Ligand profile

5BX

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

Bound to: KP13_00709 — Tryptophanyl-tRNA synthetase

Via homolog PDB 5dk4 UniProt P00953 Formula C₁₄H₁₅N₃O₂
Mol. weight 257.29 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
5BX
PDB
5dk4
UniProt (similar protein)
P00953
Target protein
KP13_00709

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 257.29 Da
LogP (Crippen) 1.77
H-bond donors 2
H-bond acceptors 3
TPSA 66.48 Ų
Rotatable bonds 2
Aromatic rings 2 / 3
Heavy atoms 19
Fraction sp³ C 0.29
Formula C₁₄H₁₅N₃O₂

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 66.5
  • −1 ≤ LogP ≤ 5 1.77
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 257.3
  • LogP ≤ 5 1.77
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 3
Veber's rules Pass
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 66.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C[C@H](c1c[nH]c2c1cccc2)[C@H]3C(=O)N=C(O3)NC
InChI 
InChI=1S/C14H15N3O2/c1-8(12-13(18)17-14(15-2)19-12)10-7-16-11-6-4-3-5-9(10)11/h3-8,12,16H,1-2H3,(H,15,17,18)/t8-,12+/m1/s1
InChIKey 
GNTVWGDQPXCYBV-PELKAZGASA-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
PF00579

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_00709.

PDB 7

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

Ligand PDB entry

ZINC 50

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)