Structure of PDB 3drr Chain A Binding Site BS01

Receptor Information
>3drr Chain A (length=558) 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
LKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVL
PQGWKGSPAIFQSSMTKILEPFRKQNPDIVICQYMDDLYVGSDLEIGQHR
TKIEELRQHLLRWGLTTPDKKHQKEPPFLWMGYELHPDKWTVQPIVLPEK
DSWTVNDIQKLVGKLNWASQIYPGIKVRQLCKLLRGTKALTEVIPLTEEA
ELELAENREILKEPVHGVYYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNL
KTGKYARMRGAHTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKETWE
TWWTEYWQATWIPEWEFVNTPPLVKLWYQLEKEPIVGAETFYVDGAANRE
TKLGKAGYVTNRGRQKVVTLTDTTNQKTELQAIYLALQDSGLEVNIVTDS
QYALGIIQAQPDQSESELVNQIIEQLIKKEKVYLAWVPAHKGIGGNEQVD
KLVSAGIR
Ligand information
Ligand IDR8E
InChIInChI=1S/C20H13Cl2N5O2/c21-12-5-11(9-23)6-14(7-12)29-18-8-13(1-3-16(18)22)28-10-17-15-2-4-19(24)25-20(15)27-26-17/h1-8H,10H2,(H3,24,25,26,27)
InChIKeyKXDIHAQCVNNLIB-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341Nc1ccc2c(COc3ccc(Cl)c(Oc4cc(Cl)cc(c4)C#N)c3)n[nH]c2n1
ACDLabs 10.04N#Cc4cc(Oc3c(Cl)ccc(OCc2nnc1nc(ccc12)N)c3)cc(Cl)c4
OpenEye OEToolkits 1.5.0c1cc(c(cc1OCc2c3ccc(nc3[nH]n2)N)Oc4cc(cc(c4)Cl)C#N)Cl
FormulaC20 H13 Cl2 N5 O2
Name3-{5-[(6-amino-1H-pyrazolo[3,4-b]pyridin-3-yl)methoxy]-2-chlorophenoxy}-5-chlorobenzonitrile
ChEMBLCHEMBL489586
DrugBankDB08460
ZINCZINC000034891728
PDB chain3drr 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

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB3drr 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.
Resolution2.89 Å
Binding residue
(original residue number in PDB)		L100 K101 K103 V106 Y188 V189 P225 F227 W229 L234 H235 P236 Y318
Binding residue
(residue number reindexed from 1)		L101 K102 K104 V107 Y189 V190 P226 F228 W230 L235 H236 P237 Y319
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=9.40,IC50=0.4nM
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:3drr, PDBe:3drr, PDBj:3drr
PDBsum3drr
PubMed18826204
UniProtP04585|POL_HV1H2 Gag-Pol polyprotein (Gene Name=gag-pol)

[Back to BioLiP]