Ligand profile

ATH

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

Bound to: KP13_05339 — Aconitate hydratase 1

Via homolog PDB 1fgh UniProt P20004 Formula C₆H₃O₇³⁻
Mol. weight 187.08 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ATH
PDB
1fgh
UniProt (similar protein)
P20004
Target protein
KP13_05339

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 187.08 Da
LogP (Crippen) -5.48
H-bond donors 1
H-bond acceptors 7
TPSA 140.62 Ų
Rotatable bonds 4
Aromatic rings 0 / 0
Heavy atoms 13
Fraction sp³ C 0.17
Formula C₆H₃O₇³⁻

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 140.6
  • −1 ≤ LogP ≤ 5 -5.48
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 187.1
  • LogP ≤ 5 -5.48
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 7
Veber's rules Fail
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 140.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C(=C(/[C@H](C(=O)[O-])O)\C(=O)[O-])/C(=O)[O-]
InChI 
InChI=1S/C6H6O7/c7-3(8)1-2(5(10)11)4(9)6(12)13/h1,4,9H,(H,7,8)(H,10,11)(H,12,13)/p-3/b2-1+/t4-/m1/s1
InChIKey 
WUUVSJBKHXDKBS-ROFOPDMZSA-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)