Structure of PDB 4b3d Chain A Binding Site BS01

Receptor Information
>4b3d Chain A (length=213) Species: 2261 (Pyrococcus furiosus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ATIGRISTGSKSLDKLLGGGIETQAITEVFGEFGSGKTQLAHTLAVMVQL
PPEEGGLNGSVMWIDTENTFRPERIREIAQNRGLDPDEVLKHIAYARAFN
SNHQMLLVQQAEDMIKELLNTDRPVKLLIVDSLTSHFRSEYIGRGALAER
QQKLAKHLADLHRLANLYDIAVFVTNQVATLRVYLRKGKGGKRIARLIDG
EAVFSITEKGIED
Ligand information
Ligand ID5MI
InChIInChI=1S/C9H9N/c1-7-2-3-9-8(6-7)4-5-10-9/h2-6,10H,1H3
InChIKeyYPKBCLZFIYBSHK-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.9.2Cc1ccc2c(c1)cc[nH]2
ACDLabs 12.01c1c(ccc2c1ccn2)C
CACTVS 3.385Cc1ccc2[nH]ccc2c1
FormulaC9 H9 N
Name5-METHYL INDOLE
ChEMBLCHEMBL112462
DrugBank
ZINCZINC000001605250
PDB chain4b3d Chain A Residue 1351 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4b3d Using a Fragment-Based Approach to Target Protein-Protein Interactions.
Resolution1.589 Å
Binding residue
(original residue number in PDB)		M169 I171 A203
Binding residue
(residue number reindexed from 1)		M62 I64 A96
Annotation score1
Binding affinityMOAD: Kd=2.1mM
PDBbind-CN: -logKd/Ki=2.68,Kd=2.1mM
BindingDB: Kd=2100000nM
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003677 DNA binding
GO:0003684 damaged DNA binding
GO:0005524 ATP binding
GO:0008094 ATP-dependent activity, acting on DNA
GO:0016887 ATP hydrolysis activity
GO:0140664 ATP-dependent DNA damage sensor activity
Biological Process
GO:0006259 DNA metabolic process
GO:0006281 DNA repair
GO:0006310 DNA recombination

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Molecular Function
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Biological Process
External links
PDB RCSB:4b3d, PDBe:4b3d, PDBj:4b3d
PDBsum4b3d
PubMed23344974
UniProtO74036|RADA_PYRFU DNA repair and recombination protein RadA (Gene Name=radA)

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