Structure of PDB 8fm8 Chain D Binding Site BS01

Receptor Information
>8fm8 Chain D (length=335) Species: 587638 (HIV-1 06TG.HT008) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KTTLFCASDAKAYEKEVHNVWATHACVPTDPNPQEMVLANVTENFNMWKN
DMVEQMHEDIISLWDESLKPCVKLTGGSAITQACPKVSFDPIPLHYCAPA
GFAILKCNNKTFNGTGPCRNVSTVQCTHGIKPVVSTQLLLNGSLAEEEII
IRSENLTNNAKTIIVHLNESVNIVCTRPNNIRQAHCNINESKWNNTLQKV
GEELAKHFPSKTIKFEPSSGGDLEITTHSFNCRGEFFYCNTSDLFNGTYR
NGTYNHTGRSSNGTITLQCKIKQIINMWQEVGRAIYAPPIEGEITCNSNI
TGLLLLRDDTETFRPGGGDMRDNWRSELYKYKVVE
Ligand information
Ligand IDY1T
InChIInChI=1S/C28H24ClF6N7O4/c1-38-8-11-2-4-13-17(6-11)42(28(45)46-10-14-19(31)21(33)23(35)22(34)20(14)32)18(9-39-27(36)37)24(13)41-26(44)25(43)40-12-3-5-15(29)16(30)7-12/h2-7,18,24,38H,8-10H2,1H3,(H,40,43)(H,41,44)(H4,36,37,39)/t18-,24+/m1/s1
InChIKeyZLEHMUPVIABTKG-KOSHJBKYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CNCc1ccc2[C@H](NC(=O)C(=O)Nc3ccc(Cl)c(F)c3)[C@@H](CNC(N)=N)N(C(=O)OCc4c(F)c(F)c(F)c(F)c4F)c2c1
OpenEye OEToolkits 2.0.7CNCc1ccc2c(c1)N(C(C2NC(=O)C(=O)Nc3ccc(c(c3)F)Cl)CNC(=N)N)C(=O)OCc4c(c(c(c(c4F)F)F)F)F
ACDLabs 12.01Clc1ccc(cc1F)NC(=O)C(=O)NC1c2ccc(cc2N(C1CNC(=N)N)C(=O)OCc1c(F)c(F)c(F)c(F)c1F)CNC
OpenEye OEToolkits 2.0.7[H]/N=C(/N)\NC[C@@H]1[C@H](c2ccc(cc2N1C(=O)OCc3c(c(c(c(c3F)F)F)F)F)CNC)NC(=O)C(=O)Nc4ccc(c(c4)F)Cl
CACTVS 3.385CNCc1ccc2[CH](NC(=O)C(=O)Nc3ccc(Cl)c(F)c3)[CH](CNC(N)=N)N(C(=O)OCc4c(F)c(F)c(F)c(F)c4F)c2c1
FormulaC28 H24 Cl F6 N7 O4
Name(pentafluorophenyl)methyl (2R,3S)-2-(carbamimidamidomethyl)-3-[2-(4-chloro-3-fluoroanilino)(oxo)acetamido]-6-[(methylamino)methyl]-2,3-dihydro-1H-indole-1-carboxylate
ChEMBL
DrugBank
ZINC
PDB chain8fm8 Chain D Residue 507 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB8fm8 Indoline CD4-mimetic compounds mediate potent and broad HIV-1 inhibition and sensitization to antibody-dependent cellular cytotoxicity.
Resolution2.47 Å
Binding residue
(original residue number in PDB)
V255 E370 S375 F376 I424 N425 M426 W427 E429 V430 G431 G473 D474 M475 R476
Binding residue
(residue number reindexed from 1)
V134 E224 S229 F230 I275 N276 M277 W278 E280 V281 G282 G318 D319 M320 R321
Annotation score1
Enzymatic activity
Enzyme Commision number ?
Gene Ontology

View graph for
Cellular Component
External links
PDB RCSB:8fm8, PDBe:8fm8, PDBj:8fm8
PDBsum8fm8
PubMed36961924
UniProtC6G099

[Back to BioLiP]