Ligand profile

6JX

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

Bound to: KP13_02055 — Queuine tRNA-ribosyltransferase

Via homolog PDB 5jgo UniProt P28720 Formula C₁₄H₁₄N₆O₃
Mol. weight 314.31 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
6JX
PDB
5jgo
UniProt (similar protein)
P28720
Target protein
KP13_02055

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 314.31 Da
LogP (Crippen) 1.58
H-bond donors 4
H-bond acceptors 6
TPSA 124.79 Ų
Rotatable bonds 4
Aromatic rings 3 / 3
Heavy atoms 23
Fraction sp³ C 0.14
Formula C₁₄H₁₄N₆O₃

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 124.8
  • −1 ≤ LogP ≤ 5 1.58
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 314.3
  • LogP ≤ 5 1.58
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 124.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CNc1[nH]c2cc3c(cc2n1)C(=O)NC(=N3)NC(=O)OCC=C
InChI 
InChI=1S/C14H14N6O3/c1-3-4-23-14(22)20-13-16-8-6-10-9(17-12(15-2)18-10)5-7(8)11(21)19-13/h3,5-6H,1,4H2,2H3,(H2,15,17,18)(H2,16,19,20,21,22)
InChIKey 
SKMZNGUSNLOOPQ-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
PF01702

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_02055.

PDB 60

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

Ligand PDB entry

ChEMBL 5

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)