Structure of PDB 6yt1 Chain A Binding Site BS01

Receptor Information
>6yt1 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
AAYSAARLHENAAGKAAAWVQRIEFARLGLPKPDWQVLLAVSRDNYERDA
ELQQRTGAVYAELAAQGWGGRWLVVGADVDPGRLAATLAPP
Ligand information
Ligand IDPK5
InChIInChI=1S/C27H37ClN6O3/c1-3-22-24(34-16-19(28)6-9-23(34)30-22)26(36)29-14-18-4-7-20(8-5-18)32-12-10-21(11-13-32)33-15-17(2)25(35)31-27(33)37/h4-5,7-8,15,19,21-24,30H,3,6,9-14,16H2,1-2H3,(H,29,36)(H,31,35,37)
InChIKeyZMLCAZKJSUZKPA-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7CCC1C(N2CC(CCC2N1)Cl)C(=O)NCc3ccc(cc3)N4CCC(CC4)N5C=C(C(=O)NC5=O)C
CACTVS 3.385CCC1NC2CCC(Cl)CN2C1C(=O)NCc3ccc(cc3)N4CCC(CC4)N5C=C(C)C(=O)NC5=O
FormulaC27 H37 Cl N6 O3
Name2-ethyl-~{N}-[[4-[4-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]piperidin-1-yl]phenyl]methyl]-1,2,3,5,6,7,8,8~{a}-octahydroimidazo[1,2-a]pyridine-3-carboxamide
ChEMBL
DrugBank
ZINC
PDB chain6yt1 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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PDB6yt1 Endeavors towards transformation of M. tuberculosis thymidylate kinase (MtbTMPK) inhibitors into potential antimycobacterial agents.
Resolution1.9 Å
Binding residue
(original residue number in PDB)		P37 L52 F70 R74 R95 N100 Y103 Y165
Binding residue
(residue number reindexed from 1)		P37 L52 F70 R74 R95 N100 Y103 Y146
Annotation score1
Binding affinityMOAD: ic50=47uM
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

View graph for
Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:6yt1, PDBe:6yt1, PDBj:6yt1
PDBsum6yt1
PubMed32823003
UniProtP9WKE1|KTHY_MYCTU Thymidylate kinase (Gene Name=tmk)

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