PDB Entry (1pot)

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Visualizer: MichelaNGLo

PDB ID: 1pot Resolution: 1.8 Å Exp. Method: X-RAY DIFFRACTION
PMID: 8897598 DOI: 10.1002/pro.5560051004
Protein
Protein Name: Spermidine/putrescine-binding periplasmic protein
Protein Class: TRANSPORTER
Uniprot ID/ACC: P0AFK9 (POTD_ECOLI) Organism: Escherichia coli
Gene Symbol: - Gene ID: 48725081
Pocket Descriptors
Volume: 615.616 Depth: 26.7313
Hydrophobicity: 0.721698 Drug Score: 0.306303
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 : 3200 nM, Kd : 3200 nM
Binding MOAD Kd : 3200 nM, Kd : 3200 nM