Ligand profile

840

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

Bound to: KP13_31484 — 3-oxoacyl-[acyl-carrier-protein] synthase 2

Via homolog PDB 3i8p UniProt P0AAI5 Formula C₂₄H₂₅NO₈
Mol. weight 455.46 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
840
PDB
3i8p
UniProt (similar protein)
P0AAI5
Target protein
KP13_31484

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 455.46 Da
LogP (Crippen) 1.96
H-bond donors 5
H-bond acceptors 7
TPSA 153.39 Ų
Rotatable bonds 5
Aromatic rings 1 / 6
Heavy atoms 33
Fraction sp³ C 0.54
Formula C₂₄H₂₅NO₈

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 153.4
  • −1 ≤ LogP ≤ 5 1.96
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 455.5
  • LogP ≤ 5 1.96
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 7
Veber's rules Fail
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 153.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C[C@@]1([C@H]2[C@@]34C[C@]35CC2(C=CC1=O)[C@H]([C@@]5(O4)C)O)CCC(=O)Nc6c(ccc(c6O)C(=O)O)O
InChI 
InChI=1S/C24H25NO8/c1-20(7-6-14(28)25-15-12(26)4-3-11(16(15)29)17(30)31)13(27)5-8-22-9-23-10-24(23,18(20)22)33-21(23,2)19(22)32/h3-5,8,18-19,26,29,32H,6-7,9-10H2,1-2H3,(H,25,28)(H,30,31)/t18-,19+,20-,21+,22?,23+,24+/m1/s1
InChIKey 
TUHIUIGYYSZKCN-KTLHRPDZSA-N

Provenance

Annotation context from LigQ_2, the internal Target step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ sequence
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_31484.

PDB 12

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

Ligand PDB entry

ChEMBL 15

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)