Abstract
Rational molecular design, whether it is aimed at generating novel pharmaceuticals, agrochemicals or other bioactives, is at heart a knowledge-based activity. At the structural level, the molecular modeller requires answers to some very basic questions about any proposed lead molecule:
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How big is this molecule — what are its molecular dimensions?
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What shape is this molecule — what is its likely conformation(s) and what are the relative conformations of its functional substructures?
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How is this molecule likely to interact at its binding site (if this structure is known), or can this molecule mimic the ligand binding properties of existing known actives?
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References
Allen, F.H., Kennard, O., Watson, D.G., Brammer, L., Orpen, A.G. and Taylor, R. (1987). Tables of bond lengths determined by X-ray and neutron diffraction. Part 1. Bond lengths in organic compounds. J. Chem. Soc., Perkin Trans. 2, S1–S19.
Orpen, A.G., Brammer, L., Allen, F.H., Kennard, O., Watson, D.G. and Taylor, R. (1989). Tables of bond lengths determined by X-ray and neutron diffraction. Part II. Organometallic compounds and coordination complexes of the d- and f-block metals. J.Chem.Soc. Dalton Trans., pp S1–S83.
Allen, F.H., Bergerhoff, G. and Sievers, R. (1987). Crystallographic Databases. International Union of Crystallography, Chester, UK.
Allen, F.H., Davies, J.E., Galloy, J.J., Johnson, O., Kennard, O., Macrae, C.F., Mitchell, E.M., Mitchell, G.F., Smith, J.M., and Watson, D.G. (1991) The Development of Versions 3 and 4 of the Cambridge Structural Database System, J. Chem.Inf. Comput. Sci., 31, 187–204.
Sayle, R. (1995). RASMOL- A Program for Structure Visualisation. University of Edinburgh and Glaxo Group Research, Stevenage, UK.
Buergi, H.-B. and Dunitz, J.D. (1993). Structure Correlation. VCH Publishers, Weinheim, Germany.
Allen, F.H. (1980). The geometry of small rings, I. Substituent-induced bond-length asymmetry in cyclopropane. Acta Cryst., B36, 81–96.
Hoffman, R. and Stohrer, W.D. (1971). The Cope rearrangement revisited. J.Amer. Chem.Soc. 93, 6941–6948.
Gilli, G., Bertolasi, V., Bellucci, F. and Ferretti, V. (1986), Stereochemistry of the R1(X=)C(sp2)-N(sp3)R2R3 fragment. Mapping the cis-trans isomerisation path by rotation around the C-N bond from crystallographic structural data. J.Amer.Chem.Soc., 108, 2420–2424.
Dunitz, J.D. (1979) X-Ray Analysis and the Structure of Organic Molecules. Cornell University Press, Ithaca, NY, USA.
Klebe, G. (1994) Mapping common molecular fragments in crystal structures to explore conformation and configuration space under the conditions of a molecular environment. J.Mol.Struct., 308, 53–89.
Allen, F.H., Doyle, M.J. and Taylor, R. (1991) Automated conformational analysis from crystallographic data. 3. 3D Pattern recognition within the Cambridge Structural Database System : Implementation and Practical Examples. Acta Cryst., B47, 50–61, 1991.
Taylor, R. and Allen, F.H. (1993). Statistical and Numerical Methods of Data Analysis. Chapter 4 in ref [6].
Allen, F.H., Doyle, M.J. and Aufder Heyde, T.P.E. Automated conformational analysis from crystallographic data. 6. Principal component analysis for n-membered carbocyclic rings (n=4,5,6). Symmetry considerations and correlations with ring-puckering parameters. Acta Cryst., B47, 412–428, 1991.
Cremer, D. and Pople, J.A. (1975). A general definition of ring puckering coordinates. J.Amer.Chem.Soc., 97, 1354–1358.
Allen, F.H., Howard, J.A.K. and Pitchford, N.A. (1996). Symmetry-modified conformational mapping and classification of the medium rings. IV. Cyclooctane and related rings. Acta Cryst., Section B, Submitted for publication.
Allen, F.H., Garner, S.E., Howard, J.A.K. and Pitchford, N.A. (1994). Symmetry-modified conformational mapping and classifcation of the medium rings from crystallographic data. III. endo-Unsaturated seven-membered rings. Acta Cryst., B50, 395–404.
Conklin, D., Fortier, S., Glasgow, J.I. and Allen, F.H. (1996). Conformational analysis from crystallographic data using conceptual clustering. Acta Cryst., Section B, In Press.
Allen, F.H., Harris, S.E. and Taylor, R. (1996). Comparison of conformational preferences in the crystalline state with theoretically predicted gas-phase Boltzmann distributions. J.Comp.-Aided.Molec.Design, In Press.
Guest, M.F., van Lenthe, J.H., Kendrick, J., Schoeffel, K., Sherwood, P. and Harrison, R.J. (1993) GAMESS-UK User’s Guide and Reference Manual. Computing for Science Ltd., Daresbury Laboratory, Warrington, UK.
Allen, F.H., Rowland, R.S., Fortier, S. and Glasgow, J.I. (1990) The Design of Intelligent Systems for Molecular Scene Analysis, Tetrahedron Computer Methodology, 3, 757–771.
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© 1998 Springer Science+Business Media Dordrecht
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Allen, F.H., Pitchford, N.A. (1998). The Cambridge Structural Database System: Conformational Analysis from Crystallographic Data. In: Codding, P.W. (eds) Structure-Based Drug Design. NATO ASI Series, vol 352. Springer, Dordrecht. https://doi.org/10.1007/978-94-015-9028-0_2
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DOI: https://doi.org/10.1007/978-94-015-9028-0_2
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