Structure of PDB 5nq5 Chain A Binding Site BS01

Receptor Information
>5nq5 Chain A (length=191) Species: 83332 (Mycobacterium tuberculosis H37Rv) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MLIAIEGVDGAGKRTLVEKLSGAFRAAGRSVATLAFPRYGQSVAADIAAE
ALHGEHGDLASSVYAMATLFALDRAGAVHTIQGLCRGYDVVILDRYVASN
AAYSAARLHENAAGKAAAWVQRIEFARLGLPKPDWQVLLARDNYERDAEL
QQRTGAVYAELAAQGWGGRWLVVGADVDPGRLAATLAPPDV
Ligand information
Ligand ID952
InChIInChI=1S/C23H25N3O3/c1-17-14-26(23(28)24-22(17)27)19-8-6-12-25(16-19)15-18-7-5-11-21(13-18)29-20-9-3-2-4-10-20/h2-5,7,9-11,13-14,19H,6,8,12,15-16H2,1H3,(H,24,27,28)/t19-/m0/s1
InChIKeyUVSXXFBEAJISCP-IBGZPJMESA-N
SMILES
SoftwareSMILES
CACTVS 3.385CC1=CN([CH]2CCCN(C2)Cc3cccc(Oc4ccccc4)c3)C(=O)NC1=O
OpenEye OEToolkits 2.0.6CC1=CN(C(=O)NC1=O)[C@H]2CCCN(C2)Cc3cccc(c3)Oc4ccccc4
CACTVS 3.385CC1=CN([C@H]2CCCN(C2)Cc3cccc(Oc4ccccc4)c3)C(=O)NC1=O
OpenEye OEToolkits 2.0.6CC1=CN(C(=O)NC1=O)C2CCCN(C2)Cc3cccc(c3)Oc4ccccc4
FormulaC23 H25 N3 O3
Name5-methyl-1-[(3~{S})-1-[(3-phenoxyphenyl)methyl]piperidin-3-yl]pyrimidine-2,4-dione
ChEMBLCHEMBL2179292
DrugBank
ZINCZINC000095571693
PDB chain5nq5 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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PDB5nq5 Structure Guided Lead Generation toward Nonchiral M. tuberculosis Thymidylate Kinase Inhibitors.
Resolution2.85 Å
Binding residue
(original residue number in PDB)		F36 L52 M66 F70 R74 R95 N100 Y103 R107
Binding residue
(residue number reindexed from 1)		F36 L52 M66 F70 R74 R95 N100 Y103 R107
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=5.00,IC50=10uM
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:5nq5, PDBe:5nq5, PDBj:5nq5
PDBsum5nq5
PubMed29510037
UniProtP9WKE1|KTHY_MYCTU Thymidylate kinase (Gene Name=tmk)

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