Ligand profile

3XN

Ligand co-crystallized with a similar protein (Protein Data Bank).

Bound to: KP13_02224 — Protein fimH

Via homolog PDB 4x5q UniProt P08191 Formula C₂₀H₂₀N₂O₈
Mol. weight 416.39 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
3XN
PDB
4x5q
UniProt (similar protein)
P08191
Target protein
KP13_02224

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 416.39 Da
LogP (Crippen) 0.72
H-bond donors 4
H-bond acceptors 9
TPSA 147.45 Ų
Rotatable bonds 5
Aromatic rings 3 / 4
Heavy atoms 30
Fraction sp³ C 0.30
Formula C₂₀H₂₀N₂O₈

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.

  • TPSA ≤ 90 Ų 147.5
  • −1 ≤ LogP ≤ 5 0.72
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 416.4
  • LogP ≤ 5 0.72
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 9
Veber's rules Fail
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 147.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1cc(ccc1n2ccc3c2ccc(c3)[N+](=O)[O-])O[C@@H]4[C@H]([C@H]([C@@H]([C@H](O4)CO)O)O)O
InChI 
InChI=1S/C20H20N2O8/c23-10-16-17(24)18(25)19(26)20(30-16)29-14-4-1-12(2-5-14)21-8-7-11-9-13(22(27)28)3-6-15(11)21/h1-9,16-20,23-26H,10H2/t16-,17-,18+,19+,20+/m1/s1
InChIKey 
CPRVANUZGRDTIH-SLHNCBLASA-N

Provenance

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

Method
LigQ nearest_k
Source
PDB
Binding sites
PF09160

External resources

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

Other ligands for this protein

Quick navigation to other ligands bound to KP13_02224.

PDB 24

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

Ligand PDB entry

ChEMBL 100

Compounds with measured inhibitory activity on this target (higher pchembl = more potent).

Compound Potency (pchembl)

ZINC 50

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

Compound Similarity (Tanimoto)