Structure of PDB 3is9 Chain A Binding Site BS01

Receptor Information
>3is9 Chain A (length=554) 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]
PISPIETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISKI
GPENPYNTPVFAIKKKDSTKWRKLVDFRELNKRTQDFWEVQLGIPHPAGL
KKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLP
QGWKGSPAIFQSSMTKILEPFAAQNPDIVIYQYMDDLYVGSDLEIGQHRT
KIEELRQHLLRWGLTTPDKKHQKEPPFLWMGYELHPDKWTVQPIVLPEKD
SWTVNDIQKLVGKLNWASQIYPGIKVRQLSKLLRGTKALTEVIPLTEEAE
LELAENREILKEPVHGVYYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLK
TGKYARMRGAHTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKETWET
WWTEYWQATWIPEWEFVNTPPLVKLWYQLEKEPIVGAETFYVDGAANRET
KLGKAGYVTNKGRQKVVPLTNTTNQKTELQAIYLALQDSGLEVNIVTDSQ
YALGIIQAQPDKSESELVNQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDK
LVSA
Ligand information
Ligand IDAC7
InChIInChI=1S/C27H26N2O8/c1-33-23(30)9-7-6-8-20(16-10-18(14-28)24(34-2)21(12-16)26(31)36-4)17-11-19(15-29)25(35-3)22(13-17)27(32)37-5/h8,10-13H,6-7,9H2,1-5H3
InChIKeyKTXLKUASBPHAEE-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385COC(=O)CCC\C=C(/c1cc(C#N)c(OC)c(c1)C(=O)OC)c2cc(C#N)c(OC)c(c2)C(=O)OC
CACTVS 3.385COC(=O)CCCC=C(c1cc(C#N)c(OC)c(c1)C(=O)OC)c2cc(C#N)c(OC)c(c2)C(=O)OC
OpenEye OEToolkits 1.7.5COc1c(cc(cc1C(=O)OC)C(=CCCCC(=O)OC)c2cc(c(c(c2)C(=O)OC)OC)C#N)C#N
FormulaC27 H26 N2 O8
Namedimethyl 3,3'-(6-methoxy-6-oxohex-1-ene-1,1-diyl)bis(5-cyano-6-methoxybenzoate)
ChEMBLCHEMBL110610
DrugBank
ZINCZINC000026850341
PDB chain3is9 Chain A Residue 556 [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]
PDB3is9 Crystallographic study of a novel subnanomolar inhibitor provides insight on the binding interactions of alkenyldiarylmethanes with human immunodeficiency virus-1 reverse transcriptase.
Resolution2.55 Å
Binding residue
(original residue number in PDB)		L100 V106 Y181 Y188 K223 F227 L228 W229 L234 H235 Y318
Binding residue
(residue number reindexed from 1)		L100 V106 Y181 Y188 K223 F227 L228 W229 L234 H235 Y318
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=6.42,IC50=0.38uM
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:3is9, PDBe:3is9, PDBj:3is9
PDBsum3is9
PubMed19775161
UniProtP03366|POL_HV1B1 Gag-Pol polyprotein (Gene Name=gag-pol)

[Back to BioLiP]