Structure of PDB 4dmn Chain A Binding Site BS01

Receptor Information
>4dmn Chain A (length=145) Species: 11698 (Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE)) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DCSPGIWQLDCTHLEGKVILVAVHVASGYIEAEVIPAETGQETAYFLLKL
AGRWPVKTVHTDNGSNFTSTTVKAACWWAGIKQEFGIESMNKELKKIIGQ
VRDQAEHLKTAVQMAVFIHNKKRKGGIGGYSAGERIVDIIATDIQ
Ligand information
Ligand ID0L9
InChIInChI=1S/C19H15BrClNO3/c1-10-16(18(25-2)19(23)24)17(11-3-6-13(21)7-4-11)14-9-12(20)5-8-15(14)22-10/h3-9,18H,1-2H3,(H,23,24)/t18-/m0/s1
InChIKeyBNDPDYQQAJUJPY-SFHVURJKSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6Cc1c(c(c2cc(ccc2n1)Br)c3ccc(cc3)Cl)C(C(=O)O)OC
ACDLabs 12.01O=C(O)C(OC)c1c(c2cc(Br)ccc2nc1C)c3ccc(Cl)cc3
OpenEye OEToolkits 1.7.6Cc1c(c(c2cc(ccc2n1)Br)c3ccc(cc3)Cl)[C@@H](C(=O)O)OC
CACTVS 3.370CO[CH](C(O)=O)c1c(C)nc2ccc(Br)cc2c1c3ccc(Cl)cc3
CACTVS 3.370CO[C@H](C(O)=O)c1c(C)nc2ccc(Br)cc2c1c3ccc(Cl)cc3
FormulaC19 H15 Br Cl N O3
Name(2S)-[6-bromo-4-(4-chlorophenyl)-2-methylquinolin-3-yl](methoxy)ethanoic acid
ChEMBLCHEMBL3259893
DrugBank
ZINC
PDB chain4dmn Chain A Residue 305 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4dmn Multimode, cooperative mechanism of action of allosteric HIV-1 integrase inhibitors.
Resolution2.45 Å
Binding residue
(original residue number in PDB)		T124 A128 W132
Binding residue
(residue number reindexed from 1)		T70 A74 W78
Annotation score1
Binding affinityMOAD: ic50=2.3uM
PDBbind-CN: -logKd/Ki=5.64,IC50=2.3uM
BindingDB: IC50=4e+2nM
Enzymatic activity
Enzyme Commision number 2.7.7.-
2.7.7.49: RNA-directed DNA polymerase.
2.7.7.7: DNA-directed DNA polymerase.
3.1.-.-
3.1.13.2: exoribonuclease H.
3.1.26.13: retroviral ribonuclease H.
3.4.23.16: HIV-1 retropepsin.
Gene Ontology
Molecular Function
GO:0003676 nucleic acid binding
Biological Process
GO:0015074 DNA integration

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:4dmn, PDBe:4dmn, PDBj:4dmn
PDBsum4dmn
PubMed22437836
UniProtP12497|POL_HV1N5 Gag-Pol polyprotein (Gene Name=gag-pol)

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