Structure of PDB 6vdk Chain C Binding Site BS06

Receptor Information
>6vdk Chain C (length=270) Species: 11676 (Human immunodeficiency virus 1) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
FLDGIDKAQEEHEKYHSNWRAMASDFNLPPVVAKEIVASCDKCQLKGEAM
HGQVDCSPGIWQLDCTHLEGKVILVAVHVASGYIEAEVIPAETGQETAYF
LLKLAGRWPVKTVHTDNGSNFTSTTVKAACWWAGIKQEFGIPYNPQSQGV
IESMNKELKKIIGQVRDQAEHLKTAVQMAVFIHNFKRKGGIGGYSAGERI
VDIIATDIQTKELQKQITKIQNFRVYYRDSRDPVWKGPAKLLWKGEGAVV
IQDNSDIKVVPRRKAKIIRD
Ligand information
Ligand IDDLU
InChIInChI=1S/C20H19F2N3O5/c1-10-4-5-30-15-9-24-8-13(17(26)18(27)16(24)20(29)25(10)15)19(28)23-7-11-2-3-12(21)6-14(11)22/h2-3,6,8,10,15,27H,4-5,7,9H2,1H3,(H,23,28)/t10-,15+/m1/s1
InChIKeyRHWKPHLQXYSBKR-BMIGLBTASA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.2CC1CCOC2N1C(=O)C3=C(C(=O)C(=CN3C2)C(=O)NCc4ccc(cc4F)F)O
CACTVS 3.370C[C@@H]1CCO[C@H]2CN3C=C(C(=O)NCc4ccc(F)cc4F)C(=O)C(=C3C(=O)N12)O
ACDLabs 12.01Fc1ccc(c(F)c1)CNC(=O)C4=CN3C(C(=O)N2C(CCOC2C3)C)=C(O)C4=O
OpenEye OEToolkits 1.7.2C[C@@H]1CCO[C@@H]2N1C(=O)C3=C(C(=O)C(=CN3C2)C(=O)NCc4ccc(cc4F)F)O
CACTVS 3.370C[CH]1CCO[CH]2CN3C=C(C(=O)NCc4ccc(F)cc4F)C(=O)C(=C3C(=O)N12)O
FormulaC20 H19 F2 N3 O5
Name(4R,12aS)-N-(2,4-difluorobenzyl)-7-hydroxy-4-methyl-6,8-dioxo-3,4,6,8,12,12a-hexahydro-2H-pyrido[1',2':4,5]pyrazino[2,1-b][1,3]oxazine-9-carboxamide;
Dolutegravir
ChEMBLCHEMBL1229211
DrugBankDB08930
ZINCZINC000058581064
PDB chain6vdk Chain C Residue 303 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6vdk A Peptide Derived from Lens Epithelium-Derived Growth Factor Stimulates HIV-1 DNA Integration and Facilitates Intasome Structural Studies.
Resolution4.5 Å
Binding residue
(original residue number in PDB)		D116 P145 Q146 E152
Binding residue
(residue number reindexed from 1)		D116 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:0008270 zinc ion binding
Biological Process
GO:0015074 DNA integration

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Molecular Function
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Biological Process
External links
PDB RCSB:6vdk, PDBe:6vdk, PDBj:6vdk
PDBsum6vdk
PubMed32061936
UniProtP12497|POL_HV1N5 Gag-Pol polyprotein (Gene Name=gag-pol)

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