PDB Entry (4jdf) Download |
||
Visualizer: MichelaNGLo |
||
PDB ID: 4jdf | Resolution: 1.69 Å | Exp. Method: X-RAY DIFFRACTION |
PMID: 23792166 | DOI: 10.1016/j.jsb.2013.06.002 | |
Protein |
|
Protein Name: Putrescine-binding periplasmic protein | |
Protein Class: TRANSPORTER | |
Uniprot ID/ACC: P31133 (POTF_ECOLI) | Organism: Escherichia coli |
Gene Symbol: - | Gene ID: 48136163 |
Pocket Descriptors | |
Volume: 979.776 | Depth: 29.5676 |
Hydrophobicity: 0.714286 | Drug Score: 0.666917 |
Pocket Similarity: Calculate |
Ligand |
||
Ligand Name: SPERMIDINE | ||
HET ID: SPD | PubChem: 1102 | |
DrugBank: DB03566 | ChEMBL: CHEMBL19612 | |
Canonical SMILES: NCCCNCCCCN | ||
Standard InChI: InChI=1S/C7H19N3/c8-4-1-2-6-10-7-3-5-9/h10H,1-9H2 | ||
Molecular Formula: C7H19N3 | Mol. Weight: 145.24586 | Heavy Atoms: 10 |
Charge: 0 | Is Chiral: False | logP: 1.4552 |
HBD: 3 | HBA: 3 | TPSA: 64.07 |
#Bonds: 9 | #Rotatable Bonds: 7 | Shape Complexity: 1.0 |
Stereocomplexity: 0.0 | Ligand Type: Small Molecule |
Binding Affinity |
|
Database Name | Value |
PDBBind | Kd : 6400000 nM |
Binding MOAD | Kd : 6400000 nM |