Ligand profile

VNY

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

Bound to: KP13_02224 — Protein fimH

Via homolog PDB 5aap UniProt Q1R2J4 Formula C₂₁H₂₄O₅
Mol. weight 356.42 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
VNY
PDB
5aap
UniProt (similar protein)
Q1R2J4
Target protein
KP13_02224

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 356.42 Da
LogP (Crippen) 1.60
H-bond donors 4
H-bond acceptors 5
TPSA 90.15 Ų
Rotatable bonds 4
Aromatic rings 2 / 3
Heavy atoms 26
Fraction sp³ C 0.33
Formula C₂₁H₂₄O₅

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 90.2
  • −1 ≤ LogP ≤ 5 1.60
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 356.4
  • LogP ≤ 5 1.60
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 90.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C/C(=C\[C@@H]1[C@H]([C@H]([C@@H]([C@H](O1)CO)O)O)O)/c2ccc(cc2)c3ccccc3
InChI 
InChI=1S/C21H24O5/c1-13(11-17-19(23)21(25)20(24)18(12-22)26-17)14-7-9-16(10-8-14)15-5-3-2-4-6-15/h2-11,17-25H,12H2,1H3/b13-11+/t17-,18-,19-,20-,21-/m1/s1
InChIKey 
CZOUTUOSDBYBBC-OBPXZMPXSA-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)