Structure of PDB 4rw8 Chain A Binding Site BS01

Receptor Information
>4rw8 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]
VPISPIETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISK
IGPENPYNTPVFAIKKKDSTKWRKLVDFRELNKRTQDFWEVQLGIPHPAG
LKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVL
PQGWKGSPAIFQSSMTKILEPFAAQNPDIVIYQYMDDLYVGSDLEIGQHR
TKIEELRQHLLRWGLTTPDKKHQKEPPFLWMGYELHPDKWTVQPIVLPEK
DSWTVNDIQKLVGKLNWASQIYPGIKVRQLSKLLRGTKALTEVIPLTEEA
ELELAENREILKEPVHGVYYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNL
KTGKYARMRGAHTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKETWE
TWWTEYWQATWIPEWEFVNTPPLVKLWYQLEKEPIVGAETFYVDGAANRE
TKLGKAGYVTNKGRQKVVPLTNTTNQKTELQAIYLALQDSGLEVNIVTDS
QYALGIIQAQPDKSESELVNQIIEQLIKKEKVYLAWVPAHKGIGGNEQ
Ligand information
Ligand ID3X6
InChIInChI=1S/C21H16ClN3O4/c22-16-12-15(4-3-8-23)13-17(14-16)29-19-6-2-1-5-18(19)28-11-10-25-9-7-20(26)24-21(25)27/h1-7,9,12-14H,10-11H2,(H,24,26,27)/b4-3+
InChIKeyQQWLDKMLZHRQRI-ONEGZZNKSA-N
SMILES
SoftwareSMILES
CACTVS 3.385Clc1cc(Oc2ccccc2OCCN3C=CC(=O)NC3=O)cc(\C=C\C#N)c1
ACDLabs 12.01N#C\C=C\c3cc(Oc2ccccc2OCCN1C=CC(=O)NC1=O)cc(Cl)c3
OpenEye OEToolkits 1.7.6c1ccc(c(c1)OCCN2C=CC(=O)NC2=O)Oc3cc(cc(c3)Cl)C=CC#N
CACTVS 3.385Clc1cc(Oc2ccccc2OCCN3C=CC(=O)NC3=O)cc(C=CC#N)c1
OpenEye OEToolkits 1.7.6c1ccc(c(c1)OCCN2C=CC(=O)NC2=O)Oc3cc(cc(c3)Cl)/C=C/C#N
FormulaC21 H16 Cl N3 O4
Name(2E)-3-(3-chloro-5-{2-[2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)ethoxy]phenoxy}phenyl)prop-2-enenitrile
ChEMBLCHEMBL3342966
DrugBank
ZINCZINC000222275052
PDB chain4rw8 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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PDB4rw8 Structure-Based Evaluation of Non-nucleoside Inhibitors with Improved Potency and Solubility That Target HIV Reverse Transcriptase Variants.
Resolution2.878 Å
Binding residue
(original residue number in PDB)
K102 K103 V106 V108 Y181 Y188 F227 W229 L234 H235 P236 Y318
Binding residue
(residue number reindexed from 1)
K103 K104 V107 V109 Y182 Y189 F228 W230 L235 H236 P237 Y319
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

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Molecular Function

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Biological Process
External links
PDB RCSB:4rw8, PDBe:4rw8, PDBj:4rw8
PDBsum4rw8
PubMed25700160
UniProtP03366|POL_HV1B1 Gag-Pol polyprotein (Gene Name=gag-pol)

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