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PDB Entry (1pot) Download |
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Visualizer: MichelaNGLo |
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| PDB ID: 1pot | Resolution: 1.8 Å | Exp. Method: X-RAY DIFFRACTION |
| PMID: 8897598 | DOI: 10.1002/pro.5560051004 | |
Protein |
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| 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 |
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| 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 |
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| Database Name | Value |
| PDBBind | Kd : 3200 nM, Kd : 3200 nM |
| Binding MOAD | Kd : 3200 nM, Kd : 3200 nM |