Ligand profile

ZINC31539924

Virtual-screening candidate from ZINC.

Bound to: KP13_13547 — Tryptophanyl-tRNA synthetase

Via homolog UniProt P00953 Formula C₁₉H₂₃N₆O₈P
Tanimoto 0.75
Mol. weight 494.40 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC31539924
UniProt (similar protein)
P00953
Tanimoto
0.747
Target protein
KP13_13547

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 494.40 Da
LogP (Crippen) -0.74
H-bond donors 5
H-bond acceptors 13
TPSA 218.16 Ų
Rotatable bonds 8
Aromatic rings 3 / 4
Heavy atoms 34
Fraction sp³ C 0.37
Formula C₁₉H₂₃N₆O₈P

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 218.2
  • −1 ≤ LogP ≤ 5 -0.74
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 494.4
  • LogP ≤ 5 -0.74
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 13
Veber's rules Fail
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 218.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@@](=O)(O)OC(=O)[C@@H](N)Cc2ccccc2)[C@@H](O)[C@H]1O
InChI 
InChI=1S/C19H23N6O8P/c20-11(6-10-4-2-1-3-5-10)19(28)33-34(29,30)31-7-12-14(26)15(27)18(32-12)25-9-24-13-16(21)22-8-23-17(13)25/h1-5,8-9,11-12,14-15,18,26-27H,6-7,20H2,(H,29,30)(H2,21,22,23)/t11-,12+,14+,15+,18+/m0/s1
InChIKey 
ZFNOOEXYTZPIQS-URQYDQELSA-N

Provenance

Annotation context from LigQ_2, the internal Target step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ nearest_k
Query
TYM
Homolog
P00953

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_13547.

PDB 7

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

Ligand PDB entry

ZINC 49

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

Compound Similarity (Tanimoto)