Structure of PDB 8dcq Chain A Binding Site BS01

Receptor Information

>8dcq Chain A (length=336) Species: 11676 (Human immunodeficiency virus 1)

PVWKDADTTLFCASDAKAYETEVHNVWATHACVPTDPNPQEIHLENVTEN
FNMWKNNMVEQMHEDIISLWDQSLQPCVVIKQACPKISFDPIPIHYCTPA
GYVILKCNDKNFNGTGPCKNVSSVQCTHGIKPVVSTQLLLNGSLAEEEII
IRSENLTNNAKTIIVHLNKSVEINCTRPSDIRKAYCEINGTKWNKVLKQV
TEKLKEHFNNKTIIFQPPSGGDLEITMHTFNCRGEFFYCNTTQLFNNTCI
MKGCNGTITLPCKIKQIINMWQGTGQAMYAPPIDGKINCVSNITGILLTR
DGGANNTSNETFRPGGGDMRDNWRSELYKYKVVQIE

Ligand information

• Ligand ID: R5K
• InChI: InChI=1S/C26H40ClN7O3/c27-19-7-9-20(10-8-19)32-23(36)24(37)33-21-11-14-26(12-3-1-4-13-26)34(18-21)17-16-30-22(35)6-2-5-15-31-25(28)29/h7-10,21H,1-6,11-18H2,(H,30,35)(H,32,36)(H,33,37)(H4,28,29,31)/t21-/m1/s1
• InChIKey: CGZSMDJLUHVSDB-OAQYLSRUSA-N
• SMILES:
  OpenEye OEToolkits 2.0.7: c1cc(ccc1NC(=O)C(=O)NC2CCC3(CCCCC3)N(C2)CCNC(=O)CCCCNC(=N)N)Cl
  CACTVS 3.385: NC(=N)NCCCCC(=O)NCCN1C[CH](CCC12CCCCC2)NC(=O)C(=O)Nc3ccc(Cl)cc3
  OpenEye OEToolkits 2.0.7: [H]/N=C(\N)/NCCCCC(=O)NCCN1C[C@@H](CCC12CCCCC2)NC(=O)C(=O)Nc3ccc(cc3)Cl
  ACDLabs 12.01: Clc1ccc(cc1)NC(=O)C(=O)NC1CCC2(CCCCC2)N(C1)CCNC(=O)CCCCNC(=N)N
  CACTVS 3.385: NC(=N)NCCCCC(=O)NCCN1C[C@@H](CCC12CCCCC2)NC(=O)C(=O)Nc3ccc(Cl)cc3
• Formula: C26 H40 Cl N7 O3
• Name: N~1~-{(3R)-1-[2-(5-carbamimidamidopentanamido)ethyl]-1-azaspiro[5.5]undecan-3-yl}-N~2~-(4-chlorophenyl)ethanediamide
• PDB chain: 8dcq Chain A Residue 511

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8dcq Characterization of a Novel CD4 Mimetic Compound YIR-821 against HIV-1 Clinical Isolates.
• Resolution: 3.2 Å
• Binding residue (original residue number in PDB): V255 E370 T375 F376 N377 F382 N425 M426 W427 G473
• Binding residue (residue number reindexed from 1): V134 E224 T229 F230 N231 F236 N269 M270 W271 G317
• Annotation score: 1

Gene Ontology

Cellular Component

• GO:0019031 viral envelope

External links

• PDB: RCSB:8dcq, PDBe:8dcq, PDBj:8dcq
• PDBsum: 8dcq
• PubMed: 36511698
• UniProt: A0A0M3KKW9