Ligand profile

VGN

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

Bound to: KP13_03859 — Dihydroorotate dehydrogenase

Via homolog PDB 2wv8 UniProt Q02127 Formula C₂₁H₁₇NO₃
Mol. weight 331.37 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
VGN
PDB
2wv8
UniProt (similar protein)
Q02127
Target protein
KP13_03859

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 331.37 Da
LogP (Crippen) 4.68
H-bond donors 2
H-bond acceptors 2
TPSA 66.40 Ų
Rotatable bonds 4
Aromatic rings 3 / 3
Heavy atoms 25
Fraction sp³ C 0.05
Formula C₂₁H₁₇NO₃

Drug-likeness

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

Permeability proxy High

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 66.4
  • −1 ≤ LogP ≤ 5 4.68
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 331.4
  • LogP ≤ 5 4.68
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 2
Veber's rules Pass
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 66.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC(=O)Nc1ccc(cc1C(=O)O)c2ccc(cc2)c3ccccc3
InChI 
InChI=1S/C21H17NO3/c1-14(23)22-20-12-11-18(13-19(20)21(24)25)17-9-7-16(8-10-17)15-5-3-2-4-6-15/h2-13H,1H3,(H,22,23)(H,24,25)
InChIKey 
XXPKIBVYLUEVCV-UHFFFAOYSA-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
PF01180

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_03859.

PDB 74

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)