Structure of PDB 4m5n Chain A Binding Site BS04

Receptor Information
>4m5n Chain A (length=160) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
HMTVAYIAIGSNLASPLEQVNAALKALGDIPESHILTVSSFYRTPPLGPQ
DQPDYLNAAVALETSLAPEELLNHTQRIELQQGRVRKAERWGPRTLDLDI
MLFGNEVINTERLTVPHYDMKNRGFMLWPLFEIAPELVFPDGEMLRQILH
TRAFDKLNKW
Ligand information
Ligand IDYH7
InChIInChI=1S/C5H5N5S/c6-3-2-4(8-1-7-2)10-5(11)9-3/h1H,(H4,6,7,8,9,10,11)
InChIKeyLQJZZLRZEPKRRQ-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6C1=NC2=C(NC(=S)N=C2N1)N
CACTVS 3.370NC1=C2N=CNC2=NC(=S)N1
ACDLabs 12.01S=C2N=C1C(N=CN1)=C(N2)N
FormulaC5 H5 N5 S
Name6-amino-1,9-dihydro-2H-purine-2-thione
ChEMBL
DrugBank
ZINCZINC000004353400
PDB chain4m5n Chain A Residue 504 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4m5n The identification, analysis and structure-based development of novel inhibitors of 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase.
Resolution2.0 Å
Binding residue
(original residue number in PDB)		T42 P44 L45 Y53 N55 D95 F123
Binding residue
(residue number reindexed from 1)		T44 P46 L47 Y55 N57 D97 F125
Annotation score1
Binding affinityMOAD: Kd=7.5uM
PDBbind-CN: -logKd/Ki=5.12,Kd=7.5uM
Enzymatic activity
Catalytic site (original residue number in PDB) R82 R92 D95 D97
Catalytic site (residue number reindexed from 1) R84 R94 D97 D99
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:4m5n, PDBe:4m5n, PDBj:4m5n
PDBsum4m5n
PubMed24613625
UniProtP26281|HPPK_ECOLI 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase (Gene Name=folK)

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