Structure of PDB 5cyq Chain A Binding Site BS01

Receptor Information
>5cyq Chain A (length=548) 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]
MVPISPIETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKIS
KIGPENPYNTPVFAIKKKDSTKWRKLVDFRELNKRTQDFWEVQLGIPHPA
GLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNV
LPQGWKGSPAIFQSSMTKILEPFAAQNPDIVIYQYMDDLYVGSDLEIGQH
RTKIEELRQHLLRWGLTTPDKKHQKEPPFLWMGYELHPDKWTVQPIVLPE
KDSWTVNDIQKLVGKLNWASQIYPGIKVRQLSKLLRGTKALTEVIPLTEE
AELELAENREILKEPVHGVYYDPSKDLIAEIQKQGQGQWTYQIYQEPFKN
LKTGKYARMRGAHTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKETW
ETWWTEYWQATWIPEWEFVNTPPLVKLWYQLEKEPIVGAETFYVDGAANR
ETKLGKAGYVTNKGRQKVVPLTNTTNQKTELQAIYLALQDSGLEVNIVTD
SQYALGIIQAQPDKSESELVNQIIEQLIKKEKVYLAWVPAHKGIGGNE
Ligand information
Ligand IDT27
InChIInChI=1S/C22H18N6/c1-15-12-18(4-3-10-23)13-16(2)21(15)27-20-9-11-25-22(28-20)26-19-7-5-17(14-24)6-8-19/h3-9,11-13H,1-2H3,(H2,25,26,27,28)/b4-3+
InChIKeyYIBOMRUWOWDFLG-ONEGZZNKSA-N
SMILES
SoftwareSMILES
CACTVS 3.370Cc1cc(C=CC#N)cc(C)c1Nc2ccnc(Nc3ccc(cc3)C#N)n2
ACDLabs 12.01N#C\C=C\c1cc(c(c(c1)C)Nc2nc(ncc2)Nc3ccc(C#N)cc3)C
OpenEye OEToolkits 1.7.6Cc1cc(cc(c1Nc2ccnc(n2)Nc3ccc(cc3)C#N)C)/C=C/C#N
CACTVS 3.370Cc1cc(/C=C/C#N)cc(C)c1Nc2ccnc(Nc3ccc(cc3)C#N)n2
OpenEye OEToolkits 1.7.6Cc1cc(cc(c1Nc2ccnc(n2)Nc3ccc(cc3)C#N)C)C=CC#N
FormulaC22 H18 N6
Name4-{[4-({4-[(E)-2-cyanoethenyl]-2,6-dimethylphenyl}amino)pyrimidin-2-yl]amino}benzonitrile;
Rilpivirine
ChEMBLCHEMBL175691
DrugBankDB08864
ZINCZINC000001554274
PDB chain5cyq Chain A Residue 601 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5cyq Rapid experimental SAD phasing and hot-spot identification with halogenated fragments.
Resolution2.147 Å
Binding residue
(original residue number in PDB)		L100 K101 K103 V179 Y181 Y188 F227 W229 L234 H235 P236 Y318
Binding residue
(residue number reindexed from 1)		L102 K103 K105 V181 Y183 Y190 F229 W231 L236 H237 P238 Y320
Annotation score1
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:5cyq, PDBe:5cyq, PDBj:5cyq
PDBsum5cyq
PubMed26870381
UniProtP03366|POL_HV1B1 Gag-Pol polyprotein (Gene Name=gag-pol)

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