PDB Entry (5yj8)

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Visualizer: MichelaNGLo

PDB ID: 5yj8 Resolution: 1.76 Å Exp. Method: X-RAY DIFFRACTION
PMID: 29645362 DOI: 10.1111/febs.14469
Protein
Protein Name: Tudor domain-containing protein 3
Protein Class: TRANSCRIPTION REGULATOR
Uniprot ID/ACC: Q9H7E2 (TDRD3_HUMAN) Organism: Homo sapiens
Gene Symbol: TDRD3 Gene ID: 81550
Pocket Descriptors
Volume: 127.232 Depth: 10.1587
Hydrophobicity: 0.765957 Drug Score: 0.0472642
Pocket Similarity: Calculate
Ligand
Ligand Name:   5-(aminomethyl)-1,3-dimethyl-benzimidazol-2-one
HET ID:   8W9 PubChem:   757168
DrugBank:   - ChEMBL:   -
Canonical SMILES:   NCc1ccc2c(c1)n(C)c(=O)n2C
Standard InChI:   InChI=1S/C10H13N3O/c1-12-8-4-3-7(6-11)5-9(8)13(2)10(12)14/h3-5H,6,11H2,1-2H3
Molecular Formula:   C10H13N3O Mol. Weight:   191.22972 Heavy Atoms:   14
Charge:   0 Is Chiral:   False logP:   1.036
HBD:   1 HBA:   4 TPSA:   52.95
#Bonds:   15 #Rotatable Bonds:   1 Shape Complexity:   0.3
Stereocomplexity:   0.0 Ligand Type:   Small Molecule
Binding Affinity
Database Name Value
Binding MOAD Kd : 104000 nM