Structure of PDB 8gd3 Chain A Binding Site BS01

Receptor Information
>8gd3 Chain A (length=343) Species: 11676 (Human immunodeficiency virus 1) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PVWKDADTTLFCASDAKAYETEVHNVWATHACVPTDPNPQEIHLENVTEN
FNMWKNNMVEQMHEDIISLWDQSLQPCVKLTGGSVIKQACPKISFDPIPI
HYCTPAGYVILKCNDKNFNGTGPCKNVSSVQCTHGIKPVVSTQLLLNGSL
AEEEIIIRSENLTNNAKTIIVHLNKSVEINCTRPSNGGDIRKAYCEINGT
KWNKVLKQVTEKLKEHFNNKTIIFQPPSGGDLEITMHSFNCRGEFFYCNT
TQLFNNTCKGCNGTITLPCKIKQIINMWQGTGQAMYAPPIDGKINCVSNI
TGILLTRDGGANNTSNETFRPGGGDMRDNWRSELYKYKVVQIE
Ligand information
Ligand IDZ1Z
InChIInChI=1S/C20H27ClFN5O4/c21-16-2-1-15(8-17(16)22)24-19(30)14-7-13(12-28)10-27(11-14)20(31)26-5-3-25(4-6-26)18(29)9-23/h1-2,8,13-14,28H,3-7,9-12,23H2,(H,24,30)/t13-,14+/m1/s1
InChIKeyIUMJQOWKMYPJNQ-KGLIPLIRSA-N
SMILES
SoftwareSMILES
CACTVS 3.385NCC(=O)N1CCN(CC1)C(=O)N2C[C@H](CO)C[C@@H](C2)C(=O)Nc3ccc(Cl)c(F)c3
ACDLabs 12.01O=C(N1CC(CC(CO)C1)C(=O)Nc1ccc(Cl)c(F)c1)N1CCN(CC1)C(=O)CN
OpenEye OEToolkits 2.0.7c1cc(c(cc1NC(=O)[C@H]2C[C@H](CN(C2)C(=O)N3CCN(CC3)C(=O)CN)CO)F)Cl
CACTVS 3.385NCC(=O)N1CCN(CC1)C(=O)N2C[CH](CO)C[CH](C2)C(=O)Nc3ccc(Cl)c(F)c3
OpenEye OEToolkits 2.0.7c1cc(c(cc1NC(=O)C2CC(CN(C2)C(=O)N3CCN(CC3)C(=O)CN)CO)F)Cl
FormulaC20 H27 Cl F N5 O4
Name(3S,5R)-N-(4-chloro-3-fluorophenyl)-1-(4-glycylpiperazine-1-carbonyl)-5-(hydroxymethyl)piperidine-3-carboxamide
ChEMBL
DrugBank
ZINC
PDB chain8gd3 Chain A Residue 512 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB8gd3 Piperidine CD4-Mimetic Compounds Expose Vulnerable Env Epitopes Sensitizing HIV-1-Infected Cells to ADCC.
Resolution2.19 Å
Binding residue
(original residue number in PDB)
V255 S256 D368 E370 F376 F382 I424 N425 M426 W427 G429 T430 M475
Binding residue
(residue number reindexed from 1)
V140 S141 D231 E233 F239 F245 I275 N276 M277 W278 G280 T281 M326
Annotation score1
Enzymatic activity
Enzyme Commision number ?
Gene Ontology

View graph for
Cellular Component
External links
PDB RCSB:8gd3, PDBe:8gd3, PDBj:8gd3
PDBsum8gd3
PubMed37243271
UniProtA0A0M3KKW9

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