Structure of PDB 1iky Chain A Binding Site BS01

Receptor Information
>1iky Chain A (length=557) 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
KKNKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLP
QGWKGSPAIFQSSMTKILEPFKKQNPDIVIYQYMDDLYVGSDLEIGQHRT
KIEELRQHLLRWGLTTPDKKHQKEPPFLWMGYELHPDKWTVQPIVLPEKD
SWTVNDIQKLVGKLNWASQIYPGIKVRQLCKLLRGTKALTEVIPLTEEAE
LELAENREILKEPVHGVYYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLK
TGKYARMRGAHTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKETWET
WWTEYWQATWIPEWEFVNTPPLVKLWYQLEKEPIVGAETFYVDGAANRET
KLGKAGYVTNKGRQKVVPLTNTTNQKTQLQAIYLALQDSGLEVNIVTDSQ
YALGIIQAQPDKSESELVNQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDK
LVSAGIR
Ligand information
Ligand IDMSD
InChIInChI=1S/C19H18N4O3S/c1-10(24)12-4-5-15(26-2)17(18(12)25)13-7-14(13)22-19(27)23-16-6-3-11(8-20)9-21-16/h3-6,9,13-14,25H,7H2,1-2H3,(H2,21,22,23,27)/t13-,14+/m0/s1
InChIKeyFSRLCMRWYUJTNT-UONOGXRCSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CC(=O)c1ccc(c(c1O)C2CC2NC(=S)Nc3ccc(cn3)C#N)OC
OpenEye OEToolkits 1.5.0CC(=O)c1ccc(c(c1O)[C@H]2C[C@H]2NC(=S)Nc3ccc(cn3)C#N)OC
CACTVS 3.341COc1ccc(C(C)=O)c(O)c1[CH]2C[CH]2NC(=S)Nc3ccc(cn3)C#N
CACTVS 3.341COc1ccc(C(C)=O)c(O)c1[C@H]2C[C@H]2NC(=S)Nc3ccc(cn3)C#N
ACDLabs 10.04S=C(Nc1ncc(C#N)cc1)NC3CC3c2c(OC)ccc(C(=O)C)c2O
FormulaC19 H18 N4 O3 S
Name1-[2-(3-ACETYL-2-HYDROXY-6-METHOXY-PHENYL)-CYCLOPROPYL]-3-(5-CYANO-PYRIDIN-2-YL)-THIOUREA
ChEMBL
DrugBankDB08212
ZINCZINC000013685243
PDB chain1iky Chain A Residue 2000 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB1iky Structural basis for the inhibitory efficacy of efavirenz (DMP-266), MSC194 and PNU142721 towards the HIV-1 RT K103N mutant.
Resolution3.0 Å
Binding residue
(original residue number in PDB)
L100 K101 N103 V179 Y181 Y188 F227 W229 L234 H235 P236 Y318
Binding residue
(residue number reindexed from 1)
L100 K101 N103 V179 Y181 Y188 F227 W229 L234 H235 P236 Y318
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=8.26,IC50=5.5nM
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

View graph for
Molecular Function

View graph for
Biological Process
External links
PDB RCSB:1iky, PDBe:1iky, PDBj:1iky
PDBsum1iky
PubMed11895437
UniProtP03366|POL_HV1B1 Gag-Pol polyprotein (Gene Name=gag-pol)

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