Ligand profile

3RY

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

Bound to: KP13_03859 — Dihydroorotate dehydrogenase

Via homolog PDB 4rka UniProt Q02127 Formula C₂₁H₁₆N₂O₃S
Mol. weight 376.44 Da
Permeability High
PAINS Alert

Identifiers

Database identifiers and provenance.

Ligand ID
3RY
PDB
4rka
UniProt (similar protein)
Q02127
Target protein
KP13_03859

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 376.44 Da
LogP (Crippen) 3.73
H-bond donors 3
H-bond acceptors 3
TPSA 78.76 Ų
Rotatable bonds 4
Aromatic rings 3 / 4
Heavy atoms 27
Fraction sp³ C 0.05
Formula C₂₁H₁₆N₂O₃S

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 78.8
  • −1 ≤ LogP ≤ 5 3.73
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 376.4
  • LogP ≤ 5 3.73
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 3
Veber's rules Pass
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 78.8
PAINS Alert

Matches PAINS filter: thio_ketone(43). May be a frequent false positive in HTS — review carefully.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1ccc2c(c1)cccc2CC3=SC(=NC3=O)Nc4ccccc4C(=O)O
InChI 
InChI=1S/C21H15N2O3S/c24-19-18(12-14-8-5-7-13-6-1-2-9-15(13)14)27-21(23-19)22-17-11-4-3-10-16(17)20(25)26/h1-11H,12H2,(H,25,26)(H,22,23,24)
InChIKey 
KGARUCYPKWKUTR-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)