) | −0.3745 (4) | 0.4204 (4) | 0.0433 (12) | |
C2 | 0.6760 (5) | −0.3165 (5) | 0.4949 (5) | 0.0427 (13) | |
H2 | 0.7225 | −0.2619 | 0.5250 | 0.051* | |
C3 | 0.5610 (5) | −0.3344 (4) | 0.5277 (4) | 0.0341 (11) | |
H3 | 0.5323 | −0.2937 | 0.5801 | 0.041* | |
C4 | 0.3666 (5) | −0.4408 (4) | 0.5086 (4) | 0.0298 (11) | |
C5 | 0.2969 (5) | −0.5156 (5) | 0.4545 (5) | 0.0364 (12) | |
H5 | 0.2179 | −0.5313 | 0.4728 | 0.044* | |
C6 | 0.3453 (5) | −0.5698 (5) | 0.3699 (4) | 0.0368 (12) | |
H6 | 0.2963 | −0.6189 | 0.3318 | 0.044* | |
C7 | 0.4615 (5) | −0.5502 (4) | 0.3448 (4) | 0.0338 (11) | |
H7 | 0.4936 | −0.5881 | 0.2919 | 0.041* | |
C8 | 0.6561 (5) | −0.4491 (4) | 0.3766 (5) | 0.0360 (12) | |
H8 | 0.6900 | −0.4897 | 0.3269 | 0.043* | |
C9 | 0.4863 (4) | −0.4148 (4) | 0.4815 (4) | 0.0275 (10) | |
C10 | 0.5346 (5) | −0.4723 (4) | 0.3988 (4) | 0.0300 (10) | |
O11 | 0.3287 (3) | −0.3871 (3) | 0.5943 (3) | 0.0337 (8) | |
C11 | 0.2272 (5) | −0.4309 (4) | 0.6415 (4) | 0.0364 (12) | |
H11 | 0.2379 | −0.5040 | 0.6456 | 0.044* | |
H12 | 0.1494 | −0.4169 | 0.5965 | 0.044* | |
C12 | 0.2195 (5) | −0.3894 (4) | 0.7526 (4) | 0.0316 (11) | |
O12 | 0.1507 (4) | −0.4322 (3) | 0.8100 (3) | 0.0391 (10) | |
N13 | 0.2886 (4) | −0.3067 (3) | 0.7833 (3) | 0.0296 (9) | |
H13 | 0.3263 | −0.2753 | 0.7364 | 0.041* | |
C13 | 0.3017 (5) | −0.2686 (4) | 0.8933 (4) | 0.0289 (10) | |
H14 | 0.2467 | −0.3070 | 0.9354 | 0.040* | |
C14 | 0.4376 (5) | −0.2791 (5) | 0.9445 (5) | 0.0365 (12) | |
H15 | 0.4438 | −0.2547 | 1.0178 | 0.044* | |
H16 | 0.4901 | −0.2361 | 0.9059 | 0.044* | |
S15 | 0.49746 (15) | −0.40805 (12) | 0.94521 (14) | 0.0483 (5) | |
C16 | 0.4082 (8) | −0.4681 (6) | 1.0394 (6) | 0.0612 (19) | |
H17 | 0.4322 | −0.5381 | 1.0474 | 0.067* | |
H18 | 0.3207 | −0.4637 | 1.0137 | 0.067* | |
H19 | 0.4239 | −0.4345 | 1.1075 | 0.067* | |
C17 | 0.2626 (5) | −0.1574 (4) | 0.8884 (4) | 0.0317 (11) | |
O17 | 0.3245 (4) | −0.0945 (3) | 0.8440 (4) | 0.0428 (10) | |
N18 | 0.1570 (4) | −0.1348 (3) | 0.9310 (4) | 0.0308 (9) | |
H20 | 0.1275 | −0.1771 | 0.9737 | 0.037* | |
C18 | 0.0913 (5) | −0.0378 (4) | 0.9046 (5) | 0.0339 (11) | |
H21 | 0.1372 | −0.0083 | 0.8494 | 0.041* | |
C19 | −0.0320 (13) | −0.0643 (11) | 0.8453 (12) | 0.035 (3) | 0.491 (12) |
H22 | −0.0793 | −0.0023 | 0.8296 | 0.042* | 0.491 (12) |
H23 | −0.0778 | −0.1056 | 0.8913 | 0.042* | 0.491 (12) |
C20 | −0.0243 (13) | −0.1215 (15) | 0.7403 (12) | 0.037 (3) | 0.491 (12) |
C21 | −0.0496 (17) | −0.224 (2) | 0.7378 (16) | 0.042 (4) | 0.491 (12) |
H24 | −0.0763 | −0.2566 | 0.7964 | 0.051* | 0.491 (12) |
C22 | −0.0330 (15) | −0.2769 (14) | 0.6416 (15) | 0.060 (5) | 0.491 (12) |
H25 | −0.0512 | −0.3459 | 0.6365 | 0.072* | 0.491 (12) |
C23 | 0.0096 (12) | −0.2280 (16) | 0.5562 (11) | 0.058 (5) | 0.491 (12) |
H26 | 0.0230 | −0.2645 | 0.4953 | 0.070* | 0.491 (12) |
C24 | 0.0316 (12) | −0.1286 (15) | 0.5605 (11) | 0.054 (4) | 0.491 (12) |
H27 | 0.0581 | −0.0958 | 0.5016 | 0.064* | 0.491 (12) |
C25 | 0.0150 (4) | −0.0725 (4) | 0.6539 (4) | 0.047 (3) | 0.491 (12) |
H28 | 0.0307 | −0.0031 | 0.6566 | 0.056* | 0.491 (12) |
C26 | 0.1111 (4) | 0.0390 (4) | 0.9963 (4) | 0.0304 (11) | |
H29 | 0.2013 | 0.0475 | 1.0166 | 0.036* | |
O26 | 0.0571 (4) | 0.0052 (4) | 1.0870 (4) | 0.0531 (14) | |
H30 | −0.0005 | 0.0345 | 1.0977 | 0.053* | |
C27 | 0.0557 (5) | 0.1417 (4) | 0.9576 (4) | 0.0285 (10) | |
O27 | −0.0411 (3) | 0.1727 (3) | 0.9914 (3) | 0.0361 (9) | |
N28 | 0.1099 (4) | 0.1918 (3) | 0.8825 (4) | 0.0281 (9) | |
C28 | 0.0501 (4) | 0.2847 (3) | 0.8367 (4) | 0.0280 (10) | |
H31 | 0.0386 | 0.3329 | 0.8941 | 0.039* | |
C29 | 0.1391 (5) | 0.3298 (4) | 0.7624 (5) | 0.0393 (13) | |
H32 | 0.1297 | 0.4029 | 0.7574 | 0.047* | |
H33 | 0.1230 | 0.3010 | 0.6910 | 0.047* | |
S30 | 0.29496 (13) | 0.29578 (11) | 0.82504 (14) | 0.0430 (5) | |
C31 | 0.2325 (5) | 0.1706 (4) | 0.8481 (5) | 0.0357 (12) | |
H34 | 0.2242 | 0.1305 | 0.7828 | 0.043* | |
H35 | 0.2859 | 0.1347 | 0.9034 | 0.043* | |
C32 | −0.0768 (5) | 0.2602 (4) | 0.7725 (4) | 0.0314 (11) | |
O32 | −0.0943 (4) | 0.1804 (3) | 0.7221 (3) | 0.0372 (9) | |
N33 | −0.1618 (4) | 0.3350 (3) | 0.7733 (4) | 0.0329 (10) | |
H36 | −0.1396 | 0.3888 | 0.8094 | 0.039* | |
C33 | −0.2910 (6) | 0.3319 (5) | 0.7165 (6) | 0.0452 (14) | |
C34 | −0.3595 (6) | 0.2375 (6) | 0.7460 (6) | 0.0542 (18) | |
H37 | −0.3618 | 0.2359 | 0.8222 | 0.054* | |
H38 | −0.3168 | 0.1784 | 0.7245 | 0.054* | |
H39 | −0.4434 | 0.2384 | 0.7101 | 0.054* | |
C35 | −0.3563 (8) | 0.4253 (8) | 0.7562 (12) | 0.105 (5) | |
H41 | −0.3574 | 0.4207 | 0.8323 | 0.105* | |
H42 | −0.4406 | 0.4286 | 0.7213 | 0.105* | |
H43 | −0.3119 | 0.4854 | 0.7397 | 0.105* | |
C36 | −0.2866 (10) | 0.3375 (7) | 0.5954 (7) | 0.070 (2) | |
H44 | −0.2453 | 0.2783 | 0.5722 | 0.070* | |
H45 | −0.2413 | 0.3971 | 0.5788 | 0.070* | |
H46 | −0.3703 | 0.3406 | 0.5592 | 0.070* | |
C19' | −0.0615 (12) | −0.0508 (8) | 0.8923 (13) | 0.033 (3) | 0.509 (12) |
H23' | −0.0891 | −0.0528 | 0.9630 | 0.040* | 0.509 (12) |
H22' | −0.1002 | 0.0075 | 0.8545 | 0.040* | 0.509 (12) |
C20' | −0.1036 (10) | −0.1475 (8) | 0.8314 (10) | 0.039 (3) | 0.509 (12) |
C25' | −0.0433 (18) | −0.176 (2) | 0.7441 (18) | 0.048 (5) | 0.509 (12) |
H28' | 0.0176 | −0.1354 | 0.7185 | 0.058* | 0.509 (12) |
C24' | −0.0816 (18) | −0.271 (2) | 0.696 (2) | 0.067 (5) | 0.509 (12) |
H27' | −0.0432 | −0.2952 | 0.6389 | 0.081* | 0.509 (12) |
C23' | −0.1733 (15) | −0.3274 (10) | 0.7337 (15) | 0.066 (5) | 0.509 (12) |
H26' | −0.1931 | −0.3899 | 0.7016 | 0.053* | 0.509 (12) |
C22' | −0.2373 (15) | −0.2978 (12) | 0.8147 (10) | 0.053 (4) | 0.509 (12) |
H25' | −0.3032 | −0.3357 | 0.8353 | 0.064* | 0.509 (12) |
C21' | −0.1993 (12) | −0.2081 (10) | 0.8649 (10) | 0.047 (3) | 0.509 (12) |
H24' | −0.2384 | −0.1868 | 0.9232 | 0.057* | 0.509 (12) |
O61 | −0.0038 (10) | −0.3377 (13) | 0.4640 (9) | 0.053 (4) | 0.366 (9) |
H62 | −0.0110 | −0.2750 | 0.4653 | 0.058* | 0.366 (9) |
H61 | −0.0802 | −0.3622 | 0.4434 | 0.058* | 0.366 (9) |
O62 | 0.0318 (18) | 0.043 (2) | 0.6072 (17) | 0.051 (6) | 0.204 (5) |
H63 | 0.1117 | 0.0352 | 0.6070 | 0.056* | 0.204 (5) |
H64 | −0.0014 | 0.0814 | 0.6527 | 0.056* | 0.204 (5) |
O63 | −0.0373 (14) | −0.1078 (14) | 0.4713 (13) | 0.034 (4) | 0.233 (6) |
H65 | −0.0717 | −0.1637 | 0.4883 | 0.038* | 0.233 (6) |
H66 | −0.0157 | −0.0658 | 0.5121 | 0.038* | 0.233 (6) |
Atomic displacement parameters (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
N1 | 0.033 (2) | 0.039 (3) | 0.061 (3) | −0.010 (2) | 0.020 (2) | −0.014 (2) |
C2 | 0.033 (3) | 0.037 (3) | 0.060 (3) | −0.010 (3) | 0.013 (2) | −0.016 (3) |
C3 | 0.030 (2) | 0.031 (3) | 0.043 (3) | −0.002 (2) | 0.013 (2) | −0.005 (2) |
C4 | 0.034 (2) | 0.026 (3) | 0.032 (2) | −0.001 (2) | 0.0124 (19) | −0.001 (2) |
C5 | 0.031 (2) | 0.036 (3) | 0.044 (3) | −0.011 (2) | 0.013 (2) | −0.005 (2) |
C6 | 0.040 (3) | 0.033 (3) | 0.037 (3) | −0.010 (2) | 0.008 (2) | −0.010 (2) |
C7 | 0.038 (3) | 0.031 (3) | 0.034 (2) | −0.001 (2) | 0.009 (2) | −0.002 (2) |
C8 | 0.034 (3) | 0.031 (3) | 0.046 (3) | 0.001 (2) | 0.016 (2) | 0.000 (2) |
C9 | 0.026 (2) | 0.023 (2) | 0.033 (2) | −0.001 (2) | 0.0051 (18) | 0.000 (2) |
C10 | 0.034 (2) | 0.022 (2) | 0.035 (2) | −0.001 (2) | 0.0077 (19) | 0.000 (2) |
O11 | 0.0347 (18) | 0.0295 (19) | 0.0401 (18) | −0.0083 (16) | 0.0174 (15) | −0.0056 (16) |
C11 | 0.034 (2) | 0.034 (3) | 0.045 (3) | −0.013 (2) | 0.022 (2) | −0.011 (2) |
C12 | 0.031 (2) | 0.026 (2) | 0.042 (3) | −0.004 (2) | 0.018 (2) | −0.004 (2) |
O12 | 0.042 (2) | 0.0281 (19) | 0.053 (2) | −0.0109 (16) | 0.0280 (17) | −0.0083 (17) |
N13 | 0.034 (2) | 0.027 (2) | 0.0289 (19) | −0.0050 (18) | 0.0088 (16) | 0.0026 (17) |
C13 | 0.033 (2) | 0.022 (2) | 0.034 (2) | −0.002 (2) | 0.0125 (19) | 0.0003 (19) |
C14 | 0.033 (3) | 0.034 (3) | 0.042 (3) | 0.001 (2) | 0.003 (2) | 0.001 (2) |
S15 | 0.0432 (8) | 0.0378 (8) | 0.0632 (9) | 0.0111 (7) | 0.0034 (7) | −0.0015 (7) |
C16 | 0.079 (5) | 0.043 (4) | 0.060 (4) | 0.006 (4) | 0.005 (4) | 0.013 (3) |
C17 | 0.037 (3) | 0.023 (2) | 0.035 (2) | −0.005 (2) | 0.007 (2) | 0.002 (2) |
O17 | 0.053 (2) | 0.0247 (19) | 0.052 (2) | −0.0087 (18) | 0.0136 (19) | 0.0083 (18) |
N18 | 0.037 (2) | 0.0164 (18) | 0.040 (2) | 0.0005 (17) | 0.0062 (17) | 0.0039 (17) |
C18 | 0.036 (3) | 0.020 (2) | 0.045 (3) | −0.002 (2) | −0.002 (2) | 0.003 (2) |
C19 | 0.031 (6) | 0.030 (6) | 0.040 (7) | 0.003 (5) | −0.008 (5) | −0.014 (6) |
C20 | 0.023 (6) | 0.036 (8) | 0.050 (7) | 0.005 (6) | 0.003 (4) | −0.003 (7) |
C21 | 0.030 (7) | 0.046 (12) | 0.048 (8) | −0.006 (11) | −0.004 (6) | −0.015 (11) |
C22 | 0.038 (7) | 0.066 (10) | 0.074 (10) | 0.005 (7) | −0.002 (7) | −0.035 (9) |
C23 | 0.037 (6) | 0.093 (13) | 0.043 (7) | 0.016 (7) | −0.003 (5) | −0.030 (8) |
C24 | 0.031 (6) | 0.088 (12) | 0.042 (6) | 0.007 (7) | 0.006 (5) | −0.019 (7) |
C25 | 0.034 (6) | 0.068 (9) | 0.038 (6) | 0.011 (6) | 0.004 (4) | −0.004 (6) |
C26 | 0.028 (2) | 0.023 (2) | 0.042 (3) | 0.004 (2) | 0.017 (2) | 0.007 (2) |
O26 | 0.061 (3) | 0.046 (3) | 0.061 (3) | 0.034 (2) | 0.044 (2) | 0.032 (2) |
C27 | 0.030 (2) | 0.023 (2) | 0.035 (2) | 0.0024 (19) | 0.0119 (18) | 0.000 (2) |
O27 | 0.0364 (19) | 0.0289 (19) | 0.047 (2) | 0.0151 (16) | 0.0217 (17) | 0.0110 (17) |
N28 | 0.0277 (19) | 0.0175 (19) | 0.042 (2) | 0.0017 (16) | 0.0149 (17) | 0.0018 (17) |
C28 | 0.030 (2) | 0.014 (2) | 0.040 (2) | 0.0020 (18) | 0.0077 (19) | −0.0002 (19) |
C29 | 0.043 (3) | 0.024 (2) | 0.053 (3) | −0.003 (2) | 0.015 (2) | 0.006 (2) |
S30 | 0.0321 (7) | 0.0322 (8) | 0.0660 (10) | −0.0076 (5) | 0.0113 (6) | 0.0108 (7) |
C31 | 0.029 (2) | 0.028 (3) | 0.053 (3) | 0.000 (2) | 0.017 (2) | 0.006 (2) |
C32 | 0.035 (3) | 0.020 (2) | 0.041 (3) | 0.002 (2) | 0.012 (2) | 0.004 (2) |
O32 | 0.0364 (19) | 0.0243 (18) | 0.052 (2) | −0.0006 (16) | 0.0112 (17) | −0.0104 (17) |
N33 | 0.036 (2) | 0.021 (2) | 0.041 (2) | 0.0022 (18) | 0.0002 (18) | −0.0033 (18) |
C33 | 0.039 (3) | 0.032 (3) | 0.061 (4) | 0.007 (2) | −0.010 (3) | −0.014 (3) |
C34 | 0.040 (3) | 0.065 (5) | 0.061 (4) | −0.011 (3) | 0.018 (3) | −0.023 (4) |
C35 | 0.051 (4) | 0.072 (6) | 0.178 (11) | 0.024 (4) | −0.043 (6) | −0.078 (7) |
C36 | 0.090 (6) | 0.047 (4) | 0.065 (4) | −0.014 (4) | −0.030 (4) | 0.019 (4) |
C19' | 0.037 (6) | 0.012 (5) | 0.049 (8) | 0.005 (4) | −0.005 (5) | 0.001 (5) |
C20' | 0.035 (5) | 0.024 (5) | 0.057 (7) | 0.008 (4) | −0.001 (5) | 0.009 (5) |
C25' | 0.029 (8) | 0.033 (11) | 0.080 (12) | 0.001 (11) | −0.007 (7) | −0.002 (13) |
C24' | 0.043 (9) | 0.084 (15) | 0.072 (12) | 0.034 (11) | −0.004 (9) | −0.004 (12) |
C23' | 0.060 (9) | 0.022 (6) | 0.106 (12) | 0.002 (6) | −0.033 (9) | 0.013 (7) |
C22' | 0.064 (8) | 0.049 (8) | 0.042 (6) | −0.002 (7) | −0.010 (6) | 0.005 (6) |
C21' | 0.052 (7) | 0.034 (6) | 0.050 (6) | −0.007 (6) | −0.016 (5) | 0.011 (6) |
O61 | 0.026 (5) | 0.091 (11) | 0.045 (6) | 0.004 (6) | 0.015 (5) | 0.007 (7) |
O62 | 0.025 (9) | 0.084 (18) | 0.048 (11) | 0.003 (11) | 0.017 (8) | 0.003 (12) |
O63 | 0.027 (7) | 0.043 (10) | 0.035 (8) | 0.001 (7) | 0.011 (6) | −0.015 (7) |
Geometric parameters (Å, º) top
N1—C8 | 1.318 (8) | O61—O62i | 1.82 (3) |
N1—C2 | 1.369 (8) | O62—O61ii | 1.82 (3) |
C2—C3 | 1.371 (7) | C2—H2 | 0.930 (6) |
C3—C9 | 1.412 (7) | C3—H3 | 0.930 (5) |
C4—C5 | 1.369 (8) | C5—H5 | 0.930 (6) |
C4—O11 | 1.389 (6) | C6—H6 | 0.930 (6) |
C4—C9 | 1.414 (7) | C7—H7 | 0.930 (5) |
C5—C6 | 1.429 (8) | C8—H8 | 0.929 (6) |
C6—C7 | 1.351 (7) | C11—H11 | 0.971 (5) |
C7—C10 | 1.416 (8) | C11—H12 | 0.970 (5) |
C8—C10 | 1.403 (7) | N13—H13 | 0.860 (4) |
C9—C10 | 1.432 (7) | C13—H14 | 0.980 (6) |
O11—C11 | 1.426 (6) | C14—H15 | 0.970 (6) |
C11—C12 | 1.511 (7) | C14—H16 | 0.970 (6) |
C12—O12 | 1.230 (6) | C16—H17 | 0.960 (8) |
C12—N13 | 1.348 (7) | C16—H18 | 0.960 (8) |
N13—C13 | 1.462 (7) | C16—H19 | 0.960 (8) |
C13—C17 | 1.524 (7) | N18—H20 | 0.860 (5) |
C13—C14 | 1.531 (7) | C18—H21 | 0.979 (6) |
C14—S15 | 1.817 (6) | C19—H22 | 0.970 (14) |
S15—C16 | 1.794 (8) | C19—H23 | 0.970 (15) |
C17—O17 | 1.238 (7) | C21—H24 | 0.93 (2) |
C17—N18 | 1.347 (7) | C22—H25 | 0.930 (18) |
N18—C18 | 1.478 (7) | C23—H26 | 0.929 (16) |
C18—C19 | 1.484 (13) | C24—H27 | 0.931 (16) |
C18—C26 | 1.529 (7) | C25—H28 | 0.930 (5) |
C18—C19' | 1.642 (14) | C26—H29 | 0.980 (4) |
C19—C20 | 1.53 (2) | O26—H30 | 0.756 (5) |
C20—C25 | 1.372 (17) | C28—H31 | 0.980 (5) |
C20—C21 | 1.37 (3) | C29—H32 | 0.970 (5) |
C21—C22 | 1.43 (3) | C29—H33 | 0.970 (6) |
C22—C23 | 1.38 (3) | C31—H34 | 0.971 (6) |
C23—C24 | 1.33 (3) | C31—H35 | 0.970 (6) |
C24—C25 | 1.416 (14) | N33—H36 | 0.860 (4) |
C26—O26 | 1.412 (6) | C34—H37 | 0.961 (8) |
C26—C27 | 1.535 (7) | C34—H38 | 0.959 (8) |
C27—O27 | 1.240 (6) | C34—H39 | 0.960 (6) |
C27—N28 | 1.341 (6) | C35—H41 | 0.959 (15) |
N28—C31 | 1.465 (6) | C35—H42 | 0.960 (9) |
N28—C28 | 1.468 (6) | C35—H43 | 0.960 (11) |
C28—C32 | 1.535 (7) | C36—H44 | 0.960 (10) |
C28—C29 | 1.535 (7) | C36—H45 | 0.960 (10) |
C29—S30 | 1.822 (6) | C36—H46 | 0.960 (10) |
S30—C31 | 1.817 (6) | C19'—H23' | 0.970 (17) |
C32—O32 | 1.230 (7) | C19'—H22' | 0.970 (12) |
C32—N33 | 1.346 (7) | C25'—H28' | 0.93 (2) |
N33—C33 | 1.485 (7) | C24'—H27' | 0.93 (3) |
C33—C34 | 1.514 (10) | C23'—H26' | 0.930 (14) |
C33—C36 | 1.530 (12) | C22'—H25' | 0.929 (16) |
C33—C35 | 1.531 (10) | C21'—H24' | 0.931 (13) |
C19'—C20' | 1.528 (18) | O61—H62 | 0.830 (17) |
C20'—C25' | 1.39 (3) | O61—H61 | 0.892 (12) |
C20'—C21' | 1.406 (18) | O62—H63 | 0.87 (2) |
C25'—C24' | 1.43 (3) | O62—H64 | 0.87 (2) |
C24'—C23' | 1.36 (3) | O63—H65 | 0.863 (18) |
C23'—C22' | 1.35 (2) | O63—H66 | 0.771 (17) |
C22'—C21' | 1.38 (2) | | |
| | | |
C8—N1—C2 | 116.7 (5) | O11—C11—H12 | 109.4 (5) |
N1—C2—C3 | 123.6 (5) | C12—C11—H11 | 109.2 (5) |
C2—C3—C9 | 119.7 (5) | C12—C11—H12 | 109.3 (5) |
C5—C4—O11 | 123.8 (4) | H11—C11—H12 | 107.9 (5) |
C5—C4—C9 | 121.0 (4) | C12—N13—H13 | 118.8 (5) |
O11—C4—C9 | 115.1 (4) | C13—N13—H13 | 118.8 (4) |
C4—C5—C6 | 120.1 (5) | N13—C13—H14 | 109.7 (4) |
C7—C6—C5 | 120.6 (5) | C14—C13—H14 | 109.6 (5) |
C6—C7—C10 | 120.2 (5) | C17—C13—H14 | 109.7 (5) |
N1—C8—C10 | 125.4 (5) | C13—C14—H15 | 108.8 (5) |
C3—C9—C4 | 125.0 (5) | C13—C14—H16 | 108.8 (5) |
C3—C9—C10 | 117.1 (4) | S15—C14—H15 | 108.7 (5) |
C4—C9—C10 | 117.9 (5) | S15—C14—H16 | 108.7 (5) |
C8—C10—C7 | 122.7 (5) | H15—C14—H16 | 107.6 (6) |
C8—C10—C9 | 117.2 (5) | S15—C16—H17 | 109.5 (6) |
C7—C10—C9 | 120.1 (4) | S15—C16—H18 | 109.4 (7) |
C4—O11—C11 | 115.3 (4) | S15—C16—H19 | 109.5 (6) |
O11—C11—C12 | 111.5 (4) | H17—C16—H18 | 109.5 (8) |
O12—C12—N13 | 123.6 (5) | H17—C16—H19 | 109.5 (8) |
O12—C12—C11 | 118.5 (5) | H18—C16—H19 | 109.4 (8) |
N13—C12—C11 | 117.8 (4) | C17—N18—H20 | 119.8 (5) |
C12—N13—C13 | 122.3 (4) | C18—N18—H20 | 119.8 (4) |
N13—C13—C17 | 107.3 (4) | N18—C18—H21 | 103.5 (5) |
N13—C13—C14 | 110.2 (4) | C19—C18—H21 | 103.6 (7) |
C17—C13—C14 | 110.4 (4) | C26—C18—H21 | 103.6 (5) |
C13—C14—S15 | 114.0 (4) | C18—C19—H22 | 108.7 (12) |
C16—S15—C14 | 101.4 (3) | C18—C19—H23 | 108.7 (12) |
O17—C17—N18 | 123.8 (5) | C20—C19—H22 | 108.7 (13) |
O17—C17—C13 | 120.1 (5) | C20—C19—H23 | 108.7 (13) |
N18—C17—C13 | 116.0 (4) | H22—C19—H23 | 107.6 (14) |
C17—N18—C18 | 120.4 (4) | C20—C21—H24 | 121 (2) |
N18—C18—C19 | 106.5 (7) | C22—C21—H24 | 121.9 (19) |
N18—C18—C26 | 112.6 (4) | C21—C22—H25 | 119.3 (19) |
C19—C18—C26 | 124.7 (8) | C23—C22—H25 | 119.4 (18) |
N18—C18—C19' | 112.2 (5) | C22—C23—H26 | 119.9 (14) |
C19—C18—C19' | 26.2 (5) | C24—C23—H26 | 119.9 (18) |
C26—C18—C19' | 100.8 (7) | C23—C24—H27 | 119.7 (17) |
C18—C19—C20 | 114.2 (12) | C25—C24—H27 | 119.8 (12) |
C25—C20—C21 | 121.5 (16) | C20—C25—H28 | 120.4 (9) |
C25—C20—C19 | 120.3 (15) | C24—C25—H28 | 120.2 (9) |
C21—C20—C19 | 118.1 (15) | C18—C26—H29 | 108.4 (4) |
C20—C21—C22 | 117 (2) | O26—C26—H29 | 108.5 (4) |
C23—C22—C21 | 121.0 (19) | C27—C26—H29 | 108.5 (4) |
C24—C23—C22 | 120.3 (13) | C26—O26—H30 | 114.1 (5) |
C23—C24—C25 | 120.5 (14) | N28—C28—H31 | 109.9 (4) |
C20—C25—C24 | 119.4 (12) | C29—C28—H31 | 109.9 (4) |
O26—C26—C18 | 111.4 (5) | C32—C28—H31 | 109.9 (4) |
O26—C26—C27 | 110.6 (4) | C28—C29—H32 | 110.8 (5) |
C18—C26—C27 | 109.3 (4) | C28—C29—H33 | 110.8 (5) |
O27—C27—N28 | 122.2 (5) | S30—C29—H32 | 110.8 (4) |
O27—C27—C26 | 119.5 (4) | S30—C29—H33 | 110.9 (5) |
N28—C27—C26 | 118.2 (4) | H32—C29—H33 | 108.8 (5) |
C27—N28—C31 | 126.7 (4) | N28—C31—H34 | 111.0 (5) |
C27—N28—C28 | 118.7 (4) | N28—C31—H35 | 111.1 (5) |
C31—N28—C28 | 114.3 (4) | S30—C31—H34 | 110.9 (4) |
N28—C28—C32 | 110.6 (4) | S30—C31—H35 | 111.0 (4) |
N28—C28—C29 | 106.6 (4) | H34—C31—H35 | 109.1 (6) |
C32—C28—C29 | 110.1 (4) | C32—N33—H36 | 117.5 (4) |
C28—C29—S30 | 104.6 (4) | C33—N33—H36 | 117.4 (5) |
C31—S30—C29 | 87.3 (3) | C33—C34—H37 | 109.5 (7) |
N28—C31—S30 | 103.7 (4) | C33—C34—H38 | 109.5 (7) |
O32—C32—N33 | 124.6 (5) | C33—C34—H39 | 109.5 (6) |
O32—C32—C28 | 121.4 (5) | H37—C34—H38 | 109.5 (7) |
N33—C32—C28 | 113.9 (4) | H37—C34—H39 | 109.5 (7) |
C32—N33—C33 | 125.1 (5) | H38—C34—H39 | 109.5 (7) |
N33—C33—C34 | 111.1 (6) | C33—C35—H41 | 109.6 (10) |
N33—C33—C36 | 109.7 (6) | C33—C35—H42 | 109.5 (8) |
C34—C33—C36 | 110.9 (6) | C33—C35—H43 | 109.4 (9) |
N33—C33—C35 | 105.2 (5) | H41—C35—H42 | 109.5 (12) |
C34—C33—C35 | 109.0 (7) | H41—C35—H43 | 109.5 (12) |
C36—C33—C35 | 110.8 (8) | H42—C35—H43 | 109.4 (9) |
C20'—C19'—C18 | 111.6 (10) | C33—C36—H44 | 109.5 (8) |
C25'—C20'—C21' | 120.9 (16) | C33—C36—H45 | 109.4 (8) |
C25'—C20'—C19' | 118.6 (16) | C33—C36—H46 | 109.5 (8) |
C21'—C20'—C19' | 120.5 (12) | H44—C36—H45 | 109.4 (9) |
C20'—C25'—C24' | 115 (2) | H44—C36—H46 | 109.4 (10) |
C23'—C24'—C25' | 121 (2) | H45—C36—H46 | 109.5 (10) |
C22'—C23'—C24' | 123.9 (18) | C20'—C19'—H23' | 109.3 (12) |
C23'—C22'—C21' | 116.2 (14) | C20'—C19'—H22' | 109.3 (9) |
C22'—C21'—C20' | 122.4 (14) | H23'—C19'—H22' | 108.0 (13) |
N1—C2—H2 | 118.2 (6) | C20'—C25'—H28' | 122.1 (19) |
C3—C2—H2 | 118.2 (6) | C24'—C25'—H28' | 122 (2) |
C2—C3—H3 | 120.1 (5) | C25'—C24'—H27' | 120 (2) |
C9—C3—H3 | 120.2 (5) | C23'—C24'—H27' | 119 (2) |
C4—C5—H5 | 120.0 (6) | C24'—C23'—H26' | 118.0 (16) |
C6—C5—H5 | 119.9 (6) | C22'—C23'—H26' | 118.1 (15) |
C5—C6—H6 | 119.7 (6) | C23'—C22'—H25' | 121.9 (15) |
C7—C6—H6 | 119.8 (6) | C21'—C22'—H25' | 121.9 (15) |
C6—C7—H7 | 119.8 (5) | C20'—C21'—H24' | 118.7 (12) |
C10—C7—H7 | 119.9 (5) | C22'—C21'—H24' | 118.8 (13) |
N1—C8—H8 | 117.3 (6) | H62—O61—H61 | 106.3 (15) |
C10—C8—H8 | 117.3 (5) | H63—O62—H64 | 124 (2) |
O11—C11—H11 | 109.4 (5) | H65—O63—H66 | 124 (2) |
Symmetry codes: (i) −x, y−1/2, −z+1; (ii) −x, y+1/2, −z+1. |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
O26—H30···O27 | 0.76 | 2.269 | 2.669 (6) | 114 |
O62—H64···O32 | 0.87 | 1.916 | 2.77 (2) | 166 |
O61—H62···O63 | 0.83 | 2.223 | 3.05 (3) | 178 |
O63—H66···O62 | 0.77 | 1.897 | 2.67 (3) | 177 |
N18—H20···O27iii | 0.86 | 2.25 | 3.038 (6) | 152 |
N33—H36···O26iv | 0.86 | 2.14 | 2.984 (7) | 169 |
O26—H30···O12iv | 0.76 | 2.145 | 2.837 (6) | 153 |
O61—H61···N1v | 0.89 | 2.075 | 2.932 (12) | 161 |
O62—H63···N1vi | 0.87 | 2.173 | 2.88 (2) | 139 |
Symmetry codes: (iii) −x, y−1/2, −z+2; (iv) −x, y+1/2, −z+2; (v) x−1, y, z; (vi) −x+1, y+1/2, −z+1. |
Experimental details
Crystal data |
Chemical formula | C33H41N5O6S2·0.803H2O |
Mr | 682.33 |
Crystal system, space group | Monoclinic, P21 |
Temperature (K) | 100 |
a, b, c (Å) | 10.7631 (4), 13.1751 (4), 12.5623 (5) |
β (°) | 96.887 (2) |
V (Å3) | 1768.54 (11) |
Z | 2 |
Radiation type | Synchrotron, λ = 0.83600 Å |
µ (mm−1) | 0.20 |
Crystal size (mm) | 0.25 × 0.10 × 0.02 |
|
Data collection |
Diffractometer | Rigaku RAXIS-IV image-plate detector diffractometer |
Absorption correction | – |
No. of measured, independent and observed [I > 2σ(I)] reflections | 5965, 3571, 3321 |
Rint | 0.070 |
(sin θ/λ)max (Å−1) | 0.624 |
|
Refinement |
R[F2 > 2σ(F2)], wR(F2), S | 0.067, 0.191, 0.99 |
No. of reflections | 3571 |
No. of parameters | 504 |
No. of restraints | 1 |
H-atom treatment | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 0.81, −0.61 |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
O26—H30···O27 | 0.76 | 2.269 | 2.669 (6) | 114 |
O62—H64···O32 | 0.87 | 1.916 | 2.77 (2) | 166 |
O61—H62···O63 | 0.83 | 2.223 | 3.05 (3) | 178 |
O63—H66···O62 | 0.77 | 1.897 | 2.67 (3) | 177 |
N18—H20···O27i | 0.86 | 2.252 | 3.038 (6) | 152 |
N33—H36···O26ii | 0.86 | 2.135 | 2.984 (7) | 169 |
O26—H30···O12ii | 0.76 | 2.145 | 2.837 (6) | 153 |
O61—H61···N1iii | 0.89 | 2.075 | 2.932 (12) | 161 |
O62—H63···N1iv | 0.87 | 2.173 | 2.88 (2) | 139 |
Symmetry codes: (i) −x, y−1/2, −z+2; (ii) −x, y+1/2, −z+2; (iii) x−1, y, z; (iv) −x+1, y+1/2, −z+1. |
Selected torsion angles for (I) in this crystal and in the complex with HIV
protease (°) topTorsion angle | This crystal | Complex |
O11-C11-C12-N13 | 12.4 (6) | 39.4 |
C11-C12-N13-C13 | -171.4 (4) | 168.8 |
C12-N13-C13-C17 | -125.3 (5) | -120.1 |
N13-C13-C14-S15 | -57.3 (5) | -161.4 |
N13-C13-C17-N18 | 112.7 (5) | 71.8 |
C13-C17-N18-C18 | -162.8 (4) | -175.9 |
C17-N18-C18-C26 | -104.8 (6) | -108.2 |
N18-C18-C19-C20* | -61.0 (12) | -54.1 |
N18-C18-C19'-C20'* | -41.7 (11) | -54.1 |
C18-C19-C20-C21 | 105.2 (17) | 98.9 |
C18-C19-C20-C25 | -70.5 (17) | -81.2 |
C18-C19'-C20'-C21' | 139.1 (11) | 98.9 |
C18-C19'-C20'-C25' | -39.2 (17) | -81.2 |
N18-C18-C26-O26 | -65.1 (6) | -74.9 |
N18-C18-C26-C27 | 172.3 (4) | 165.1 |
C18-C26-C27-N28 | -66.8 (6) | -88.4 |
O26-C26-C27-O27 | -14.2 (7) | -32.5 |
C26-C27-N28-C28 | 173.7 (4) | 169.1 |
C27-N28-C28-C32 | -65.8 (6) | -64.7 |
N28-C28-C29-S30 | -32.3 (4) | 23.6 |
N28-C28-C32-N33 | 148.8 (4) | 145.6 |
C28-C32-N33-C33 | 179.0 (5) | -169.6 |
C32-N33-C33-C34 | 53.4 (8) | 54.5 |
*The phenyl group is disordered on two sites. |
Kynostatin (KNI-272), hereinafter (I), a peptide mimic containing an allophenylnorstatin residue [Apns, (2S,3S)-3-amino-2-hydroxy-4-phenylbutyric acid; Mimoto et al., 1991], was designed based on the substrate transition state concept for aspartic protease inhibition (Kiso, 1996; Kiso et al., 1999). Compound (I) showed high selectivity and potent inhibitory activity (Ki = 0.0055 nM) for HIV protease (Mimoto et al., 1992), and also displayed good pharmacokinetics and an excellent therapeutic index (Kageyama et al., 1993). Compound (I) is composed of five modules, namely 5-isoquinolyloxy acetic acid (iQoa), methylthioalanine (Mta), Apns, thioproline (Thz) and tert-butyl amine, as shown the Scheme. Crystals of (I) were grown from various alcohol solutions, and the crystal structure obtained from aqueous hexylene glycol is reported here. \sch
The molecular structure of (I) is shown in Fig.1. The phenyl group of the Apns residue is disordered, with two alternate orientations. Analysis of the electron-density map (Fig. 2) shows that rotation of the phenyl ring about the C18—C19 and C19—C20 bonds creates space for the binding of three disordered water molecules whose total site occupancy is 0.8. The water molecules are linked to each other by hydrogen bonds [Table 1; O61···O63 = 3.05 (3) and O63···O62 = 2.67 (3) Å] and interact with the peptide [O62···O32 = 2.77 (2), O61···N1 = 2.932 (12) and O62···N1 = 2.88 (2) Å]. Hydrogen bonds are also formed between the peptides; N18···O27 = 3.038 (6), N33···O26 = 2.984 (7) and O26···O12 = 2.837 (6) Å.
The peptide backbone of (I) is twisted (Fig. 2), and the conformation is different from a β-turn or extended (β-sheet) structure. The structural features of (I) seem to be similar to those of the molecule in the complex with HIV protease (Baldwin et al., 1995). Selected torsion angles are listed in Table 2, to compare the backbone structures of the two compounds. The angles involving the atoms of the Mta residue are significantly different in the free and complex structures (e.g. N13—C13—C14—S15), and the thiazolidine ring is puckered differently (N28—C28—C29—S30). In contrast, the backbone conformation of the Apns-Thz-Tbu moiety observed in the crystal of (I) is closely related to that observed in the enzyme complex. Furthermore, it is known that the range of observed solution conformations of this fragment is rather limited (Ohno et al., 1996). Thus, it is suggested that the Apns-Thz-tBu fragment has a relatively rigid conformation, which is nearly optimal for tight interactions between the Apns moiety of (I) and the catalytic centre of the HIV protease active site.