Literature DB >> 21202093

Trichodermin (4β-acet-oxy-12,13-epoxy-trichothec-9-ene).

Shao-Yuan Chen, Chu-Long Zhang, Yu-Zhe Chen, Fu-Cheng Lin.

Abstract

In the title natural product, C(17)H(24)O(4), which is a very potent inhibitor of protein synthesis in mammalian cells, the five-membered ring displays an envelope conformation, whereas the two six-membered rings show different conformations, viz. chair and half-chair.

Entities: CellLine Chemical Disease Gene Species

Year: 2008 PMID： 21202093 PMCID： PMC2960951 DOI： 10.1107/S1600536808006168

Source DB: PubMed Journal: Acta Crystallogr Sect E Struct Rep Online ISSN： 1600-5368

Related literature

For related literature, see: Nielsen et al. (2005 ▶); Wei et al. (1974 ▶); Zhang et al. (2007 ▶). For details of ring puckering analysis, see: Cremer & Pople (1975 ▶).

Experimental

Crystal data

C17H24O4 M = 292.36 Orthorhombic, a = 7.0127 (3) Å b = 8.4102 (3) Å c = 26.2786 (10) Å V = 1549.86 (10) Å3 Z = 4 Mo Kα radiation μ = 0.09 mm−1 T = 293 (2) K 0.41 × 0.40 × 0.37 mm

Data collection

Rigaku R-AXIS RAPID IP diffractometer Absorption correction: none 14719 measured reflections 2046 independent reflections 1726 reflections with I > 2σ(I) R int = 0.027

Refinement

R[F 2 > 2σ(F 2)] = 0.036 wR(F 2) = 0.104 S = 1.11 2046 reflections 195 parameters H-atom parameters constrained Δρmax = 0.18 e Å−3 Δρmin = −0.13 e Å−3 Data collection: PROCESS-AUTO (Rigaku, 1998 ▶); cell refinement: PROCESS-AUTO; data reduction: CrystalStructure (Rigaku/MSC, 2002 ▶); program(s) used to solve structure: SIR92 (Altomare et al., 1993 ▶); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 ▶); molecular graphics: ORTEP-3 for Windows (Farrugia, 1997 ▶); software used to prepare material for publication: WinGX (Farrugia, 1999 ▶). Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536808006168/hb2704sup1.cif Structure factors: contains datablocks I. DOI: 10.1107/S1600536808006168/hb2704Isup2.hkl Additional supplementary materials: crystallographic information; 3D view; checkCIF report

C₁₇H₂₄O₄	D_x = 1.253 Mg m⁻³
M_r = 292.36	Melting point = 319–320 K
Orthorhombic, P2₁2₁2₁	Mo Kα radiation λ = 0.71073 Å
Hall symbol: P 2ac 2ab	Cell parameters from 9452 reflections
a = 7.0127 (3) Å	θ = 3.2–27.0º
b = 8.4102 (3) Å	µ = 0.09 mm⁻¹
c = 26.2786 (10) Å	T = 293 (2) K
V = 1549.86 (10) Å³	Chunk, colorless
Z = 4	0.41 × 0.40 × 0.37 mm
F₀₀₀ = 632.00

Rigaku R-AXIS RAPID IP diffractometer	2046 independent reflections
Radiation source: fine-focus sealed tube	1726 reflections with I > 2σ(I)
Monochromator: graphite	R_int = 0.027
Detector resolution: 10.0 pixels mm^-1	θ_max = 27.4º
T = 291(2) K	θ_min = 3.0º
ω scans	h = −9→9
Absorption correction: none	k = −9→10
14719 measured reflections	l = −34→33

Refinement on F²	Hydrogen site location: inferred from neighbouring sites
Least-squares matrix: full	H-atom parameters constrained
R[F² > 2σ(F²)] = 0.036	w = 1/[σ²(F_o²) + (0.0625P)² + 0.0793P] where P = (F_o² + 2F_c²)/3
wR(F²) = 0.104	(Δ/σ)_max < 0.001
S = 1.11	Δρ_max = 0.18 e Å⁻³
2046 reflections	Δρ_min = −0.13 e Å⁻³
195 parameters	Extinction correction: SHELXL97 (Sheldrick, 2008), Fc^*=kFc[1+0.001xFc²λ³/sin(2θ)]^-1/4
Primary atom site location: structure-invariant direct methods	Extinction coefficient: 0.032 (3)
Secondary atom site location: difference Fourier map

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.

	x	y	z	U_iso*/U_eq
C14	0.6512 (4)	0.9319 (2)	0.36688 (10)	0.0589 (6)
H14A	0.6793	1.0017	0.3390	0.088*
H14B	0.7086	0.9727	0.3974	0.088*
H14C	0.5156	0.9253	0.3714	0.088*
C7	0.4588 (3)	0.6081 (3)	0.39880 (9)	0.0533 (5)
H7A	0.3918	0.7071	0.4051	0.064*
H7B	0.4180	0.5680	0.3660	0.064*
C8	0.4061 (3)	0.4884 (3)	0.43987 (9)	0.0589 (6)
H8A	0.4140	0.5397	0.4729	0.071*
H8B	0.2752	0.4548	0.4348	0.071*
C13	0.4905 (3)	0.7268 (3)	0.27735 (9)	0.0641 (6)
H13A	0.4452	0.6423	0.2553	0.077*
H13B	0.3912	0.7860	0.2947	0.077*
O2	0.6596 (2)	0.81223 (19)	0.26194 (6)	0.0629 (4)
C15	0.7438 (4)	0.6934 (3)	0.45039 (7)	0.0564 (5)
H15A	0.6641	0.7780	0.4626	0.085*
H15B	0.8732	0.7299	0.4482	0.085*
H15C	0.7369	0.6051	0.4735	0.085*
C5	0.7308 (3)	0.7668 (2)	0.35565 (7)	0.0433 (4)
C18	1.1534 (4)	1.1714 (3)	0.34760 (9)	0.0627 (6)
H18A	1.2106	1.2347	0.3739	0.094*
H18B	1.0445	1.2262	0.3341	0.094*
H18C	1.2444	1.1536	0.3209	0.094*
C6	0.6749 (3)	0.6406 (2)	0.39726 (7)	0.0421 (4)
C12	0.6697 (3)	0.7020 (2)	0.30416 (7)	0.0465 (5)
C9	0.5325 (3)	0.3449 (2)	0.43982 (8)	0.0525 (5)
C16	0.4718 (4)	0.2079 (3)	0.47267 (9)	0.0676 (6)
H16A	0.5618	0.1226	0.4692	0.101*
H16B	0.3478	0.1721	0.4622	0.101*
H16C	0.4669	0.2415	0.5076	0.101*
O4	1.0964 (3)	0.9811 (2)	0.41353 (6)	0.0741 (5)
C17	1.0918 (3)	1.0153 (2)	0.36930 (9)	0.0506 (5)
O3	1.0281 (2)	0.91593 (16)	0.33263 (5)	0.0502 (4)
C4	0.9533 (3)	0.7633 (2)	0.34927 (8)	0.0440 (4)
H4	1.0141	0.7309	0.3812	0.053*
C11	0.7705 (3)	0.4800 (2)	0.38357 (7)	0.0419 (4)
H11	0.9069	0.4892	0.3911	0.050*
C10	0.6935 (3)	0.3431 (2)	0.41348 (8)	0.0486 (5)
H10	0.7641	0.2495	0.4136	0.058*
C2	0.8015 (3)	0.5625 (2)	0.29623 (7)	0.0461 (4)
H2	0.7955	0.5252	0.2609	0.055*
O1	0.7508 (2)	0.43802 (14)	0.33066 (5)	0.0462 (3)
C3	0.9936 (3)	0.6396 (2)	0.30725 (8)	0.0497 (5)
H3A	1.0438	0.6907	0.2770	0.060*
H3B	1.0849	0.5610	0.3189	0.060*

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
C14	0.0555 (13)	0.0392 (9)	0.0820 (14)	0.0064 (9)	0.0048 (11)	−0.0083 (10)
C7	0.0408 (11)	0.0516 (10)	0.0675 (13)	0.0032 (9)	0.0035 (10)	−0.0066 (10)
C8	0.0493 (12)	0.0608 (12)	0.0667 (13)	−0.0051 (11)	0.0101 (10)	−0.0109 (11)
C13	0.0542 (13)	0.0734 (14)	0.0648 (13)	0.0018 (12)	−0.0151 (11)	0.0026 (12)
O2	0.0649 (10)	0.0625 (9)	0.0612 (9)	0.0067 (8)	−0.0071 (8)	0.0092 (7)
C15	0.0640 (13)	0.0531 (10)	0.0520 (11)	−0.0085 (11)	0.0012 (10)	−0.0139 (9)
C5	0.0388 (9)	0.0374 (8)	0.0537 (10)	0.0026 (8)	−0.0021 (8)	−0.0079 (8)
C18	0.0740 (16)	0.0468 (11)	0.0672 (13)	−0.0104 (11)	0.0040 (12)	−0.0033 (10)
C6	0.0401 (10)	0.0383 (9)	0.0480 (10)	0.0012 (7)	−0.0008 (8)	−0.0095 (8)
C12	0.0442 (10)	0.0446 (10)	0.0508 (10)	0.0015 (8)	−0.0046 (9)	−0.0020 (8)
C9	0.0568 (12)	0.0509 (11)	0.0497 (10)	−0.0096 (10)	−0.0015 (10)	−0.0071 (9)
C16	0.0737 (16)	0.0677 (13)	0.0613 (13)	−0.0158 (13)	0.0082 (12)	0.0011 (11)
O4	0.1000 (14)	0.0670 (10)	0.0553 (9)	−0.0305 (10)	−0.0103 (9)	−0.0022 (8)
C17	0.0456 (11)	0.0478 (10)	0.0583 (12)	−0.0069 (9)	−0.0008 (9)	−0.0065 (9)
O3	0.0536 (8)	0.0426 (7)	0.0543 (8)	−0.0087 (6)	−0.0013 (6)	−0.0036 (6)
C4	0.0412 (10)	0.0386 (9)	0.0524 (10)	−0.0014 (8)	−0.0021 (8)	−0.0025 (8)
C11	0.0401 (10)	0.0399 (8)	0.0457 (10)	0.0007 (8)	−0.0017 (8)	−0.0067 (7)
C10	0.0531 (12)	0.0406 (9)	0.0521 (10)	−0.0014 (9)	−0.0032 (9)	−0.0061 (8)
C2	0.0498 (11)	0.0437 (9)	0.0447 (9)	0.0012 (9)	0.0008 (8)	−0.0087 (8)
O1	0.0520 (8)	0.0385 (6)	0.0481 (7)	−0.0008 (6)	−0.0003 (6)	−0.0100 (5)
C3	0.0452 (11)	0.0453 (10)	0.0586 (11)	0.0037 (8)	0.0051 (9)	−0.0071 (9)

O1—C2	1.429 (2)	C15—H15B	0.9600
O1—C11	1.441 (2)	C15—H15C	0.9600
O2—C12	1.447 (2)	C5—C12	1.521 (3)
O2—C13	1.444 (3)	C5—C4	1.569 (3)
O3—C4	1.454 (2)	C5—C6	1.574 (3)
O3—C17	1.351 (2)	C18—C17	1.496 (3)
O4—C17	1.198 (3)	C18—H18A	0.9600
C9—C10	1.325 (3)	C18—H18B	0.9600
C14—C5	1.526 (2)	C18—H18C	0.9600
C14—H14A	0.9600	C6—C11	1.550 (2)
C14—H14B	0.9600	C12—C2	1.508 (3)
C14—H14C	0.9600	C9—C16	1.501 (3)
C7—C8	1.522 (3)	C16—H16A	0.9600
C7—C6	1.540 (3)	C16—H16B	0.9600
C7—H7A	0.9700	C16—H16C	0.9600
C7—H7B	0.9700	C4—C3	1.543 (3)
C8—C9	1.497 (3)	C4—H4	0.9800
C8—H8A	0.9700	C11—C10	1.495 (3)
C8—H8B	0.9700	C11—H11	0.9800
C13—C12	1.456 (3)	C10—H10	0.9300
C13—H13A	0.9700	C2—C3	1.523 (3)
C13—H13B	0.9700	C2—H2	0.9800
C15—C6	1.543 (3)	C3—H3A	0.9700
C15—H15A	0.9600	C3—H3B	0.9700

C5—C14—H14A	109.5	C11—C6—C5	108.57 (14)
C5—C14—H14B	109.5	O2—C12—C13	59.67 (13)
H14A—C14—H14B	109.5	O2—C12—C2	114.98 (16)
C5—C14—H14C	109.5	C13—C12—C2	125.02 (19)
H14A—C14—H14C	109.5	O2—C12—C5	117.80 (16)
H14B—C14—H14C	109.5	C13—C12—C5	128.51 (19)
C8—C7—C6	112.00 (18)	C2—C12—C5	103.23 (15)
C8—C7—H7A	109.2	C10—C9—C8	120.9 (2)
C6—C7—H7A	109.2	C10—C9—C16	122.2 (2)
C8—C7—H7B	109.2	C8—C9—C16	116.76 (19)
C6—C7—H7B	109.2	C9—C16—H16A	109.5
H7A—C7—H7B	107.9	C9—C16—H16B	109.5
C9—C8—C7	112.90 (18)	H16A—C16—H16B	109.5
C9—C8—H8A	109.0	C9—C16—H16C	109.5
C7—C8—H8A	109.0	H16A—C16—H16C	109.5
C9—C8—H8B	109.0	H16B—C16—H16C	109.5
C7—C8—H8B	109.0	O4—C17—O3	123.5 (2)
H8A—C8—H8B	107.8	O4—C17—C18	125.0 (2)
O2—C13—C12	59.88 (13)	O3—C17—C18	111.50 (19)
O2—C13—H13A	117.8	C17—O3—C4	116.79 (15)
C12—C13—H13A	117.8	O3—C4—C3	108.30 (15)
O2—C13—H13B	117.8	O3—C4—C5	111.98 (16)
C12—C13—H13B	117.8	C3—C4—C5	105.74 (16)
H13A—C13—H13B	114.9	O3—C4—H4	110.2
C13—O2—C12	60.45 (13)	C3—C4—H4	110.2
C6—C15—H15A	109.5	C5—C4—H4	110.2
C6—C15—H15B	109.5	O1—C11—C10	106.50 (15)
H15A—C15—H15B	109.5	O1—C11—C6	113.33 (15)
C6—C15—H15C	109.5	C10—C11—C6	113.11 (15)
H15A—C15—H15C	109.5	O1—C11—H11	107.9
H15B—C15—H15C	109.5	C10—C11—H11	107.9
C12—C5—C14	113.27 (18)	C6—C11—H11	107.9
C12—C5—C4	100.28 (16)	C9—C10—C11	125.0 (2)
C14—C5—C4	113.68 (16)	C9—C10—H10	117.5
C12—C5—C6	107.84 (15)	C11—C10—H10	117.5
C14—C5—C6	112.86 (16)	O1—C2—C12	109.28 (15)
C4—C5—C6	108.03 (16)	O1—C2—C3	114.30 (16)
C17—C18—H18A	109.5	C12—C2—C3	100.66 (14)
C17—C18—H18B	109.5	O1—C2—H2	110.7
H18A—C18—H18B	109.5	C12—C2—H2	110.7
C17—C18—H18C	109.5	C3—C2—H2	110.7
H18A—C18—H18C	109.5	C2—O1—C11	114.05 (13)
H18B—C18—H18C	109.5	C2—C3—C4	105.12 (15)
C7—C6—C15	109.60 (17)	C2—C3—H3A	110.7
C7—C6—C11	106.10 (16)	C4—C3—H3A	110.7
C15—C6—C11	108.99 (17)	C2—C3—H3B	110.7
C7—C6—C5	112.52 (16)	C4—C3—H3B	110.7
C15—C6—C5	110.89 (15)	H3A—C3—H3B	108.8

D—H···A	D—H	H···A	D···A	D—H···A
C14—H14a···O2	0.96	2.58	2.936 (3)	102

Table 1

Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
C14—H14a⋯O2	0.96	2.58	2.936 (3)	102

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