Structure of PDB 4rfr Chain B Binding Site BS01

Receptor Information
>4rfr Chain B (length=201) Species: 562 (Escherichia coli) [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 IDRHN
InChIInChI=1S/C15H8O6/c16-9-3-1-2-7-11(9)14(19)12-8(13(7)18)4-6(15(20)21)5-10(12)17/h1-5,16-17H,(H,20,21)
InChIKeyFCDLCPWAQCPTKC-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=C(O)c3cc2C(=O)c1cccc(O)c1C(=O)c2c(O)c3
CACTVS 3.370OC(=O)c1cc(O)c2C(=O)c3c(O)cccc3C(=O)c2c1
OpenEye OEToolkits 1.7.0c1cc2c(c(c1)O)C(=O)c3c(cc(cc3O)C(=O)O)C2=O
FormulaC15 H8 O6
Name4,5-dihydroxy-9,10-dioxo-9,10-dihydroanthracene-2-carboxylic acid;
Rhein;
Rhubarb Yellow
ChEMBLCHEMBL418068
DrugBankDB13174
ZINCZINC000004098704
PDB chain4rfr Chain B Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4rfr Rhein Inhibits AlkB Repair Enzymes and Sensitizes Cells to Methylated DNA Damage.
Resolution1.5 Å
Binding residue
(original residue number in PDB)		N120 Y122 L128 D133 I143 S145 F154 W178 H187 I189 R204 N206 T208
Binding residue
(residue number reindexed from 1)		N107 Y109 L115 D120 I130 S132 F141 W165 H174 I176 R191 N193 T195
Annotation score1
Binding affinityMOAD: Kd=0.29uM
PDBbind-CN: -logKd/Ki=6.54,Kd=0.29uM
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:4rfr, PDBe:4rfr, PDBj:4rfr
PDBsum4rfr
PubMed27015802
UniProtP05050|ALKB_ECOLI Alpha-ketoglutarate-dependent dioxygenase AlkB (Gene Name=alkB)

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