The natural diterpenoid kamebacetal A

Kamebacetal A, or (1S*,2S*,8S*,9R*,11R*,15S*,16S*,18R*)-15,18-dihydroxy-16-methoxy-12,12-di­methyl-6-methyl­ene-17-oxapenta­cyclo­[7.6.2.1^5,8.0^1,11.0^2,8]­octadecan-7-one, C₂₁H₃₀O₅, is a natural diterpenoid which has cytotoxic and antibacterial activity. The mol­ecule contains five six-membered rings and one five-membered ring. Ring A adopts a chair conformation, rings B, C, E and F adopt boat conformations, and ring D adopts an envelope conformation. The conjugated α-methyl­ene­cyclo­pentanone is the active part of the mol­ecule due to ring strain.

Key indicators

• Single-crystal X-ray study
• T = 289 K
• Mean [sigma](C-C) = 0.004 Å
• R factor = 0.043
• wR factor = 0.089
• Data-to-parameter ratio = 9.8

checkCIF/PLATON results

No syntax errors found



Alert level C
PLAT125_ALERT_4_C No _symmetry_space_group_name_Hall Given .......          ?

Alert level G
REFLT03_ALERT_4_G Please check that the estimate of the number of Friedel pairs is
            correct. If it is not, please give the correct count in the
            _publ_section_exptl_refinement section of the submitted CIF.
           From the CIF: _diffrn_reflns_theta_max           27.49
           From the CIF: _reflns_number_total               2354
           Count of symmetry unique reflns         2353
           Completeness (_total/calc)            100.04%
           TEST3: Check Friedels for noncentro structure
           Estimate of Friedel pairs measured         1
           Fraction of Friedel pairs measured     0.000
           Are heavy atom types Z>Si present           no

   0 ALERT level A = In general: serious problem
   0 ALERT level B = Potentially serious problem
   1 ALERT level C = Check and explain
   1 ALERT level G = General alerts; check

   0 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
   0 ALERT type 2 Indicator that the structure model may be wrong or deficient
   0 ALERT type 3 Indicator that the structure quality may be low
   2 ALERT type 4 Improvement, methodology, query or suggestion

---

Computing details

Data collection: XSCANS (Siemens, 1994); cell refinement: XSCANS; data reduction: SHELXTL (Siemens, 1991); program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: XP in SHELXTL; software used to prepare material for publication: SHELXTL.

(1S,2S,8S,9R,11R,15S,16S,18R)-15,18-dihydroxy-16-methoxy-12,12-dimethyl- 6-methylene-17-oxapentacyclo[7.6.2.1^5,8.0^1,11.0^2,8]octadecan-7-one

Crystal data

C21H30O5	Dx = 1.344 Mg m^−3
Mr = 362.45	Mo Kα radiation, λ = 0.71073 Å
Orthorhombic, P212121	Cell parameters from 38 reflections
a = 7.804 (1) Å	θ = 2.8–15.0°
b = 12.078 (2) Å	µ = 0.09 mm^−1
c = 19.007 (3) Å	T = 289 K
V = 1791.5 (5) Å^3	Plate, colourless
Z = 4	0.52 × 0.42 × 0.20 mm
F(000) = 784

Data collection

Siemens P4 diffractometer	Rint = 0.016
Radiation source: normal-focus sealed tube	θmax = 27.5°, θmin = 2.0°
Graphite monochromator	h = 0→10
ω scans	k = 0→15
2425 measured reflections	l = −1→24
2354 independent reflections	3 standard reflections every 97 reflections
1396 reflections with I > 2σ(I)	intensity decay: 1.3%

Refinement

Refinement on F^2	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F^2 > 2σ(F^2)] = 0.043	H atoms treated by a mixture of independent and constrained refinement
wR(F^2) = 0.089	w = 1/[σ^2(Fo^2) + (0.0369P)^2] where P = (Fo^2 + 2Fc^2)/3
S = 0.88	(Δ/σ)max = 0.025
2354 reflections	Δρmax = 0.17 e Å^−3
241 parameters	Δρmin = −0.16 e Å^−3
0 restraints	Extinction correction: SHELXL97 (Sheldrick, 1997), Fc^*=kFc[1+0.001xFc^2λ^3/sin(2θ)]^-1/4
Primary atom site location: structure-invariant direct methods	Extinction coefficient: 0.0096 (10)

Special details

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 (Ų)

	x	y	z	Uiso*/Ueq
O17	0.6579 (3)	0.44170 (18)	0.34155 (10)	0.0379 (6)
O2	0.9913 (3)	0.69681 (19)	0.43328 (14)	0.0500 (7)
H2O	1.0212	0.6372	0.4166	0.060*
O3	0.9349 (3)	0.48885 (18)	0.37339 (11)	0.0402 (6)
O4	0.5660 (3)	0.24903 (16)	0.46566 (13)	0.0445 (6)
H4O	0.6212	0.1922	0.4724	0.053*
O5	0.2645 (3)	0.4571 (2)	0.50351 (13)	0.0570 (7)
C1	0.7039 (4)	0.6144 (2)	0.40523 (15)	0.0279 (7)
C2	0.6688 (4)	0.5547 (2)	0.47728 (14)	0.0281 (7)
H2	0.5941	0.6035	0.5048	0.034*
C3	0.8278 (4)	0.5309 (3)	0.52281 (15)	0.0395 (8)
H3A	0.9153	0.4970	0.4936	0.047*
H3B	0.8731	0.6005	0.5402	0.047*
C4	0.7906 (4)	0.4546 (3)	0.58553 (16)	0.0450 (9)
H4A	0.7398	0.4979	0.6231	0.054*
H4B	0.8977	0.4243	0.6028	0.054*
C5	0.6689 (4)	0.3587 (3)	0.56634 (16)	0.0391 (8)
H5	0.7009	0.2903	0.5907	0.047*
C6	0.4849 (5)	0.3890 (3)	0.58032 (18)	0.0405 (9)
C7	0.4150 (4)	0.4360 (3)	0.51430 (17)	0.0367 (8)
C8	0.5640 (4)	0.4456 (2)	0.46228 (15)	0.0289 (7)
C9	0.5089 (4)	0.4465 (3)	0.38584 (15)	0.0309 (7)
H9	0.4372	0.3814	0.3767	0.037*
C10	0.4090 (4)	0.5498 (3)	0.36745 (16)	0.0367 (8)
H10A	0.3084	0.5551	0.3972	0.044*
H10B	0.3712	0.5459	0.3189	0.044*
C11	0.5238 (4)	0.6533 (2)	0.37806 (15)	0.0294 (7)
H11	0.4724	0.6936	0.4175	0.035*
C12	0.5170 (4)	0.7344 (3)	0.31515 (16)	0.0368 (8)
C13	0.6346 (5)	0.8316 (3)	0.33182 (18)	0.0443 (9)
H13A	0.5869	0.8734	0.3708	0.053*
H13B	0.6400	0.8803	0.2913	0.053*
C14	0.8159 (5)	0.7939 (3)	0.35091 (17)	0.0444 (9)
H14A	0.8656	0.7551	0.3112	0.053*
H14B	0.8863	0.8583	0.3605	0.053*
C15	0.8168 (4)	0.7179 (3)	0.41494 (17)	0.0357 (8)
H15	0.7670	0.7603	0.4539	0.043*
C16	0.7733 (4)	0.5314 (3)	0.35183 (16)	0.0310 (8)
H16	0.7885	0.5696	0.3068	0.037*
C18	0.6662 (4)	0.3426 (2)	0.48564 (16)	0.0342 (7)
H18	0.7817	0.3407	0.4654	0.041*
C19	0.5624 (5)	0.6863 (3)	0.24283 (15)	0.0513 (10)
H19A	0.5195	0.6120	0.2394	0.062*
H19B	0.6846	0.6859	0.2371	0.062*
H19C	0.5115	0.7310	0.2067	0.062*
C20	0.3297 (5)	0.7773 (3)	0.31030 (18)	0.0482 (10)
H20A	0.3246	0.8385	0.2781	0.058*
H20B	0.2921	0.8011	0.3560	0.058*
H20C	0.2566	0.7189	0.2938	0.058*
C21	1.0122 (4)	0.4214 (3)	0.32041 (19)	0.0537 (10)
H21A	0.9357	0.3623	0.3081	0.064*
H21B	1.1175	0.3910	0.3380	0.064*
H21C	1.0355	0.4656	0.2795	0.064*
C22	0.3954 (6)	0.3806 (3)	0.6386 (2)	0.0645 (12)
H22A	0.2823	0.4049	0.6397	0.077*
H22B	0.4451	0.3505	0.6787	0.077*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
O17	0.0372 (12)	0.0398 (13)	0.0366 (12)	−0.0044 (13)	0.0028 (11)	−0.0129 (11)
O2	0.0365 (14)	0.0466 (15)	0.0668 (18)	−0.0110 (12)	−0.0045 (14)	−0.0030 (14)
O3	0.0306 (12)	0.0459 (14)	0.0440 (13)	0.0038 (12)	0.0014 (12)	−0.0124 (11)
O4	0.0426 (14)	0.0250 (11)	0.0661 (16)	0.0020 (11)	−0.0059 (14)	−0.0017 (12)
O5	0.0326 (13)	0.0672 (17)	0.0712 (18)	0.0073 (14)	0.0109 (13)	0.0227 (16)
C1	0.0262 (17)	0.0290 (16)	0.0283 (16)	−0.0024 (15)	0.0013 (14)	−0.0030 (14)
C2	0.0304 (16)	0.0269 (15)	0.0269 (15)	−0.0009 (15)	0.0012 (15)	−0.0035 (14)
C3	0.0417 (19)	0.0424 (19)	0.0345 (17)	−0.0065 (19)	−0.0085 (17)	−0.0027 (16)
C4	0.051 (2)	0.048 (2)	0.0354 (18)	0.000 (2)	−0.0099 (17)	0.0072 (18)
C5	0.049 (2)	0.0309 (18)	0.0371 (19)	0.0043 (19)	−0.0055 (18)	0.0097 (15)
C6	0.051 (2)	0.0306 (18)	0.0400 (19)	−0.0028 (18)	0.0060 (18)	0.0069 (16)
C7	0.0339 (18)	0.0277 (17)	0.048 (2)	−0.0011 (17)	0.0053 (17)	0.0004 (16)
C8	0.0263 (15)	0.0250 (15)	0.0353 (17)	−0.0011 (15)	−0.0020 (14)	−0.0020 (14)
C9	0.0222 (16)	0.0295 (16)	0.0410 (18)	−0.0064 (16)	0.0011 (15)	−0.0050 (15)
C10	0.0345 (17)	0.0399 (18)	0.0356 (18)	−0.0030 (18)	−0.0042 (15)	0.0054 (16)
C11	0.0306 (18)	0.0296 (16)	0.0280 (16)	0.0010 (15)	0.0027 (15)	−0.0022 (14)
C12	0.048 (2)	0.0307 (18)	0.0312 (17)	0.0015 (17)	0.0026 (17)	0.0032 (14)
C13	0.058 (2)	0.0323 (18)	0.043 (2)	0.0018 (19)	0.0058 (19)	0.0106 (16)
C14	0.052 (2)	0.0355 (19)	0.046 (2)	−0.0126 (19)	0.011 (2)	0.0025 (17)
C15	0.0333 (19)	0.0354 (18)	0.0384 (18)	−0.0078 (17)	0.0069 (17)	−0.0044 (16)
C16	0.0297 (16)	0.0348 (19)	0.0285 (17)	−0.0015 (15)	0.0010 (14)	−0.0019 (15)
C18	0.0317 (17)	0.0308 (16)	0.0399 (18)	0.0013 (17)	−0.0042 (17)	−0.0008 (15)
C19	0.065 (2)	0.056 (2)	0.0325 (18)	0.004 (2)	0.001 (2)	0.0101 (17)
C20	0.054 (2)	0.045 (2)	0.046 (2)	0.014 (2)	−0.004 (2)	0.0075 (18)
C21	0.040 (2)	0.050 (2)	0.071 (3)	0.0094 (19)	0.002 (2)	−0.020 (2)
C22	0.076 (3)	0.066 (3)	0.052 (2)	0.003 (2)	0.013 (2)	0.016 (2)

Geometric parameters (Å, º)

O17—C16	1.423 (4)	C9—C10	1.512 (4)
O17—C9	1.436 (3)	C9—H9	0.9800
O2—C15	1.429 (4)	C10—C11	1.551 (4)
O2—H2O	0.8200	C10—H10A	0.9700
O3—C16	1.422 (3)	C10—H10B	0.9700
O3—C21	1.429 (4)	C11—C12	1.547 (4)
O4—C18	1.426 (4)	C11—H11	0.9800
O4—H4O	0.8200	C12—C13	1.524 (4)
O5—C7	1.218 (3)	C12—C19	1.534 (4)
C1—C16	1.526 (4)	C12—C20	1.554 (5)
C1—C15	1.541 (4)	C13—C14	1.530 (5)
C1—C11	1.569 (4)	C13—H13A	0.9700
C1—C2	1.572 (4)	C13—H13B	0.9700
C2—C3	1.540 (4)	C14—C15	1.524 (4)
C2—C8	1.576 (4)	C14—H14A	0.9700
C2—H2	0.9800	C14—H14B	0.9700
C3—C4	1.535 (4)	C15—H15	0.9800
C3—H3A	0.9700	C16—H16	0.9800
C3—H3B	0.9700	C18—H18	0.9800
C4—C5	1.542 (4)	C19—H19A	0.9600
C4—H4A	0.9700	C19—H19B	0.9600
C4—H4B	0.9700	C19—H19C	0.9600
C5—C6	1.505 (4)	C20—H20A	0.9600
C5—C18	1.546 (4)	C20—H20B	0.9600
C5—H5	0.9800	C20—H20C	0.9600
C6—C22	1.313 (5)	C21—H21A	0.9600
C6—C7	1.482 (4)	C21—H21B	0.9600
C7—C8	1.531 (4)	C21—H21C	0.9600
C8—C9	1.515 (4)	C22—H22A	0.9300
C8—C18	1.543 (4)	C22—H22B	0.9300
C16—O17—C9	113.7 (2)	C12—C11—H11	105.3
C15—O2—H2O	109.5	C10—C11—H11	105.3
C16—O3—C21	112.2 (2)	C1—C11—H11	105.3
C18—O4—H4O	109.5	C13—C12—C19	109.8 (3)
C16—C1—C15	114.2 (2)	C13—C12—C11	107.9 (3)
C16—C1—C11	107.2 (2)	C19—C12—C11	116.4 (3)
C15—C1—C11	108.0 (2)	C13—C12—C20	108.8 (3)
C16—C1—C2	109.9 (2)	C19—C12—C20	106.9 (3)
C15—C1—C2	111.6 (2)	C11—C12—C20	106.8 (3)
C11—C1—C2	105.6 (2)	C12—C13—C14	112.1 (3)
C3—C2—C1	115.8 (2)	C12—C13—H13A	109.2
C3—C2—C8	111.4 (2)	C14—C13—H13A	109.2
C1—C2—C8	108.4 (2)	C12—C13—H13B	109.2
C3—C2—H2	106.9	C14—C13—H13B	109.2
C1—C2—H2	106.9	H13A—C13—H13B	107.9
C8—C2—H2	106.9	C15—C14—C13	111.9 (3)
C4—C3—C2	113.3 (3)	C15—C14—H14A	109.2
C4—C3—H3A	108.9	C13—C14—H14A	109.2
C2—C3—H3A	108.9	C15—C14—H14B	109.2
C4—C3—H3B	108.9	C13—C14—H14B	109.2
C2—C3—H3B	108.9	H14A—C14—H14B	107.9
H3A—C3—H3B	107.7	O2—C15—C14	107.9 (3)
C3—C4—C5	112.6 (2)	O2—C15—C1	115.4 (3)
C3—C4—H4A	109.1	C14—C15—C1	112.9 (3)
C5—C4—H4A	109.1	O2—C15—H15	106.7
C3—C4—H4B	109.1	C14—C15—H15	106.7
C5—C4—H4B	109.1	C1—C15—H15	106.7
H4A—C4—H4B	107.8	O17—C16—O3	109.0 (2)
C6—C5—C4	111.3 (3)	O17—C16—C1	111.5 (2)
C6—C5—C18	101.1 (3)	O3—C16—C1	111.1 (2)
C4—C5—C18	109.7 (3)	O17—C16—H16	108.4
C6—C5—H5	111.4	O3—C16—H16	108.4
C4—C5—H5	111.4	C1—C16—H16	108.4
C18—C5—H5	111.4	O4—C18—C8	106.2 (2)
C22—C6—C7	123.2 (3)	O4—C18—C5	111.8 (3)
C22—C6—C5	129.6 (3)	C8—C18—C5	101.0 (2)
C7—C6—C5	107.2 (3)	O4—C18—H18	112.4
O5—C7—C6	125.3 (3)	C8—C18—H18	112.4
O5—C7—C8	127.4 (3)	C5—C18—H18	112.4
C6—C7—C8	107.2 (3)	C12—C19—H19A	109.5
C9—C8—C7	113.9 (3)	C12—C19—H19B	109.5
C9—C8—C18	115.4 (2)	H19A—C19—H19B	109.5
C7—C8—C18	98.4 (3)	C12—C19—H19C	109.5
C9—C8—C2	108.3 (2)	H19A—C19—H19C	109.5
C7—C8—C2	109.9 (2)	H19B—C19—H19C	109.5
C18—C8—C2	110.7 (2)	C12—C20—H20A	109.5
O17—C9—C10	108.4 (3)	C12—C20—H20B	109.5
O17—C9—C8	109.4 (2)	H20A—C20—H20B	109.5
C10—C9—C8	111.9 (3)	C12—C20—H20C	109.5
O17—C9—H9	109.0	H20A—C20—H20C	109.5
C10—C9—H9	109.0	H20B—C20—H20C	109.5
C8—C9—H9	109.0	O3—C21—H21A	109.5
C9—C10—C11	109.7 (2)	O3—C21—H21B	109.5
C9—C10—H10A	109.7	H21A—C21—H21B	109.5
C11—C10—H10A	109.7	O3—C21—H21C	109.5
C9—C10—H10B	109.7	H21A—C21—H21C	109.5
C11—C10—H10B	109.7	H21B—C21—H21C	109.5
H10A—C10—H10B	108.2	C6—C22—H22A	120.0
C12—C11—C10	113.0 (2)	C6—C22—H22B	120.0
C12—C11—C1	118.4 (3)	H22A—C22—H22B	120.0
C10—C11—C1	108.6 (2)
C16—C1—C2—C3	77.5 (3)	C15—C1—C11—C12	49.1 (3)
C15—C1—C2—C3	−50.1 (3)	C2—C1—C11—C12	168.5 (2)
C11—C1—C2—C3	−167.2 (3)	C16—C1—C11—C10	56.1 (3)
C16—C1—C2—C8	−48.4 (3)	C15—C1—C11—C10	179.6 (2)
C15—C1—C2—C8	−176.1 (2)	C2—C1—C11—C10	−61.0 (3)
C11—C1—C2—C8	66.9 (3)	C10—C11—C12—C13	−179.9 (3)
C1—C2—C3—C4	−169.6 (2)	C1—C11—C12—C13	−51.4 (4)
C8—C2—C3—C4	−45.1 (3)	C10—C11—C12—C19	−55.9 (4)
C2—C3—C4—C5	40.8 (4)	C1—C11—C12—C19	72.5 (4)
C3—C4—C5—C6	−92.2 (3)	C10—C11—C12—C20	63.4 (3)
C3—C4—C5—C18	18.9 (4)	C1—C11—C12—C20	−168.2 (3)
C4—C5—C6—C22	−86.3 (4)	C19—C12—C13—C14	−73.9 (3)
C18—C5—C6—C22	157.2 (4)	C11—C12—C13—C14	53.9 (4)
C4—C5—C6—C7	92.0 (3)	C20—C12—C13—C14	169.4 (3)
C18—C5—C6—C7	−24.4 (3)	C12—C13—C14—C15	−59.6 (4)
C22—C6—C7—O5	−10.9 (6)	C13—C14—C15—O2	−173.8 (3)
C5—C6—C7—O5	170.6 (3)	C13—C14—C15—C1	57.4 (4)
C22—C6—C7—C8	172.5 (3)	C16—C1—C15—O2	−55.3 (4)
C5—C6—C7—C8	−6.0 (3)	C11—C1—C15—O2	−174.4 (3)
O5—C7—C8—C9	−20.2 (5)	C2—C1—C15—O2	70.1 (3)
C6—C7—C8—C9	156.2 (3)	C16—C1—C15—C14	69.5 (3)
O5—C7—C8—C18	−142.8 (4)	C11—C1—C15—C14	−49.6 (3)
C6—C7—C8—C18	33.6 (3)	C2—C1—C15—C14	−165.2 (3)
O5—C7—C8—C2	101.5 (4)	C9—O17—C16—O3	120.0 (3)
C6—C7—C8—C2	−82.0 (3)	C9—O17—C16—C1	−3.1 (3)
C3—C2—C8—C9	−137.7 (2)	C21—O3—C16—O17	63.8 (3)
C1—C2—C8—C9	−9.3 (3)	C21—O3—C16—C1	−172.9 (3)
C3—C2—C8—C7	97.3 (3)	C15—C1—C16—O17	−175.9 (2)
C1—C2—C8—C7	−134.2 (3)	C11—C1—C16—O17	−56.3 (3)
C3—C2—C8—C18	−10.3 (3)	C2—C1—C16—O17	57.9 (3)
C1—C2—C8—C18	118.2 (3)	C15—C1—C16—O3	62.3 (3)
C16—O17—C9—C10	62.9 (3)	C11—C1—C16—O3	−178.2 (2)
C16—O17—C9—C8	−59.4 (3)	C2—C1—C16—O3	−63.9 (3)
C7—C8—C9—O17	−172.9 (2)	C9—C8—C18—O4	−52.8 (3)
C18—C8—C9—O17	−60.1 (3)	C7—C8—C18—O4	68.7 (3)
C2—C8—C9—O17	64.6 (3)	C2—C8—C18—O4	−176.3 (2)
C7—C8—C9—C10	67.0 (3)	C9—C8—C18—C5	−169.6 (3)
C18—C8—C9—C10	179.7 (3)	C7—C8—C18—C5	−48.1 (3)
C2—C8—C9—C10	−55.6 (3)	C2—C8—C18—C5	67.0 (3)
O17—C9—C10—C11	−58.6 (3)	C6—C5—C18—O4	−67.0 (3)
C8—C9—C10—C11	62.1 (3)	C4—C5—C18—O4	175.3 (2)
C9—C10—C11—C12	132.7 (3)	C6—C5—C18—C8	45.5 (3)
C9—C10—C11—C1	−0.7 (3)	C4—C5—C18—C8	−72.2 (3)
C16—C1—C11—C12	−74.4 (3)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
O2—H2O···O3	0.82	2.08	2.793 (3)	145
O4—H4O···O5^i	0.82	2.17	2.990 (3)	177
C20—H20A···O17^ii	0.96	2.60	3.505 (4)	158

Symmetry codes: (i) x+1/2, −y+1/2, −z+1; (ii) −x+1, y+1/2, −z+1/2.