Structure of PDB 5yj8 Chain A Binding Site BS01

Receptor Information
>5yj8 Chain A (length=60) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
HHHHHMMWKPGDECFALYWEDNKFYRAEVEALHSSGMTAVVKFIDYGNYE
EVLLSNIKPI
Ligand information
Ligand ID8W9
InChIInChI=1S/C10H13N3O/c1-12-8-4-3-7(6-11)5-9(8)13(2)10(12)14/h3-5H,6,11H2,1-2H3
InChIKeyGDVGETHSXBLPHM-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6CN1c2ccc(cc2N(C1=O)C)CN
CACTVS 3.385CN1C(=O)N(C)c2cc(CN)ccc12
FormulaC10 H13 N3 O
Name5-(aminomethyl)-1,3-dimethyl-benzimidazol-2-one
ChEMBL
DrugBank
ZINCZINC000000215305
PDB chain5yj8 Chain A Residue 701 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB5yj8 Structural plasticity of the TDRD3 Tudor domain probed by a fragment screening hit.
Resolution1.762 Å
Binding residue
(original residue number in PDB)		Y566 Y573 F591 Y594 N596
Binding residue
(residue number reindexed from 1)		Y18 Y25 F43 Y46 N48
Annotation score1
Binding affinityMOAD: Kd=0.104mM
PDBbind-CN: -logKd/Ki=3.98,Kd=0.104mM
Enzymatic activity
Enzyme Commision number ?
External links
PDB RCSB:5yj8, PDBe:5yj8, PDBj:5yj8
PDBsum5yj8
PubMed29645362
UniProtQ9H7E2|TDRD3_HUMAN Tudor domain-containing protein 3 (Gene Name=TDRD3)

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