Structure of PDB 4dkv Chain B Binding Site BS01

Receptor Information

>4dkv Chain B (length=339) Species: 11676 (Human immunodeficiency virus 1)

VWKDADTTLFCASDAKAHETEVHNVWATHACVPTDPNPQEIHLENVTENF
NMWKNNMVEQMQEDVISLWDQSLQPCVKLTGGSVIKQACPKISFDPIPIH
YCTPAGYVILKCNDKNFNGTGPCKNVSSVQCTHGIKPVVSTQLLLNGSLA
EEEIIIRSENLTNNAKTIIVHLNKSVEINCTRPSNGDIRKAYCEINGTKW
NKVLKQVTEKLKEHFNNKTIIFQPPSGGDLEITMHSFNCRGEFFYCNTTQ
LFNNTCINGTITLPCKIKQIINMWQGTGQAMYAPPIDGKINCVSNITGIL
LTRDGGANNTSNETFRPGGGNIKDNWRSELYKYKVVQIE

Ligand information

• Ligand ID: 0KW
• InChI: InChI=1S/C20H25ClN4O3S/c1-12-16(9-11-26)29-20(23-12)17(15-4-2-3-10-22-15)25-19(28)18(27)24-14-7-5-13(21)6-8-14/h5-8,15,17,22,26H,2-4,9-11H2,1H3,(H,24,27)(H,25,28)/t15-,17-/m0/s1
• InChIKey: CXKXTRRHRJSSBG-RDJZCZTQSA-N
• SMILES:
  OpenEye OEToolkits 1.7.6: Cc1c(sc(n1)[C@H]([C@@H]2CCCCN2)NC(=O)C(=O)Nc3ccc(cc3)Cl)CCO
  CACTVS 3.370: Cc1nc(sc1CCO)[C@@H](NC(=O)C(=O)Nc2ccc(Cl)cc2)[C@@H]3CCCCN3
  ACDLabs 12.01: O=C(NC(c1nc(c(s1)CCO)C)C2NCCCC2)C(=O)Nc3ccc(Cl)cc3
  CACTVS 3.370: Cc1nc(sc1CCO)[CH](NC(=O)C(=O)Nc2ccc(Cl)cc2)[CH]3CCCCN3
  OpenEye OEToolkits 1.7.6: Cc1c(sc(n1)C(C2CCCCN2)NC(=O)C(=O)Nc3ccc(cc3)Cl)CCO
• Formula: C20 H25 Cl N4 O3 S
• Name: N-(4-chlorophenyl)-N'-{(S)-[5-(2-hydroxyethyl)-4-methyl-1,3-thiazol-2-yl][(2S)-piperidin-2-yl]methyl}ethanediamide
• ZINC: ZINC000084757164
• PDB chain: 4dkv Chain B Residue 511

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4dkv Binding mode characterization of NBD series CD4-mimetic HIV-1 entry inhibitors by X-ray structure and resistance study.
• Resolution: 2.1847 Å
• Binding residue (original residue number in PDB): E370 I371 S375 F376 N425 W427 G429
• Binding residue (residue number reindexed from 1): E231 I232 S236 F237 N272 W274 G276
• Annotation score: 1

Gene Ontology

Cellular Component

• GO:0019031 viral envelope

External links

• PDB: RCSB:4dkv, PDBe:4dkv, PDBj:4dkv
• PDBsum: 4dkv
• PubMed: 25001301
• UniProt: A0A0M3KKW9