Structure of PDB 8gd0 Chain A Binding Site BS01

Receptor Information

>8gd0 Chain A (length=340) Species: 11676 (Human immunodeficiency virus 1)

VWKDADTTLFCASDAKAYETEVHNVWATHACVPTDPNPQEIHLENVTENF
NMWKNNMVEQMHEDIISLWDQSLQPCVKLTGGSVIKQACPKISFDPIPIH
YCTPAGYVILKCNDKNFNGTGPCKNVSSVQCTHGIKPVVSTQLLLNGSLA
EEEIIIRSENLTNNAKTIIVHLNKSVEINCTRPSNDIRKAYCEINGTKWN
KVLKQVTEKLKEHFNNKTIIFQPPSGGDLEITMHTFNCRGEFFYCNTTQL
FNNTCIGCNGTITLPCKIKQIINMWQGTGQAMYAPPIDGKINCVSNITGI
LLTRDGGANNTSNETFRPGGGDMRDNWRSELYKYKVVQIE

Ligand information

• Ligand ID: Z3F
• InChI: InChI=1S/C18H24ClFN4O2/c1-22-7-9-23(10-8-22)18(26)24-6-2-3-13(12-24)17(25)21-14-4-5-15(19)16(20)11-14/h4-5,11,13H,2-3,6-10,12H2,1H3,(H,21,25)/t13-/m0/s1
• InChIKey: KORUUSLMTDCGIB-ZDUSSCGKSA-N
• SMILES:
  CACTVS 3.385: CN1CCN(CC1)C(=O)N2CCC[C@@H](C2)C(=O)Nc3ccc(Cl)c(F)c3
  CACTVS 3.385: CN1CCN(CC1)C(=O)N2CCC[CH](C2)C(=O)Nc3ccc(Cl)c(F)c3
  OpenEye OEToolkits 2.0.7: CN1CCN(CC1)C(=O)N2CCCC(C2)C(=O)Nc3ccc(c(c3)F)Cl
  OpenEye OEToolkits 2.0.7: CN1CCN(CC1)C(=O)N2CCC[C@@H](C2)C(=O)Nc3ccc(c(c3)F)Cl
  ACDLabs 12.01: O=C(N1CCN(C)CC1)N1CCCC(C1)C(=O)Nc1ccc(Cl)c(F)c1
• Formula: C18 H24 Cl F N4 O2
• Name: (3S)-N-(4-chloro-3-fluorophenyl)-1-(4-methylpiperazine-1-carbonyl)piperidine-3-carboxamide
• PDB chain: 8gd0 Chain A Residue 513

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8gd0 Piperidine CD4-Mimetic Compounds Expose Vulnerable Env Epitopes Sensitizing HIV-1-Infected Cells to ADCC.
• Resolution: 2.4 Å
• Binding residue (original residue number in PDB): V255 T257 E370 T375 F376 F382 N425 M426 W427 G429 T430 G473 M475
• Binding residue (residue number reindexed from 1): V139 T141 E230 T235 F236 F242 N273 M274 W275 G277 T278 G321 M323
• Annotation score: 1

Gene Ontology

Cellular Component

• GO:0019031 viral envelope

External links

• PDB: RCSB:8gd0, PDBe:8gd0, PDBj:8gd0
• PDBsum: 8gd0
• PubMed: 37243271
• UniProt: A0A0M3KKW9