Ligand profile

KEM

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

Bound to: KP13_04610 — 2-hydroxy-6-oxononadienedioate/2-hydroxy-6- oxononatrienedioate hydrolase

Via homolog PDB 2wuf UniProt P9WNH5 Formula C₁₉H₂₅O₆⁻
Mol. weight 349.40 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
KEM
PDB
2wuf
UniProt (similar protein)
P9WNH5
Target protein
KP13_04610

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 349.40 Da
LogP (Crippen) 0.60
H-bond donors 1
H-bond acceptors 6
TPSA 111.57 Ų
Rotatable bonds 7
Aromatic rings 0 / 2
Heavy atoms 25
Fraction sp³ C 0.68
Formula C₁₉H₂₅O₆⁻

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 111.6
  • −1 ≤ LogP ≤ 5 0.60
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 349.4
  • LogP ≤ 5 0.60
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 7
  • TPSA ≤ 140 Ų 111.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C[C@H](\C=C\C(=O)C(=O)[O-])C(=O)CC[C@@H]1[C@H]2CC[C@@H]([C@]2(CCC1=O)C)O
InChI 
InChI=1S/C19H26O6/c1-11(3-6-16(22)18(24)25)14(20)7-4-12-13-5-8-17(23)19(13,2)10-9-15(12)21/h3,6,11-13,17,23H,4-5,7-10H2,1-2H3,(H,24,25)/p-1/b6-3+/t11-,12-,13-,17+,19+/m1/s1
InChIKey 
PAPYZGVUTPWUFW-WDRCEGBMSA-M

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
PF00561

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_04610.

PDB 22

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)