Structure of PDB 4dkr Chain A Binding Site BS01

Receptor Information
>4dkr Chain A (length=339) Species: 11686 (Human immunodeficiency virus type 1 (BRU ISOLATE)) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VWKDADTTLFCASDAKAHETEVHNVWATHACVPTDPNPQEIHLENVTENF
NMWKNNMVEQMQEDVISLWDQSLQPCVKLTGGSVIKQACPKISFDPIPIH
YCTPAGYVILKCNDKNFNGTGPCKNVSSVQCTHGIKPVVSTQLLLNGSLA
EEEIIIRSENLTNNAKTIIVHLNKSVEINCTRPSNGDIRKAYCEINGTKW
NKVLKQVTEKLKEHFNNKTIIFQPPSGGDLEITMHSFNCRGEFFYCNTTQ
LFNNTCINGTITLPCKIKQIINMWQGTGQAMYAPPIDGKINCVSNITGIL
LTRDGGANNTSNETFRPGGGNIKDNWRSELYKYKVVQIE
Ligand information
Ligand ID0LJ
InChIInChI=1S/C18H17ClFN5O2/c19-12-6-5-10(8-13(12)20)23-16(26)17(27)25-15-11-4-2-1-3-9(11)7-14(15)24-18(21)22/h1-6,8,14-15H,7H2,(H,23,26)(H,25,27)(H4,21,22,24)/t14-,15-/m1/s1
InChIKeyICNIHLCRBSFIFO-HUUCEWRRSA-N
SMILES
SoftwareSMILES
CACTVS 3.370NC(=N)N[CH]1Cc2ccccc2[CH]1NC(=O)C(=O)Nc3ccc(Cl)c(F)c3
OpenEye OEToolkits 1.7.6[H]/N=C(/N)\N[C@@H]1Cc2ccccc2[C@H]1NC(=O)C(=O)Nc3ccc(c(c3)F)Cl
OpenEye OEToolkits 1.7.6c1ccc2c(c1)CC(C2NC(=O)C(=O)Nc3ccc(c(c3)F)Cl)NC(=N)N
CACTVS 3.370NC(=N)N[C@@H]1Cc2ccccc2[C@H]1NC(=O)C(=O)Nc3ccc(Cl)c(F)c3
ACDLabs 12.01Clc1ccc(cc1F)NC(=O)C(=O)NC3c2ccccc2CC3NC(=[N@H])N
FormulaC18 H17 Cl F N5 O2
NameN-[(1R,2R)-2-carbamimidamido-2,3-dihydro-1H-inden-1-yl]-N'-(4-chloro-3-fluorophenyl)ethanediamide
ChEMBLCHEMBL2219814
DrugBank
ZINCZINC000095556243
PDB chain4dkr Chain A Residue 513 [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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PDB4dkr Structure-Based Design, Synthesis, and Characterization of Dual Hotspot Small-Molecule HIV-1 Entry Inhibitors.
Resolution1.8 Å
Binding residue
(original residue number in PDB)		S256 T257 D368 E370 I371 S375 F376 N425 W427 G429 G473
Binding residue
(residue number reindexed from 1)		S140 T141 D229 E231 I232 S236 F237 N272 W274 G276 G320
Annotation score1
Binding affinityMOAD: Kd=0.3uM
PDBbind-CN: -logKd/Ki=6.52,Kd=0.30uM
Enzymatic activity
Enzyme Commision number ?
Gene Ontology

View graph for
Cellular Component
External links
PDB RCSB:4dkr, PDBe:4dkr, PDBj:4dkr
PDBsum4dkr
PubMed22497421
UniProtQ0ED31

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