Structure of PDB 4m5h Chain A Binding Site BS02

Receptor Information
>4m5h 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 IDYH2
InChIInChI=1S/C13H10N6OS/c14-5-7-1-3-8(4-2-7)6-21-13-16-9-10(18-13)17-12(15)19-11(9)20/h1-4H,6H2,(H4,15,16,17,18,19,20)
InChIKeyGWZOSZRSFBULCC-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385NC1=Nc2[nH]c(SCc3ccc(cc3)C#N)nc2C(=O)N1
OpenEye OEToolkits 1.7.6c1cc(ccc1CSc2[nH]c3c(n2)C(=O)NC(=N3)N)C#N
ACDLabs 12.01N#Cc1ccc(cc1)CSc3nc2c(N=C(N)NC2=O)n3
FormulaC13 H10 N6 O S
Name4-{[(2-amino-6-oxo-6,9-dihydro-1H-purin-8-yl)sulfanyl]methyl}benzonitrile
ChEMBLCHEMBL3233202
DrugBank
ZINCZINC000004639554
PDB chain4m5h Chain A Residue 302 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB4m5h The identification, analysis and structure-based development of novel inhibitors of 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase.
Resolution1.11 Å
Binding residue
(original residue number in PDB)		T42 P43 L45 G46 Y53 N55 W89 R121 F123
Binding residue
(residue number reindexed from 1)		T43 P44 L46 G47 Y54 N56 W90 R122 F124
Annotation score1
Binding affinityMOAD: Kd=29uM
PDBbind-CN: -logKd/Ki=4.54,Kd=29uM
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:4m5h, PDBe:4m5h, PDBj:4m5h
PDBsum4m5h
PubMed24613625
UniProtP26281|HPPK_ECOLI 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase (Gene Name=folK)

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