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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 [sigma](C-C) = 0.004 Å
R = 0.048
wR = 0.116
Data-to-parameter ratio = 18.9
Details
Open access

Cyclolinopeptide B methanol trisolvate

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-H...O 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-H...O and O-H...O 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[Matsumoto, T., Shishido, A., Morita, H., Itokawa, H. & Takeya, K. (2002). Tetrahedron, 58, 5135-5140.]), Morita et al. (1999[Morita, H., Shishido, A., Matsumoto, T., Itokawa, H. & Takeya, K. (1999). Tetrahedron, 55, 967-976.]) and Matsumoto et al. (2001[Matsumoto, T., Shishido, A., Morita, H., Itokawa, H. & Takeya, K. (2001). Phytochemistry, 57, 251-260.]), 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[Di Blasio, B., Benedetti, E., Pavone, C. & Goodman, M. (1987). Biopolymers, 26, 2099-2102.], 1989[Di Blasio, B., Benedetti, E., Pavone, C. & Temussi, P. A. (1989). J. Am. Chem. Soc. 111, 9089-9092.]); Matsumoto et al. (2002[Matsumoto, T., Shishido, A., Morita, H., Itokawa, H. & Takeya, K. (2002). Tetrahedron, 58, 5135-5140.]); Quail et al. (2009[Quail, J. W., Shen, J., Reaney, M. J. T. & Sammynaiken, R. (2009). Acta Cryst. E65, o1913-o1914.]). For the X-ray single-crystal structure of cyclolinopeptide K, see: Jadhav et al. (2011[Jadhav, P., Schatte, G., Labiuk, S., Burnett, P.-G., Li, B., Okinyo-Owiti, D., Reaney, M., Grochulski, P., Fodje, M. & Sammynaiken, R. (2011). Acta Cryst. E67, o2360-o2361.]). For the synthesis of cyclopeptides, see: Rovero et al. (1991[Rovero, P., Quartara, L. & Fabbri, G. (1991). Tetrahedron Lett. 32, 2639-2642.]); Ghadiri et al. (1993[Ghadiri, M. R., Granja, J. R., Milligan, R. A., McRee, D. E. & Khazanovich, N. (1993). Nature (London), 366, 324-327.]). For the immuno-suppressive activity of CLP-A, see: Wieczorek et al. (1991[Wieczorek, Z., Bengsston, B., Trojnar, I. & Siemion, I. Z. (1991). Peptide Res. 4, 275-283.]) and for its cytoproctective ability, see: Gaymes et al. (1997[Gaymes, T. J., Cebrat, M., Siemion, I. Z. & Kay, J. E. (1997). FEBS Lett. 418, 224-227.]). For the biomolecular interaction with human albumin of CLP-A, see: Rempel et al. (2010[Rempel, B., Gui, B., Maley, J., Reaney, M. & Sammynaiken, R. (2010). J. Biomed. Biotechnol. 2010, 1-8.]). For details of the CORN rule, see: Cahn et al. (1966[Cahn, R. S., Ingold, C. K. & Prelog, V. (1966). Angew. Chem. Int. Ed. 5, 385-415.]). For details of the absolute structure, see: Flack & Bernardinelli (2000[Flack, H. D. & Bernardinelli, G. (2000). J. Appl. Cryst. 33, 1143-1148.]).

[Scheme 1]

Experimental

Crystal data
  • C56H83N9O9S·3CH4O

  • Mr = 1154.50

  • Monoclinic, P 21

  • a = 10.374 (2) Å

  • b = 19.624 (4) Å

  • c = 15.576 (4) Å

  • [beta] = 100.0653 (13)°

  • V = 3122.1 (12) Å3

  • Z = 2

  • Synchrotron radiation

  • [lambda] = 0.68878 Å

  • [mu] = 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[Bruker (2008). SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]) Tmin = 0.985, Tmax = 0.988

  • 177237 measured reflections

  • 15255 independent reflections

  • 13940 reflections with I > 2[sigma](I)

  • Rint = 0.055

Refinement
  • R[F2 > 2[sigma](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

  • [Delta][rho]max = 0.64 e Å-3

  • [Delta][rho]min = -0.34 e Å-3

  • Absolute structure: Flack (1983[Flack, H. D. (1983). Acta Cryst. A39, 876-881.]), 7080 Friedel pairs

  • Flack parameter: 0.09 (7)

Table 1
Hydrogen-bond geometry (Å, °)

D-H...A D-H H...A D...A D-H...A
N1-H1D...O7 0.87 (3) 2.29 (3) 3.046 (3) 145 (3)
N2-H2D...O8 0.87 (3) 2.11 (3) 2.923 (3) 155 (3)
N7-H7D...O3 0.84 (3) 2.18 (3) 2.956 (3) 153 (3)
N8-H8D...O2i 0.83 (3) 2.52 (3) 3.274 (3) 151 (3)
N9-H9D...O60 0.91 (3) 2.00 (3) 2.896 (3) 169 (3)
N6-H6D...O70ii 0.77 (3) 2.34 (3) 3.071 (3) 159 (3)
O60-H60...O1i 0.95 (4) 1.79 (4) 2.705 (3) 160 (4)
O70-H70...O4iii 1.01 (3) 1.91 (2) 2.861 (3) 157 (3)
O80-H80...O9iv 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

  [varphi] [psi] [omega] [chi]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[Canadian Light Source (2007). MXDC. Canadian Light Source, Saskatoon, Saskatchewan, Canada.]); cell refinement: SAINT (Bruker, 2008[Bruker (2008). SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]); data reduction: SAINT; program(s) used to solve structure: SIR2004 (Burla et al., 2005[Burla, M. C., Caliandro, R., Camalli, M., Carrozzini, B., Cascarano, G. L., De Caro, L., Giacovazzo, C., Polidori, G. & Spagna, R. (2005). J. Appl. Cryst. 38, 381-388.]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); molecular graphics: CAMERON (Watkin et al., 1993[Watkin, D. J., Prout, C. K. & Pearce, L. J. (1993). CAMERON. Chemical Crystallography Laboratory, Oxford, England.]) and SHELXTL (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); software used to prepare material for publication: publCIF (Westrip, 2010[Westrip, S. P. (2010). J. Appl. Cryst. 43, 920-925.]).


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.

References

Bruker (2008). SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.
Burla, M. C., Caliandro, R., Camalli, M., Carrozzini, B., Cascarano, G. L., De Caro, L., Giacovazzo, C., Polidori, G. & Spagna, R. (2005). J. Appl. Cryst. 38, 381-388.  [ISI] [CrossRef] [ChemPort] [details]
Cahn, R. S., Ingold, C. K. & Prelog, V. (1966). Angew. Chem. Int. Ed. 5, 385-415.  [ChemPort]
Canadian Light Source (2007). MXDC. Canadian Light Source, Saskatoon, Saskatchewan, Canada.
Di Blasio, B., Benedetti, E., Pavone, C. & Goodman, M. (1987). Biopolymers, 26, 2099-2102.  [CrossRef] [ChemPort] [PubMed] [ISI]
Di Blasio, B., Benedetti, E., Pavone, C. & Temussi, P. A. (1989). J. Am. Chem. Soc. 111, 9089-9092.  [CrossRef] [ChemPort] [ISI]
Flack, H. D. (1983). Acta Cryst. A39, 876-881.  [CrossRef] [details]
Flack, H. D. & Bernardinelli, G. (2000). J. Appl. Cryst. 33, 1143-1148.  [ISI] [CrossRef] [ChemPort] [details]
Gaymes, T. J., Cebrat, M., Siemion, I. Z. & Kay, J. E. (1997). FEBS Lett. 418, 224-227.  [CrossRef] [ChemPort] [PubMed] [ISI]
Ghadiri, M. R., Granja, J. R., Milligan, R. A., McRee, D. E. & Khazanovich, N. (1993). Nature (London), 366, 324-327.  [CrossRef] [ChemPort] [PubMed] [ISI]
Jadhav, P., Schatte, G., Labiuk, S., Burnett, P.-G., Li, B., Okinyo-Owiti, D., Reaney, M., Grochulski, P., Fodje, M. & Sammynaiken, R. (2011). Acta Cryst. E67, o2360-o2361.  [CSD] [CrossRef] [details]
Matsumoto, T., Shishido, A., Morita, H., Itokawa, H. & Takeya, K. (2001). Phytochemistry, 57, 251-260.  [ISI] [CrossRef] [PubMed] [ChemPort]
Matsumoto, T., Shishido, A., Morita, H., Itokawa, H. & Takeya, K. (2002). Tetrahedron, 58, 5135-5140.  [ISI] [CrossRef] [ChemPort]
Morita, H., Shishido, A., Matsumoto, T., Itokawa, H. & Takeya, K. (1999). Tetrahedron, 55, 967-976.  [ISI] [CrossRef] [ChemPort]
Quail, J. W., Shen, J., Reaney, M. J. T. & Sammynaiken, R. (2009). Acta Cryst. E65, o1913-o1914.  [CSD] [CrossRef] [details]
Rempel, B., Gui, B., Maley, J., Reaney, M. & Sammynaiken, R. (2010). J. Biomed. Biotechnol. 2010, 1-8.  [CrossRef]
Rovero, P., Quartara, L. & Fabbri, G. (1991). Tetrahedron Lett. 32, 2639-2642.  [CrossRef] [ChemPort] [ISI]
Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.  [CrossRef] [details]
Watkin, D. J., Prout, C. K. & Pearce, L. J. (1993). CAMERON. Chemical Crystallography Laboratory, Oxford, England.
Westrip, S. P. (2010). J. Appl. Cryst. 43, 920-925.  [ISI] [CrossRef] [ChemPort] [details]
Wieczorek, Z., Bengsston, B., Trojnar, I. & Siemion, I. Z. (1991). Peptide Res. 4, 275-283.  [ChemPort]


Acta Cryst (2012). E68, o50-o51   [ doi:10.1107/S1600536811051488 ]

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