Structure of PDB 5nr7 Chain A Binding Site BS01

Receptor Information
>5nr7 Chain A (length=188) Species: 83332 (Mycobacterium tuberculosis H37Rv) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MLIAIEGVDGAGKRTLVEKLSGAFRAAGRSVATLAFPRYGQSVAADIAAE
ALHGEHGDLASSVYAMATLFALDRAGAVHTIQGLCRGYDVVILDRYVASN
AAYSAARLHENAAGKAAAWVQRIEFARLGLPKPDWQVLLAVSAELRDAEL
QQRTGAVYAELAAQGWGGRWLVVGADVDPGRLAATLAP
Ligand information
Ligand IDYUI
InChIInChI=1S/C26H25ClN4O3/c1-17-15-31(26(33)29-25(17)32)20-9-11-30(12-10-20)16-19-14-24(22-7-2-3-8-23(22)28-19)34-21-6-4-5-18(27)13-21/h2-8,13-15,20H,9-12,16H2,1H3,(H,29,32,33)
InChIKeyDAZGAHYHWTYXTL-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6CC1=CN(C(=O)NC1=O)C2CCN(CC2)Cc3cc(c4ccccc4n3)Oc5cccc(c5)Cl
CACTVS 3.385CC1=CN(C2CCN(CC2)Cc3cc(Oc4cccc(Cl)c4)c5ccccc5n3)C(=O)NC1=O
FormulaC26 H25 Cl N4 O3
Name1-[1-[[4-(3-chloranylphenoxy)quinolin-2-yl]methyl]piperidin-4-yl]-5-methyl-pyrimidine-2,4-dione
ChEMBLCHEMBL4105150
DrugBank
ZINC
PDB chain5nr7 Chain A Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5nr7 Structure Guided Lead Generation toward Nonchiral M. tuberculosis Thymidylate Kinase Inhibitors.
Resolution2.35 Å
Binding residue
(original residue number in PDB)		P37 L52 H53 F70 R74 R95 S99 N100 Y103
Binding residue
(residue number reindexed from 1)		P37 L52 H53 F70 R74 R95 S99 N100 Y103
Annotation score1
Binding affinityMOAD: ic50=0.95uM
PDBbind-CN: -logKd/Ki=6.02,IC50=0.95uM
Enzymatic activity
Enzyme Commision number 2.7.4.9: dTMP kinase.
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0004798 thymidylate kinase activity
GO:0005524 ATP binding
GO:0005525 GTP binding
GO:0016301 kinase activity
GO:0042803 protein homodimerization activity
GO:0046872 metal ion binding
Biological Process
GO:0006227 dUDP biosynthetic process
GO:0006233 dTDP biosynthetic process
GO:0006235 dTTP biosynthetic process
GO:0009165 nucleotide biosynthetic process
GO:0016310 phosphorylation
GO:0046044 TMP metabolic process
GO:0046940 nucleoside monophosphate phosphorylation
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5nr7, PDBe:5nr7, PDBj:5nr7
PDBsum5nr7
PubMed29510037
UniProtP9WKE1|KTHY_MYCTU Thymidylate kinase (Gene Name=tmk)

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