Structure of PDB 3c6u Chain A Binding Site BS01

Receptor Information
>3c6u 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
PQGWKGSPAIFQSSMTKILEPFRKQNPDIVIYQYMDDLYVGSDLEIGQHR
TKIEELRQHLLRWGLTTPDKKHQKEPPFLWMGYELHPDKWTVQPIVLPEK
DSWTVNDIQKLVGKLNWASQIYPGIKVRQLCKLLRGTKALTEVIPLTEEA
ELELAENREILKEPVHGVYYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNL
KTGKYARMRGAHTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKETWE
TWWTEYWQATWIPEWEFVNTPPLVKLWYQLEKEPIVGAETFYVDGAANRE
TKLGKAGYVTNRGRQKVVTLTDTTNQKTELQAIYLALQDSGLEVNIVTDS
QYALGIIQAQPDQSESELVNQIIEQLIKKEKVYLAWVPAHKGIGGNEQVD
KLVSAGIR
Ligand information
Ligand IDM22
InChIInChI=1S/C21H13Cl2N3O2/c22-14-7-13(11-24)8-16(9-14)28-21-10-15(5-6-18(21)23)27-12-20-17-3-1-2-4-19(17)25-26-20/h1-10H,12H2,(H,25,26)
InChIKeyWHCLIFOVZDANCU-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04N#Cc4cc(Oc3c(Cl)ccc(OCc2nnc1ccccc12)c3)cc(Cl)c4
OpenEye OEToolkits 1.5.0c1ccc2c(c1)c(n[nH]2)COc3ccc(c(c3)Oc4cc(cc(c4)Cl)C#N)Cl
CACTVS 3.341Clc1cc(Oc2cc(OCc3n[nH]c4ccccc34)ccc2Cl)cc(c1)C#N
FormulaC21 H13 Cl2 N3 O2
Name3-chloro-5-[2-chloro-5-(1H-indazol-3-ylmethoxy)phenoxy]benzonitrile
ChEMBLCHEMBL402823
DrugBankDB08154
ZINCZINC000029044989
PDB chain3c6u Chain A Residue 561 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3c6u The design and synthesis of diaryl ether second generation HIV-1 non-nucleoside reverse transcriptase inhibitors (NNRTIs) with enhanced potency versus key clinical mutations.
Resolution2.7 Å
Binding residue
(original residue number in PDB)		L100 K103 V106 Y181 Y188 G190 F227 W229 L234 H235 P236 Y318
Binding residue
(residue number reindexed from 1)		L101 K104 V107 Y182 Y189 G191 F228 W230 L235 H236 P237 Y319
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=8.87,IC50=1.35nM
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:3c6u, PDBe:3c6u, PDBj:3c6u
PDBsum3c6u
PubMed18396399
UniProtP04585|POL_HV1H2 Gag-Pol polyprotein (Gene Name=gag-pol)

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