Ligand profile

164

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

Bound to: KP13_00976 — 2-succinyl-6-hydroxy-2, 4-cyclohexadiene-1-carboxylate synthase

Via homolog PDB 4myd UniProt P37355 Formula C₁₁H₁₂O₆
Mol. weight 240.21 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
164
PDB
4myd
UniProt (similar protein)
P37355
Target protein
KP13_00976

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 240.21 Da
LogP (Crippen) -0.02
H-bond donors 3
H-bond acceptors 4
TPSA 111.90 Ų
Rotatable bonds 5
Aromatic rings 0 / 1
Heavy atoms 17
Fraction sp³ C 0.36
Formula C₁₁H₁₂O₆

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 111.9
  • −1 ≤ LogP ≤ 5 -0.02
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 240.2
  • LogP ≤ 5 -0.02
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 111.9
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C1=C[C@H]([C@@H](C(=C1)C(=O)CCC(=O)O)C(=O)O)O
InChI 
InChI=1S/C11H12O6/c12-7(4-5-9(14)15)6-2-1-3-8(13)10(6)11(16)17/h1-3,8,10,13H,4-5H2,(H,14,15)(H,16,17)/t8-,10-/m1/s1
InChIKey 
QJYRAJSESKVEAE-PSASIEDQSA-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
PF12697

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_00976.

PDB 1

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

Ligand PDB entry

ChEMBL 100

Compounds with measured inhibitory activity on this target (higher pchembl = more potent).

Compound Potency (pchembl)

ZINC 50

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

Compound Similarity (Tanimoto)