Structure of PDB 4kv8 Chain A Binding Site BS01

Receptor Information
>4kv8 Chain A (length=554) Species: 11706 (HIV-1 M:B_HXB2R) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PISPIETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISKI
GPENPYNTPVFAIKKKDSTKWRKLVDFRELNKRTQDFWEVQLGIPHPAGL
KKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLP
QGWKGSPAIFQSSMTKILEPFRKQNPDIVIYQYMDDLYVGSDLEIGQHRT
KIEELRQHLLRWGLTTPDKKHQKEPPFLWMGYELHPDKWTVQPIVLPEKD
SWTVNDIQKLVGKLNWASQIYPGIKVRQLCKLLRGTKALTEVIPLTEEAE
LELAENREILKEPVHGVYYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLK
TGKYARMRGAHTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKETWET
WWTEYWQATWIPEWEFVNTPPLVKLWYQLEKEPIVGAETFYVDGAANRET
KLGKAGYVTNRGRQKVVTLTDTTNQKTELQAIYLALQDSGLEVNIVTDSQ
YALGIIQAQPDQSESELVNQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDK
LVSA
Ligand information
Ligand ID1WT
InChIInChI=1S/C25H24N5O3/c1-3-29-23-19(25(31)28(2)21-9-6-12-26-24(21)29)15-17(16-27-23)11-14-33-22-10-13-30(32)20-8-5-4-7-18(20)22/h4-10,12-13,15-16,32H,3,11,14H2,1-2H3
InChIKeyPQGWYSJEHPHRGI-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CCN1c2ncccc2N(C)C(=O)c3cc(CCOc4ccn(O)c5ccccc45)cnc13
OpenEye OEToolkits 1.7.6CCN1c2c(cccn2)N(C(=O)c3c1ncc(c3)CCOC4=CC=[N](c5c4cccc5)O)C
FormulaC25 H24 N5 O3
Name11-ethyl-5-methyl-8-[2-(1-oxidanylquinolin-4-yl)oxyethyl]dipyrido[3,2-[1,4]diazepin-6-one
ChEMBL
DrugBank
ZINC
PDB chain4kv8 Chain A Residue 602 [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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PDB4kv8 N- versus O-alkylation: Utilizing NMR methods to establish reliable primary structure determinations for drug discovery.
Resolution2.3 Å
Binding residue
(original residue number in PDB)		L100 K101 K103 K104 S105 V106 Y181 Y188 P225 F227 W229 L234 H235 P236 Y318
Binding residue
(residue number reindexed from 1)		L100 K101 K103 K104 S105 V106 Y181 Y188 P225 F227 W229 L234 H235 P236 Y318
Annotation score1
Binding affinityMOAD: ic50=17nM
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:4kv8, PDBe:4kv8, PDBj:4kv8
PDBsum4kv8
PubMed23809849
UniProtP04585|POL_HV1H2 Gag-Pol polyprotein (Gene Name=gag-pol)

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