Structure of PDB 3drs Chain A Binding Site BS01

Receptor Information
>3drs Chain A (length=549) Species: 11706 (HIV-1 M:B_HXB2R) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SPISPIETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISK
IGPENPYNTPVFAIKKKDSTKWRKLVDFRELNKRTQDFWEVQLGIPHPAG
LKKNKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVL
PQGWKGSPAIFQSSMTKILEPFRKQNPDIVIYQYMDDLYVGSDLEIGQHR
TKIEELRQHLLRWGLTTPDKKHQKEPPFLWMGYELHPDKWTVQPIVLPEK
DSWTVNDIQKLVGKLNWASQIYPGIKVRQLCKLLRGTKALTEVIPLTEEA
ELELAENREILKEPVHGVYYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNL
KTGKYARMRGAHTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKETWE
TWWTEYWQATWIPEWEFVNTPPLVKLWYQLEKEPIVGAETFYVDGAANRE
TKLGKAGYVTNRGRQKVVTLTDTTNQKTELQAIYLALQDSGLEVNIVTDS
QYALGIIQAQPDQSESELVNQIIEQLIKKEKVYLAWVPAHKGIGGNEQV
Ligand information
Ligand IDR8D
InChIInChI=1S/C20H12Cl2N4O2/c21-13-6-12(10-23)7-15(8-13)28-19-9-14(3-4-17(19)22)27-11-18-16-2-1-5-24-20(16)26-25-18/h1-9H,11H2,(H,24,25,26)
InChIKeySVMHTBVIPYVDIL-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341Clc1cc(Oc2cc(OCc3n[nH]c4ncccc34)ccc2Cl)cc(c1)C#N
OpenEye OEToolkits 1.5.0c1cc2c(n[nH]c2nc1)COc3ccc(c(c3)Oc4cc(cc(c4)Cl)C#N)Cl
ACDLabs 10.04N#Cc4cc(Oc3c(Cl)ccc(OCc2nnc1ncccc12)c3)cc(Cl)c4
FormulaC20 H12 Cl2 N4 O2
Name3-chloro-5-[2-chloro-5-(1H-pyrazolo[3,4-b]pyridin-3-ylmethoxy)phenoxy]benzonitrile
ChEMBLCHEMBL491019
DrugBankDB08459
ZINCZINC000034891664
PDB chain3drs 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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PDB3drs Discovery of 3-{5-[(6-Amino-1H-pyrazolo[3,4-b]pyridine-3-yl)methoxy]-2-chlorophenoxy}-5-chlorobenzonitrile (MK-4965): A Potent, Orally Bioavailable HIV-1 Non-Nucleoside Reverse Transcriptase Inhibitor with Improved Potency against Key Mutant Viruses.
Resolution3.15 Å
Binding residue
(original residue number in PDB)		L100 K101 N103 V106 V108 Y181 Y188 F227 L234 H235 P236 Y318
Binding residue
(residue number reindexed from 1)		L101 K102 N104 V107 V109 Y182 Y189 F228 L235 H236 P237 Y319
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=9.30,IC50=0.5nM
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:3drs, PDBe:3drs, PDBj:3drs
PDBsum3drs
PubMed18826204
UniProtP04585|POL_HV1H2 Gag-Pol polyprotein (Gene Name=gag-pol)

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