Structure of PDB 6v3k Chain A Binding Site BS06

Receptor Information
>6v3k Chain A (length=259) Species: 11698,273057 [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
FLDGIDKAQEEHEKYHSNWRAMASDFNLPPVVAKEIVASCDKCQLKGEAM
HGQVDCSPGIWQLDCTHLEGKVILVAVHVASGYIEAEVIPAETGQETAYF
LLKLAGRWPVKTVHTDNGSNFTSTTVKAACWWAGIKQEFGIPYNPQSQGV
IESMNKELKKIIGQVRDQAEHLKTAVQMAVFIHNFKRKGGIGGYSAGERI
VDIIATDIQTKELQKQITKIQNFRVYYGPAKLLWKGEGAVVIQDNSDIKV
VPRRKAKII
Ligand information
Ligand IDQUW
InChIInChI=1S/C21H22F2N4O4/c22-14-6-5-13(16(23)9-14)11-26-20(29)17-18(24)15-8-12(4-2-1-3-7-28)10-25-19(15)27(31)21(17)30/h5-6,8-10,28,31H,1-4,7,11,24H2,(H,26,29)
InChIKeyKDSNFIUIIYYHGI-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6c1cc(c(cc1F)F)CNC(=O)C2=C(c3cc(cnc3N(C2=O)O)CCCCCO)N
CACTVS 3.385NC1=C(C(=O)NCc2ccc(F)cc2F)C(=O)N(O)c3ncc(CCCCCO)cc13
FormulaC21 H22 F2 N4 O4
Name4-azanyl-N-[[2,4-bis(fluoranyl)phenyl]methyl]-1-oxidanyl-2-oxidanylidene-6-(5-oxidanylpentyl)-1,8-naphthyridine-3-carboxamide
ChEMBLCHEMBL4101122
DrugBank
ZINCZINC000263620641
PDB chain6v3k Chain A Residue 304 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6v3k Structural basis for strand-transfer inhibitor binding to HIV intasomes.
Resolution3.4 Å
Binding residue
(original residue number in PDB)		D64 D116 Y143 P145 Q146 E152
Binding residue
(residue number reindexed from 1)		D64 D116 Y143 P145 Q146 E152
Annotation score1
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
GO:0003677 DNA binding
GO:0004521 RNA endonuclease activity
GO:0008270 zinc ion binding
Biological Process
GO:0015074 DNA integration
Cellular Component
GO:0005737 cytoplasm

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6v3k, PDBe:6v3k, PDBj:6v3k
PDBsum6v3k
PubMed32001521
UniProtP12497|POL_HV1N5 Gag-Pol polyprotein (Gene Name=gag-pol);
P39476|DN7D_SACS2 DNA-binding protein 7d (Gene Name=sso7d)

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