Ligand profile

TRA

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

Bound to: KP13_05339 — Aconitate hydratase 1

Via homolog PDB 1aco UniProt P20004 Formula C₆H₃O₆³⁻
Mol. weight 171.08 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
TRA
PDB
1aco
UniProt (similar protein)
P20004
Target protein
KP13_05339

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 171.08 Da
LogP (Crippen) -4.45
H-bond donors 0
H-bond acceptors 6
TPSA 120.39 Ų
Rotatable bonds 4
Aromatic rings 0 / 0
Heavy atoms 12
Fraction sp³ C 0.17
Formula C₆H₃O₆³⁻

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 120.4
  • −1 ≤ LogP ≤ 5 -4.45
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 171.1
  • LogP ≤ 5 -4.45
  • H-bond donors ≤ 5 0
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 120.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C(/C(=C\C(=O)[O-])/C(=O)[O-])C(=O)[O-]
InChI 
InChI=1S/C6H6O6/c7-4(8)1-3(6(11)12)2-5(9)10/h1H,2H2,(H,7,8)(H,9,10)(H,11,12)/p-3/b3-1+
InChIKey 
GTZCVFVGUGFEME-HNQUOIGGSA-K

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
PF00330' 'PF00694

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_05339.

PDB 10

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

Ligand PDB entry

ZINC 14

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

Compound Similarity (Tanimoto)