Ligand profile

0JR

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

Bound to: KP13_03141 — Uridine kinase

Via homolog PDB 4gi7 UniProt B5XYG3 Formula C₁₅H₂₃N₃O₄
Mol. weight 309.37 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
0JR
PDB
4gi7
UniProt (similar protein)
B5XYG3
Target protein
KP13_03141

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 309.37 Da
LogP (Crippen) -0.42
H-bond donors 4
H-bond acceptors 5
TPSA 111.55 Ų
Rotatable bonds 8
Aromatic rings 1 / 1
Heavy atoms 22
Fraction sp³ C 0.53
Formula C₁₅H₂₃N₃O₄

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 111.6
  • −1 ≤ LogP ≤ 5 -0.42
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 309.4
  • LogP ≤ 5 -0.42
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 111.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC(C)(CO)[C@H](C(=O)NCCC(=O)NCc1cccnc1)O
InChI 
InChI=1S/C15H23N3O4/c1-15(2,10-19)13(21)14(22)17-7-5-12(20)18-9-11-4-3-6-16-8-11/h3-4,6,8,13,19,21H,5,7,9-10H2,1-2H3,(H,17,22)(H,18,20)/t13-/m0/s1
InChIKey 
VXNNKPMWKMAMDX-ZDUSSCGKSA-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
PF00485

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_03141.

PDB 11

Ligands co-crystallized with this protein (structural evidence).

Ligand PDB entry

ChEMBL 2

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)