Ligand profile

MDY

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

Bound to: VK055_1513 — dihydroorotate dehydrogenase

Via homolog PDB 3g0u UniProt Q02127 Formula C₁₈H₁₅ClN₂O₃
Mol. weight 342.78 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
MDY
PDB
3g0u
UniProt (similar protein)
Q02127
Target protein
VK055_1513

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 342.78 Da
LogP (Crippen) 4.31
H-bond donors 2
H-bond acceptors 4
TPSA 82.35 Ų
Rotatable bonds 4
Aromatic rings 2 / 2
Heavy atoms 24
Fraction sp³ C 0.11
Formula C₁₈H₁₅ClN₂O₃

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 82.4
  • −1 ≤ LogP ≤ 5 4.31
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 342.8
  • LogP ≤ 5 4.31
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 82.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC(=C(C#N)C(=O)Nc1ccc(cc1Cl)c2ccccc2OC)O
InChI 
InChI=1S/C18H15ClN2O3/c1-11(22)14(10-20)18(23)21-16-8-7-12(9-15(16)19)13-5-3-4-6-17(13)24-2/h3-9,22H,1-2H3,(H,21,23)
InChIKey 
YUDQXOMZBLEWBH-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 VK055_1513.

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)