Structure of PDB 8dxg Chain A Binding Site BS01

Receptor Information
>8dxg Chain A (length=556) 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]
MVPISPIETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKIS
KIGPENPYNTPVFAIKKKDSTKWRKLVDFRELNKRTQDFWEVQLGIPHPA
GLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNV
LPQGWKGSPAIFQSSMTKILEPFAAQNPDIVIYQYMDDLYVGSDLEIGQH
RTKIEELRQHLLRWGLTTPDKKHQKEPPFLWMGYELHPDKWTVQPIVLPE
KDSWTVNDIQKLVGKLNWASQIYPGIKVRQLSKLLRGTKALTEVIPLTEE
AELELAENREILKEPVHGVYYDPSKDLIAEIQKQGQGQWTYQIYQEPFKN
LKTGKYARMRGAHTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKETW
ETWWTEYWQATWIPEWEFVNTPPLVKLWYQLEKEPIVGAETFYVDGAANR
ETKLGKAGYVTNKGRQKVVPLTNTTNQKTELQAIYLALQDSGLEVNIVTD
SQYALGIIQAQPDKSESELVNQIIEQLIKKEKVYLAWVPAHKGIGGNEQV
DKLVSA
Ligand information
Ligand IDU4D
InChIInChI=1S/C6H4F3NO/c7-6(8,9)4-1-2-5(11)10-3-4/h1-3H,(H,10,11)
InChIKeyBYRJSCNPUHYZQE-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7c1cc(ncc1C(F)(F)F)O
CACTVS 3.385Oc1ccc(cn1)C(F)(F)F
ACDLabs 12.01FC(F)(F)c1cnc(O)cc1
FormulaC6 H4 F3 N O
Name5-(trifluoromethyl)pyridin-2-one
ChEMBL
DrugBank
ZINCZINC000008698270
PDB chain8dxg Chain A Residue 601 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB8dxg Halo Library, a Tool for Rapid Identification of Ligand Binding Sites on Proteins Using Crystallographic Fragment Screening.
Resolution2.1 Å
Binding residue
(original residue number in PDB)		K22 Q23 W24 P59 F61
Binding residue
(residue number reindexed from 1)		K24 Q25 W26 P61 F63
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
View graph for
Biological Process
External links
PDB RCSB:8dxg, PDBe:8dxg, PDBj:8dxg
PDBsum8dxg
PubMed37115705
UniProtP03366|POL_HV1B1 Gag-Pol polyprotein (Gene Name=gag-pol)

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