Structure of PDB 1ikv Chain A Binding Site BS01

Receptor Information
>1ikv Chain A (length=556) 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
KKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQ
GWKGSPAIFQSSMTKILEPFKKQNPDIVIYQYMDDLYVGSDLEIGQHRTK
IEELRQHLLRWGLTTPDKKHQKEPPFLWMGYELHPDKWTVQPIVLPEKDS
WTVNDIQKLVGKLNWASQIYPGIKVRQLCKLLRGTKALTEVIPLTEEAEL
ELAENREILKEPVHGVYYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLKT
GKYARMRGAHTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKETWETW
WTEYWQATWIPEWEFVNTPPLVKLWYQLEKEPIVGAETFYVDGAANRETK
LGKAGYVTNKGRQKVVPLTNTTNQKTQLQAIYLALQDSGLEVNIVTDSQY
ALGIIQAQPDKSESELVNQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDKL
VSAGIR
Ligand information
Ligand IDEFZ
InChIInChI=1S/C14H9ClF3NO2/c15-9-3-4-11-10(7-9)13(14(16,17)18,21-12(20)19-11)6-5-8-1-2-8/h3-4,7-8H,1-2H2,(H,19,20)/t13-/m0/s1
InChIKeyXPOQHMRABVBWPR-ZDUSSCGKSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6c1cc2c(cc1Cl)[C@@](OC(=O)N2)(C#CC3CC3)C(F)(F)F
CACTVS 3.370FC(F)(F)[C@]1(OC(=O)Nc2ccc(Cl)cc12)C#CC3CC3
ACDLabs 12.01FC(F)(F)C3(C#CC1CC1)OC(=O)Nc2c3cc(Cl)cc2
CACTVS 3.370FC(F)(F)[C]1(OC(=O)Nc2ccc(Cl)cc12)C#CC3CC3
OpenEye OEToolkits 1.7.6c1cc2c(cc1Cl)C(OC(=O)N2)(C#CC3CC3)C(F)(F)F
FormulaC14 H9 Cl F3 N O2
Name(-)-6-CHLORO-4-CYCLOPROPYLETHYNYL-4-TRIFLUOROMETHYL-1,4-DIHYDRO-2H-3,1-BENZOXAZIN-2-ONE;
DMP-266;
Efavirenz
ChEMBLCHEMBL223228
DrugBankDB00625
ZINCZINC000002020233
PDB chain1ikv Chain A Residue 2000 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1ikv 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 V106 V179 Y181 Y188 G190 W229 L234 H235 Y318
Binding residue
(residue number reindexed from 1)		L100 K101 V105 V178 Y180 Y187 G189 W228 L233 H234 Y317
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=6.28,IC50=520nM
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:1ikv, PDBe:1ikv, PDBj:1ikv
PDBsum1ikv
PubMed11895437
UniProtP03366|POL_HV1B1 Gag-Pol polyprotein (Gene Name=gag-pol)

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