Ligand profile

9E0

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

Bound to: KP13_13547 — Tryptophanyl-tRNA synthetase

Via homolog PDB 7cms UniProt P00953 Formula C₁₂H₁₁NO₂S
Mol. weight 233.29 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
9E0
PDB
7cms
UniProt (similar protein)
P00953
Target protein
KP13_13547

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 233.29 Da
LogP (Crippen) 2.83
H-bond donors 2
H-bond acceptors 2
TPSA 53.09 Ų
Rotatable bonds 1
Aromatic rings 2 / 3
Heavy atoms 16
Fraction sp³ C 0.25
Formula C₁₂H₁₁NO₂S

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 53.1
  • −1 ≤ LogP ≤ 5 2.83
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 233.3
  • LogP ≤ 5 2.83
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 2
Veber's rules Pass
  • Rotatable bonds ≤ 10 1
  • TPSA ≤ 140 Ų 53.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C[C@H]1c2c[nH]c3c2c(ccc3)S[C@H]1C(=O)O
InChI 
InChI=1S/C12H11NO2S/c1-6-7-5-13-8-3-2-4-9(10(7)8)16-11(6)12(14)15/h2-6,11,13H,1H3,(H,14,15)/t6-,11+/m0/s1
InChIKey 
DKHFLDXCKWDVMF-UPONEAKYSA-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_13547.

PDB 6

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)