Structure of PDB 4m5k Chain A Binding Site BS05

Receptor Information
>4m5k Chain A (length=159) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MTVAYIAIGSNLASPLEQVNAALKALGDIPESHILTVSSFYRTPPLGPQD
QPDYLNAAVALETSLAPEELLNHTQRIELQQGRVRKAERWGPRTLDLDIM
LFGNEVINTERLTVPHYDMKNRGFMLWPLFEIAPELVFPDGEMLRQILHT
RAFDKLNKW
Ligand information
Ligand IDYH3
InChIInChI=1S/C14H13N5O2S/c1-7-3-2-4-8(5-7)9(20)6-22-14-16-10-11(18-14)17-13(15)19-12(10)21/h2-5H,6H2,1H3,(H4,15,16,17,18,19,21)
InChIKeyKDLSQBTYPBZMRM-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6Cc1cccc(c1)C(=O)CSc2[nH]c3c(n2)C(=O)NC(=N3)N
CACTVS 3.385Cc1cccc(c1)C(=O)CSc2[nH]c3N=C(N)NC(=O)c3n2
ACDLabs 12.01O=C(c1cccc(c1)C)CSc3nc2c(N=C(N)NC2=O)n3
FormulaC14 H13 N5 O2 S
Name2-amino-8-{[2-(3-methylphenyl)-2-oxoethyl]sulfanyl}-1,9-dihydro-6H-purin-6-one
ChEMBLCHEMBL3233208
DrugBank
ZINCZINC000098209638
PDB chain4m5k Chain A Residue 305 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4m5k The identification, analysis and structure-based development of novel inhibitors of 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase.
Resolution1.296 Å
Binding residue
(original residue number in PDB)		T42 P43 L45 Y53 N55 W89 D117 R121 F123
Binding residue
(residue number reindexed from 1)		T43 P44 L46 Y54 N56 W90 D118 R122 F124
Annotation score1
Binding affinityMOAD: Kd=5.9uM
PDBbind-CN: -logKd/Ki=5.23,Kd=5.9uM
Enzymatic activity
Catalytic site (original residue number in PDB) R82 R92 D95 D97
Catalytic site (residue number reindexed from 1) R83 R93 D96 D98
Enzyme Commision number 2.7.6.3: 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase.
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0003848 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase activity
GO:0005524 ATP binding
GO:0016301 kinase activity
Biological Process
GO:0009396 folic acid-containing compound biosynthetic process
GO:0016310 phosphorylation
GO:0046654 tetrahydrofolate biosynthetic process
GO:0046656 folic acid biosynthetic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:4m5k, PDBe:4m5k, PDBj:4m5k
PDBsum4m5k
PubMed24613625
UniProtP26281|HPPK_ECOLI 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase (Gene Name=folK)

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