Ligand profile

1X9

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

Bound to: KP13_01032 — 3-oxoacyl-[acyl-carrier-protein] synthase 1

Via homolog PDB 4ls7 UniProt O34340 Formula C₁₂H₁₇NO₃
Mol. weight 223.27 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
1X9
PDB
4ls7
UniProt (similar protein)
O34340
Target protein
KP13_01032

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 223.27 Da
LogP (Crippen) 1.11
H-bond donors 1
H-bond acceptors 3
TPSA 72.69 Ų
Rotatable bonds 7
Aromatic rings 0 / 1
Heavy atoms 16
Fraction sp³ C 0.50
Formula C₁₂H₁₇NO₃

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 72.7
  • −1 ≤ LogP ≤ 5 1.11
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 223.3
  • LogP ≤ 5 1.11
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 3
Veber's rules Pass
  • Rotatable bonds ≤ 10 7
  • TPSA ≤ 140 Ų 72.7
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C/C=C/C/C=C/CCC(=O)[C@@H]1[C@@H](O1)C(=O)N
InChI 
InChI=1S/C12H17NO3/c1-2-3-4-5-6-7-8-9(14)10-11(16-10)12(13)15/h2-3,5-6,10-11H,4,7-8H2,1H3,(H2,13,15)/b3-2+,6-5+/t10-,11-/m1/s1
InChIKey 
GVEZIHKRYBHEFX-NQQPLRFYSA-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
PF00109' 'PF02801

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_01032.

PDB 16

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)