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Figure 4 | BMC Bioinformatics

Figure 4

From: Multiple virtual screening approaches for finding new Hepatitis c virus RNA-dependent RNA polymerase inhibitors: Structure-based screens and molecular dynamics for the pursue of new poly pharmacological inhibitors

Figure 4

Interaction pharmacophore of three NNI binding sites compiled from structural superpositionand alignment of relevant PDB coordinates for thumb I (A), palm II (B) and palm III (C), respectively. The essential interactions shown are described in the results section. A) shows formation of hydrogen bond with ARG503 side chain and a hydrogen acceptor from the ligand B) HCV-796 inhibitor interacts with both side-chains of SER 365 -forms hydrogen bond with a hydrogen donor- and ARG200, in addition to arene-cation bond between the latter and the aromatic benzene ring of the benzofuran nucleus and H-bond donar with ASN 306 (not common for all pdb) C) The pocket seems to be narrow and only two polar interactions were computed with residues: ASN316 and TYR195, showing a tightly closed proximity contour with almost no solvent exposure by the ligand.

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BMC Bioinformatics

ISSN: 1471-2105

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