Structure of PDB 9c9m Chain A Binding Site BS07

Receptor Information

>9c9m Chain A (length=261) Species: 11676 (Human immunodeficiency virus 1)

FLDGIDKAQEEHEKYHSNWRAMASDFNLPPVVAKEIVASCDKCQLKGEAM
HGQVDCSPGIWQLDCTHLEGKVILVAVHVASGYIEAEVIPAETGQETAYF
LLKLAGRWPVKTVHTDNGSNFTSTTVKAACWWAGIKQEFGIPYNPQSQGV
IESMNKELKKIIGQVRDQAEHLKTAVQMAVFIHNFKRKGGIGGYSAGERI
VDIIATDIQTKELQKQITKIQNFRVYYRKGPAKLLWKGEGAVVIQDNSDI
KVVPRRKAKII

Ligand information

• Ligand ID: DLU
• InChI: InChI=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
• InChIKey: RHWKPHLQXYSBKR-BMIGLBTASA-N
• SMILES:
  OpenEye OEToolkits 1.7.2: CC1CCOC2N1C(=O)C3=C(C(=O)C(=CN3C2)C(=O)NCc4ccc(cc4F)F)O
  CACTVS 3.370: C[C@@H]1CCO[C@H]2CN3C=C(C(=O)NCc4ccc(F)cc4F)C(=O)C(=C3C(=O)N12)O
  ACDLabs 12.01: Fc1ccc(c(F)c1)CNC(=O)C4=CN3C(C(=O)N2C(CCOC2C3)C)=C(O)C4=O
  OpenEye OEToolkits 1.7.2: C[C@@H]1CCO[C@@H]2N1C(=O)C3=C(C(=O)C(=CN3C2)C(=O)NCc4ccc(cc4F)F)O
  CACTVS 3.370: C[CH]1CCO[CH]2CN3C=C(C(=O)NCc4ccc(F)cc4F)C(=O)C(=C3C(=O)N12)O
• Formula: C20 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
• ChEMBL: CHEMBL1229211
• DrugBank: DB08930
• ZINC: ZINC000058581064
• PDB chain: 9c9m Chain F Residue 101

Receptor-Ligand Complex Structure

Structure summary

• PDB: 9c9m HIV-1 Intasomes Assembled with Excess Integrase C-Terminal Domain Protein Facilitate Structural Studies by Cryo-EM and Reveal the Role of the Integrase C-terminal Tail in HIV-1 Integration
• Resolution: 2.01 Å
• Binding residue (original residue number in PDB): D64 D116 G118 P145 Q146 E152
• Binding residue (residue number reindexed from 1): D64 D116 G118 P145 Q146 E152
• Annotation score: 1

External links

• PDB: RCSB:9c9m, PDBe:9c9m, PDBj:9c9m
• PDBsum: 9c9m
• PubMed: 39066328
• UniProt: P12497|POL_HV1N5 Gag-Pol polyprotein (Gene Name=gag-pol)