Cyclo­linopeptide B methanol tris­olvate

Schatte, G.; Labiuk, S.; Li, B.; Burnett, P.-G.; Reaney, M.; Grochulski, P.; Fodje, M.; Yang, J.; Sammynaiken, R.

doi:10.1107/S1600536811051488

Volume 68
Part 1
Pages o50-o51
January 2012

Received 22 November 2011
Accepted 29 November 2011
Online 7 December 2011

Key indicators
Single-crystal Synchrotron study
T = 100 K
Mean (C-C) = 0.004 Å
R = 0.048
wR = 0.116
Data-to-parameter ratio = 18.9
Details

Cyclolinopeptide B methanol trisolvate

Gabriele Schatte,^a ^* Shaunivan Labiuk,^b Bonnie Li,^c Peta-Gaye Burnett,^c Martin Reaney,^c Pawel Grochulski,^b Michel Fodje,^b Jian Yang ^d and Ramaswami Sammynaiken ^a ^*

^aSaskatchewan Structural Sciences Centre, University of Saskatchewan, Saskatoon, Saskatchewan, Canada S7N 5C9,^bCanadian Light Source Inc., University of Saskatchewan, Saskatoon, Saskatchewan, Canada S7N 0X4,^cCollege of Agriculture & Bioresources, University of Saskatchewan, Saskatoon, Saskatchewan, Canada S7N 5A8, and ^dCollege of Pharmacy and Nutrition, University of Saskatchewan, Saskatoon, Saskatchewan, Canada S7N 5C9
Correspondence e-mail: gabriele.schatte@usask.ca, r.sammynaiken@usask.ca

The title compound, C₅₆H₈₃N₉O₉S·3CH₃OH, is a methanol trisolvate of the cyclolinopeptide cyclo(Met¹-Leu²-Ile³-Pro⁴-Pro⁵-Phe⁶-Phe⁷-Val⁸-Ile⁹) (henceforth referred to as CLP-B), which was isolated from flaxseed oil. All the amino acid residues are in an L-configuration based on the CORN rule. The cyclic nonapeptide exhibits eight trans peptide bonds and one cis peptide bond observed between the two proline residues. The conformation is stabilized by an [alpha] -turn and two consecutive [beta] -turns each containing a N-HO hydrogen bond between the carbonyl group O atom of the first residue and the amide group H atom of the fourth ( [alpha] -turn) or the third residue ( [beta] -turns), repectively. In the crystal, the components of the structure are linked by N-HO and O-HO hydrogen bonds into chains parallel to the a axis.

Related literature

For the isolation of cyclolinopeptides A to B, B to E, F to I and characterization by multi-dimensional NMR spectroscopy, see: Matsumoto et al. (2002), Morita et al. (1999) and Matsumoto et al. (2001), respectively. For the isolation of the related cyclolinopeptide A and its structure determination by single X-ray diffraction in the presence of different solvates, see: Di Blasio et al. (1987, 1989); Matsumoto et al. (2002); Quail et al. (2009). For the X-ray single-crystal structure of cyclolinopeptide K, see: Jadhav et al. (2011). For the synthesis of cyclopeptides, see: Rovero et al. (1991); Ghadiri et al. (1993). For the immuno-suppressive activity of CLP-A, see: Wieczorek et al. (1991) and for its cytoproctective ability, see: Gaymes et al. (1997). For the biomolecular interaction with human albumin of CLP-A, see: Rempel et al. (2010). For details of the CORN rule, see: Cahn et al. (1966). For details of the absolute structure, see: Flack & Bernardinelli (2000).

Experimental

Crystal data

C₅₆H₈₃N₉O₉S·3CH₄O
M_r = 1154.50
Monoclinic, P 2₁
a = 10.374 (2) Å
b = 19.624 (4) Å
c = 15.576 (4) Å
= 100.0653 (13)°
V = 3122.1 (12) Å³
Z = 2
Synchrotron radiation
= 0.68878 Å
= 0.12 mm^-1
T = 100 K
0.13 × 0.10 × 0.10 mm

Data collection

300mm 16K Rayonix MX300 HE CCD detector with an ACCEL MD2 microdiffractometer
Absorption correction: multi-scan (SADABS; Bruker, 2008) T_min = 0.985, T_max = 0.988
177237 measured reflections
15255 independent reflections
13940 reflections with I > 2(I)
R_int = 0.055

Refinement

R[F² > 2(F²)] = 0.048
wR(F²) = 0.116
S = 1.12
15255 reflections
809 parameters
2 restraints
H atoms treated by a mixture of independent and constrained refinement
_max = 0.64 e Å^-3
_min = -0.34 e Å^-3
Absolute structure: Flack (1983), 7080 Friedel pairs
Flack parameter: 0.09 (7)

Table 1
Hydrogen-bond geometry (Å, °)

D-HA	D-H	HA	DA	D-HA
N1-H1DO7	0.87 (3)	2.29 (3)	3.046 (3)	145 (3)
N2-H2DO8	0.87 (3)	2.11 (3)	2.923 (3)	155 (3)
N7-H7DO3	0.84 (3)	2.18 (3)	2.956 (3)	153 (3)
N8-H8DO2ⁱ	0.83 (3)	2.52 (3)	3.274 (3)	151 (3)
N9-H9DO60	0.91 (3)	2.00 (3)	2.896 (3)	169 (3)
N6-H6DO70ⁱⁱ	0.77 (3)	2.34 (3)	3.071 (3)	159 (3)
O60-H60O1ⁱ	0.95 (4)	1.79 (4)	2.705 (3)	160 (4)
O70-H70O4ⁱⁱⁱ	1.01 (3)	1.91 (2)	2.861 (3)	157 (3)
O80-H80O9^iv	0.94 (6)	1.86 (6)	2.786 (3)	165 (5)
Symmetry codes: (i) x+1, y, z; (ii) $[-x, y-{\script{1\over 2}}, -z]$ ; (iii) $[-x, y+{\script{1\over 2}}, -z]$ ; (iv) $[-x, y+{\script{1\over 2}}, -z+1]$ .

Table 2
Backbone torsion angles [varphi] , [psi] , [omega] and side chain torsion angle [chi] 1 (°)in CLP-B

				1
Met¹	-83.2 (3)	-3.7 (3)	174.6 (2)	-56.0 (3)
Leu²	53.4 (3)	42.8 (3)	-172.4 (2)	-48.7 (3)
Ile³	-117.2 (3)	99.9 (2)	172.9 (2)	-61.9 (3)
Pro⁴	-76.8 (3)	157.2 (2)	-174.4 (2)	32.3 (2)
Pro⁵	-91.4 (3)	-4.6 (3)	-9.8 (3)	34.2 (2)
Phe⁶	-98.9 (3)	-23.7 (3)	-166.6 (2)	-75.2 (2)
Phe⁷	-116.6 (2)	72.7 (3)	-171.5 (2)	-59.6 (3)
Val⁸	-63.9 (3)	-43.7 (3)	-162.8 (2)	-66.1 (19)
Ile⁹	-69.8 (3)	-19.9 (3)	-177.1 (2)	-155.2 (2)

Data collection: MXDC, Macromolecular Crystallography Data Collector (Canadian Light Source, 2007); cell refinement: SAINT (Bruker, 2008); data reduction: SAINT; program(s) used to solve structure: SIR2004 (Burla et al., 2005); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: CAMERON (Watkin et al., 1993) and SHELXTL (Sheldrick, 2008); software used to prepare material for publication: publCIF (Westrip, 2010).

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: LH5387 ).

Acknowledgements

Funding for this research was contributed by The Agriculture Development Fund (ADF) administered by the Saskatchewan Ministry of Agriculture (SMA), the Total Utililization Flax Genomics and the National Sciences and Engineering Research Council (NSERC). The data collection was performed at the Canadian Light Source (CLS), which is supported by the Natural Sciences and Engineering Research Council of Canada, the National Research Council Canada, the Canadian Institutes of Health Research, the Province of Saskatchewan, Western Economic Diversification Canada and the University of Saskatchewan.

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organic compounds