Structure of PDB 4h4m Chain A Binding Site BS01

Receptor Information
>4h4m Chain A (length=548) 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]
PISPIETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISKI
GPENPYNTPVFAIKKKDSTKWRKLVDFRELNKRTQDFWEVQLGIPHPAGL
KKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLP
QGWKGSPAIFQSSMTKILEPFAAQNPDIVIYQYMDDLYVGSDLEIGQHRT
KIEELRQHLLRWGLTTPDKKHQKEPPFLWMGYELHPDKWTVQPIVLPEKD
SWTVNDIQKLVGKLNWASQIYPGIKVRQLSKLLRGTKALTEVIPLTEEAE
LELAENREILKEPVHGVYYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLK
TGKYARMRGAHTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKETWET
WWTEYWQATWIPEWEFVNTPPLVKLWYQLEKEPIVGAETFYVDGAANRET
KLGKAGYVTNKGRQKVVPLTNTTNQKTELQAIYLALQDSGLEVNIVTDSQ
YALGIIQAQPDKSESELVNQIIEQLIKKEKVYLAWVPAHKGIGGNEQV
Ligand information
Ligand ID494
InChIInChI=1S/C21H15Cl2N3O4/c22-15-3-4-18(30-17-11-14(2-1-6-24)10-16(23)12-17)19(13-15)29-9-8-26-7-5-20(27)25-21(26)28/h1-5,7,10-13H,8-9H2,(H,25,27,28)/b2-1+
InChIKeyLXPGWIGXHHBGJC-OWOJBTEDSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6c1cc(c(cc1Cl)OCCN2C=CC(=O)NC2=O)Oc3cc(cc(c3)Cl)/C=C/C#N
OpenEye OEToolkits 1.7.6c1cc(c(cc1Cl)OCCN2C=CC(=O)NC2=O)Oc3cc(cc(c3)Cl)C=CC#N
CACTVS 3.370Clc1ccc(Oc2cc(Cl)cc(\C=C\C#N)c2)c(OCCN3C=CC(=O)NC3=O)c1
CACTVS 3.370Clc1ccc(Oc2cc(Cl)cc(C=CC#N)c2)c(OCCN3C=CC(=O)NC3=O)c1
ACDLabs 12.01N#C\C=C\c3cc(Oc2ccc(Cl)cc2OCCN1C=CC(=O)NC1=O)cc(Cl)c3
FormulaC21 H15 Cl2 N3 O4
Name(2E)-3-(3-chloro-5-{4-chloro-2-[2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)ethoxy]phenoxy}phenyl)prop-2-enenitrile
ChEMBLCHEMBL1923490
DrugBank
ZINCZINC000073196585
PDB chain4h4m 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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PDB4h4m Crystal Structures of HIV-1 Reverse Transcriptase with Picomolar Inhibitors Reveal Key Interactions for Drug Design.
Resolution2.85 Å
Binding residue
(original residue number in PDB)		P95 L100 K102 K103 V106 V108 Y181 Y188 W229 L234 P236 Y318
Binding residue
(residue number reindexed from 1)		P95 L100 K102 K103 V106 V108 Y181 Y188 W229 L234 P236 Y318
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=8.52,IC50=3.0nM
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:4h4m, PDBe:4h4m, PDBj:4h4m
PDBsum4h4m
PubMed23163887
UniProtP03366|POL_HV1B1 Gag-Pol polyprotein (Gene Name=gag-pol)

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