PDB Entry (5yj8) Download |
||
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 |