Ligand profile

3XO

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

Bound to: KP13_02224 — Protein fimH

Via homolog PDB 4x5r UniProt P08191 Formula C₂₁H₂₆ClN₃O₈
Mol. weight 483.91 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
3XO
PDB
4x5r
UniProt (similar protein)
P08191
Target protein
KP13_02224

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 483.91 Da
LogP (Crippen) -1.39
H-bond donors 5
H-bond acceptors 11
TPSA 152.03 Ų
Rotatable bonds 6
Aromatic rings 2 / 4
Heavy atoms 33
Fraction sp³ C 0.52
Formula C₂₁H₂₆ClN₃O₈

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 152.0
  • −1 ≤ LogP ≤ 5 -1.39
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 483.9
  • LogP ≤ 5 -1.39
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 11
Veber's rules Fail
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 152.0
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CN1CCN(CC1)C2=C(C(=O)C2=O)Nc3ccc(c(c3)Cl)O[C@@H]4[C@H]([C@H]([C@@H]([C@H](O4)CO)O)O)O
InChI 
InChI=1S/C21H26ClN3O8/c1-24-4-6-25(7-5-24)15-14(17(28)18(15)29)23-10-2-3-12(11(22)8-10)32-21-20(31)19(30)16(27)13(9-26)33-21/h2-3,8,13,16,19-21,23,26-27,30-31H,4-7,9H2,1H3/t13-,16-,19+,20+,21+/m1/s1
InChIKey 
OVFSRWMGARZIAS-YVNBQAQUSA-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)