Structure of PDB 3t3y Chain A Binding Site BS02

Receptor Information
>3t3y Chain A (length=199) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AAGAVILRRFAFNAAEQLIRDINDVASQSPFRQMVTPGGYTMSVAMTNCG
HLGWTTHRQGYLYSPIDPQTNKPWPAMPQSFHNLCQRAATAAGYPDFQPD
ACLINRYAPGAKLSLHQDKDEPDLRAPIVSVSLGLPAIFQFGGLKRNDPL
KRLLLEHGDVVVWGGESRLFYHGIQPLKAGFHPLTIDCRYNLTFRQAGK
Ligand information
Ligand IDMD6
InChIInChI=1S/C8H8N2O4/c11-5-2-1-3-9-7(5)8(14)10-4-6(12)13/h1-3,11H,4H2,(H,10,14)(H,12,13)
InChIKeyIZQMRNMMPSNPJM-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.370OC(=O)CNC(=O)c1ncccc1O
ACDLabs 12.01O=C(c1ncccc1O)NCC(=O)O
OpenEye OEToolkits 1.7.2c1cc(c(nc1)C(=O)NCC(=O)O)O
FormulaC8 H8 N2 O4
NameN-[(3-hydroxypyridin-2-yl)carbonyl]glycine
ChEMBLCHEMBL1256568
DrugBank
ZINCZINC000033978615
PDB chain3t3y Chain A Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3t3y Dynamic combinatorial mass spectrometry leads to inhibitors of a 2-oxoglutarate-dependent nucleic Acid demethylase.
Resolution2.001 Å
Binding residue
(original residue number in PDB)		Y122 L128 H131 D133 S145 W178 H187 I189 R204 N206 T208
Binding residue
(residue number reindexed from 1)		Y107 L113 H116 D118 S130 W163 H172 I174 R189 N191 T193
Annotation score1
Binding affinityMOAD: ic50=3.4uM
PDBbind-CN: -logKd/Ki=5.47,IC50=3.4uM
Enzymatic activity
Enzyme Commision number 1.14.11.33: DNA oxidative demethylase.
Gene Ontology
Molecular Function
GO:0005515 protein binding
GO:0008198 ferrous iron binding
GO:0035515 oxidative RNA demethylase activity
GO:0035516 broad specificity oxidative DNA demethylase activity
GO:0046872 metal ion binding
GO:0051213 dioxygenase activity
Biological Process
GO:0006281 DNA repair
GO:0006307 DNA alkylation repair
GO:0035513 oxidative RNA demethylation
GO:0042245 RNA repair
GO:0070989 oxidative demethylation
GO:0072702 response to methyl methanesulfonate
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:3t3y, PDBe:3t3y, PDBj:3t3y
PDBsum3t3y
PubMed22263962
UniProtP05050|ALKB_ECOLI Alpha-ketoglutarate-dependent dioxygenase AlkB (Gene Name=alkB)

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