Structure of PDB 8u6h Chain A Binding Site BS01

Receptor Information
>8u6h Chain A (length=550) Species: 11678 (Human immunodeficiency virus type 1 BH10) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ISPIETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISKIG
PENPYNTPVFAIKKKDSTKWRKLVDFRELNKRTQDFWEVQLGIPHPAGLK
KKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQ
GWKGSPAIFQSSMTKILEPFAAQNPDIVIYQYMDDLYVGSDLEIGQHRTK
IEELRQHLLRWGLTTPDKKHQKEPPFLWMGYELHPDKWTVQPIVLDSWTV
NDIQKLVGKLNWASQIYPGIKVRQLSKLLRGTKALTEVIPLTEEAELELA
ENREILKEPVHGVYYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLKTGKY
ARMRGAHTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKETWETWWTE
YWQATWIPEWEFVNTPPLVKLWYQLEKEPIVGAETFYVDGAANRETKLGK
AGYVTNKGRQKVVPLTNTTNQKTELQAIYLALQDSGLEVNIVTDSQYALG
IIQAQPDKSESELVNQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDKLVSA
Ligand information
Ligand IDVVE
InChIInChI=1S/C25H19Cl2N3O4/c1-2-24(31)30-21-6-4-3-5-20(21)29(25(30)32)9-10-33-23-14-17(26)7-8-22(23)34-19-12-16(15-28)11-18(27)13-19/h3-8,11-14H,2,9-10H2,1H3
InChIKeyLGSPOOOHYUJKNO-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7CCC(=O)N1c2ccccc2N(C1=O)CCOc3cc(ccc3Oc4cc(cc(c4)Cl)C#N)Cl
CACTVS 3.385CCC(=O)N1C(=O)N(CCOc2cc(Cl)ccc2Oc3cc(Cl)cc(c3)C#N)c4ccccc14
ACDLabs 12.01N#Cc1cc(cc(Cl)c1)Oc1ccc(Cl)cc1OCCN1c2ccccc2N(C(=O)CC)C1=O
FormulaC25 H19 Cl2 N3 O4
Name3-chloro-5-{4-chloro-2-[2-(2-oxo-3-propanoyl-2,3-dihydro-1H-benzimidazol-1-yl)ethoxy]phenoxy}benzonitrile
ChEMBL
DrugBank
ZINC
PDB chain8u6h Chain A Residue 601 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB8u6h Covalent and noncovalent strategies for targeting Lys102 in HIV-1 reverse transcriptase.
Resolution2.99 Å
Binding residue
(original residue number in PDB)		L100 K102 K103 K104 V106 V108 V179 Y181 Y188 F227 L234 P236 Y318
Binding residue
(residue number reindexed from 1)		L99 K101 K102 K103 V105 V107 V178 Y180 Y187 F226 L233 P235 Y314
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:0003964 RNA-directed DNA polymerase activity
GO:0004523 RNA-DNA hybrid ribonuclease activity
Biological Process
GO:0006278 RNA-templated DNA biosynthetic process

View graph for
Molecular Function
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Biological Process
External links
PDB RCSB:8u6h, PDBe:8u6h, PDBj:8u6h
PDBsum8u6h
PubMed37883896
UniProtP03366|POL_HV1B1 Gag-Pol polyprotein (Gene Name=gag-pol)

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