Binder profile

ZINC5158649

Virtual-screening candidate from ZINC.

Bound to: PA0206 — spermidine/putrescine ABC transporter ATP-binding protein

Via homolog UniProt Q9KIF7 C12H16N5O6P
Tanimoto 0.72
Mol. weight 357.26 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC5158649
UniProt (similar protein)
Q9KIF7
Tanimoto
0.721
Target protein
PA0206

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 357.26 Da
LogP (Crippen) 0.23
H-bond donors 2
H-bond acceptors 11
TPSA 143.84 Ų
Rotatable bonds 3
Aromatic rings 2 / 4
Heavy atoms 24
Fraction sp³ C 0.58
Formula C12H16N5O6P

Drug-likeness

Descriptor-based ADME screening flags from SMILES. These are not experimental toxicity results.

Permeability proxy Check

Estimated from TPSA and LogP only: TPSA ≤ 90 Ų and −1 ≤ LogP ≤ 5 are treated as a favorable small-molecule permeability screen.

Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 357.3
  • LogP ≤ 5 0.23
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 11
Veber's rules Fail
  • Rotatable bonds ≤ 10 3
  • TPSA ≤ 140 Ų 143.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCO[P@@]1(=O)OC[C@@H]2O[C@@H](n3cnc4c(N)ncnc43)[C@@H](O)[C@@H]2O1
InChI 
InChI=1S/C12H16N5O6P/c1-2-20-24(19)21-3-6-9(23-24)8(18)12(22-6)17-5-16-7-10(13)14-4-15-11(7)17/h4-6,8-9,12,18H,2-3H2,1H3,(H2,13,14,15)/t6-,8-,9+,12+,24-/m0/s1
InChIKey 
TXRXEHHGCBJORG-OSMNKBTPSA-N

Provenance

Annotation context from LigQ_2, the internal TPW step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ nearest_k
Query
2BA
Homolog
Q9KIF7

External resources

Open this ligand in third-party databases and cheminformatics tools.

Other binders for this protein

Quick navigation to other ligands bound to PA0206.

PDB 6

Ligands co-crystallized with this protein (structural evidence).

Ligand PDB entry

ZINC 49

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)