Structure of PDB 1bqn Chain A Binding Site BS01

Receptor Information
>1bqn Chain A (length=558) Species: 11676 (Human immunodeficiency virus 1) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PISPIETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISKI
GPENPYNTPVFAIKKKDSTKWRKLVDFRELNKRTQDFWEVQLGIPHPAGL
KKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLP
QGWKGSPAIFQSSMTKILEPFKKQNPDIVIYQYMDDLLVGSDLEIGQHRT
KIEELRQHLLRWGLTTPDKKHQKEPPFLWMGYELHPDKWTVQPIVLPQKD
SWTVNDIQKLVGKLNWASQIYPGIKVRQLSKLLRGTKALTEVIPLTEEAE
LELAENREILKEPVHGVYYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLK
TGKYARMRGAHTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKETWET
WWTEYWQATWIPEWEFVNTPPLVKLWYQLEKEPIVGAETFYVDGAANRET
KLGKAGYVTNKGRQKVVPLTNTTNQKTELQAIYLALQDSGLEVNIVTDSQ
YALGIIQAQPDKSESELVNQIIEQLIKKEKVYLAWVPAHKGIGGNQQVDK
LVSAGIRK
Ligand information
Ligand IDHBY
InChIInChI=1S/C15H20N2O3S2/c1-9(2)20-15(18)17-12-7-10(19-3)5-6-11(12)16-14(21)13(17)8-22-4/h5-7,9,13H,8H2,1-4H3,(H,16,21)/t13-/m0/s1
InChIKeyGWKIPRVERALPRD-ZDUSSCGKSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CC(C)OC(=O)N1c2cc(ccc2NC(=S)[C@@H]1CSC)OC
OpenEye OEToolkits 1.5.0CC(C)OC(=O)N1c2cc(ccc2NC(=S)C1CSC)OC
CACTVS 3.341COc1ccc2NC(=S)[CH](CSC)N(C(=O)OC(C)C)c2c1
ACDLabs 10.04S=C2Nc1c(cc(OC)cc1)N(C(=O)OC(C)C)C2CSC
CACTVS 3.341COc1ccc2NC(=S)[C@H](CSC)N(C(=O)OC(C)C)c2c1
FormulaC15 H20 N2 O3 S2
Name(S)-4-ISOPROPOXYCARBONYL-6-METHOXY-3-METHYLTHIOMETHYL-3,4-DIHYDROQUINOXALIN-2(1H)-THIONE;
HBY 097
ChEMBLCHEMBL430488
DrugBankDB07885
ZINCZINC000003870431
PDB chain1bqn Chain A Residue 559 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1bqn Structures of Tyr188Leu mutant and wild-type HIV-1 reverse transcriptase complexed with the non-nucleoside inhibitor HBY 097: inhibitor flexibility is a useful design feature for reducing drug resistance.
Resolution3.3 Å
Binding residue
(original residue number in PDB)		L100 K101 V106 Y181 L188 V189 G190 W229 L234 H235 Y318
Binding residue
(residue number reindexed from 1)		L100 K101 V106 Y181 L188 V189 G190 W229 L234 H235 Y318
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=6.22,IC50=0.60uM
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:1bqn, PDBe:1bqn, PDBj:1bqn
PDBsum1bqn
PubMed9813120
UniProtP03366|POL_HV1B1 Gag-Pol polyprotein (Gene Name=gag-pol)

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