PDB Entry (4jdf)

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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