Structure of PDB 5kgx Chain A Binding Site BS01

Receptor Information
>5kgx Chain A (length=136) Species: 11676 (Human immunodeficiency virus 1) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
CSPGIWQLDCTHLEGKVILVAVHVASGYIEAEVIPAETGQETAYFLLKLA
GRWPVKTVHTDNGSNFTSTTVKTACWWAGIKQEESMNKELKKIIGQVRDQ
AEHLKTAVQMAVFIHNKKRKGYSAGERIVDIIATDI
Ligand information
Ligand ID7SK
InChIInChI=1S/C24H27NO4/c1-24(2,3)29-22(23(26)27)21-20(17-9-5-6-10-18(17)25(21)4)16-11-12-19-15(14-16)8-7-13-28-19/h5-6,9-12,14,22H,7-8,13H2,1-4H3,(H,26,27)/t22-/m0/s1
InChIKeyJEETZBQOULTRJG-QFIPXVFZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6CC(C)(C)O[C@@H](c1c(c2ccccc2n1C)c3ccc4c(c3)CCCO4)C(=O)O
OpenEye OEToolkits 2.0.6CC(C)(C)OC(c1c(c2ccccc2n1C)c3ccc4c(c3)CCCO4)C(=O)O
CACTVS 3.385Cn1c2ccccc2c(c3ccc4OCCCc4c3)c1[CH](OC(C)(C)C)C(O)=O
CACTVS 3.385Cn1c2ccccc2c(c3ccc4OCCCc4c3)c1[C@H](OC(C)(C)C)C(O)=O
ACDLabs 12.01C(=O)(O)C(c4c(c2ccc1OCCCc1c2)c3ccccc3n4C)OC(C)(C)C
FormulaC24 H27 N O4
Name(2S)-tert-butoxy[3-(3,4-dihydro-2H-1-benzopyran-6-yl)-1-methyl-1H-indol-2-yl]acetic acid
ChEMBL
DrugBank
ZINCZINC000584905394
PDB chain5kgx Chain A Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5kgx Indole-based allosteric inhibitors of HIV-1 integrase.
Resolution2.67 Å
Binding residue
(original residue number in PDB)		A169 E170 H171 T174 M178
Binding residue
(residue number reindexed from 1)		A101 E102 H103 T106 M110
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=4.80,IC50=16uM
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

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Molecular Function
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Biological Process
External links
PDB RCSB:5kgx, PDBe:5kgx, PDBj:5kgx
PDBsum5kgx
PubMed27568085
UniProtP12497|POL_HV1N5 Gag-Pol polyprotein (Gene Name=gag-pol)

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