Structure of PDB 3t4h Chain B Binding Site BS02

Receptor Information
>3t4h Chain B (length=201) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PLAAGAVILRRFAFNAAEQLIRDINDVASQSPFRQMVTPGGYTMSVAMTN
CGHLGWTTHRQGYLYSPIDPQTNKPWPAMPQSFHNLCQRAATAAGYPDFQ
PDACLINRYAPGAKLSLHQDKDEPDLRAPIVSVSLGLPAIFQFGGLKRND
PLKRLLLEHGDVVVWGGESRLFYHGIQPLKAGFHPLTIDCRYNLTFRQAG
K
Ligand information
Ligand IDMD5
InChIInChI=1S/C12H12N2O7S/c15-10(12(18)19)13-9(11(16)17)6-22-5-7-2-1-3-8(4-7)14(20)21/h1-4,9H,5-6H2,(H,13,15)(H,16,17)(H,18,19)/t9-/m0/s1
InChIKeyOBSYIMVMIJBTMQ-VIFPVBQESA-N
SMILES
SoftwareSMILES
CACTVS 3.370OC(=O)[CH](CSCc1cccc(c1)[N+]([O-])=O)NC(=O)C(O)=O
OpenEye OEToolkits 1.7.2c1cc(cc(c1)[N+](=O)[O-])CSC[C@@H](C(=O)O)NC(=O)C(=O)O
OpenEye OEToolkits 1.7.2c1cc(cc(c1)[N+](=O)[O-])CSCC(C(=O)O)NC(=O)C(=O)O
ACDLabs 12.01O=[N+]([O-])c1cc(ccc1)CSCC(C(=O)O)NC(=O)C(=O)O
CACTVS 3.370OC(=O)[C@H](CSCc1cccc(c1)[N+]([O-])=O)NC(=O)C(O)=O
FormulaC12 H12 N2 O7 S
NameN-(carboxycarbonyl)-S-(3-nitrobenzyl)-L-cysteine
ChEMBLCHEMBL2030869
DrugBank
ZINCZINC000084653793
PDB chain3t4h Chain B Residue 217 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3t4h Dynamic combinatorial mass spectrometry leads to inhibitors of a 2-oxoglutarate-dependent nucleic Acid demethylase.
Resolution1.65 Å
Binding residue
(original residue number in PDB)		N120 Y122 L128 H131 S145 F154 W178 S182 H187 I189 R204 N206 T208 R210
Binding residue
(residue number reindexed from 1)		N107 Y109 L115 H118 S132 F141 W165 S169 H174 I176 R191 N193 T195 R197
Annotation score1
Binding affinityMOAD: ic50=5.2uM
PDBbind-CN: -logKd/Ki=5.28,IC50=5.2uM
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:3t4h, PDBe:3t4h, PDBj:3t4h
PDBsum3t4h
PubMed22263962
UniProtP05050|ALKB_ECOLI Alpha-ketoglutarate-dependent dioxygenase AlkB (Gene Name=alkB)

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