Ligand profile

CHEMBL4578643

Bioactivity hit from ChEMBL on a similar protein.

Bound to: KP13_02726 — S-adenosylmethionine synthase

Via homolog UniProt P31153 Formula C₂₅H₂₃N₃O₂
pchembl 7.00 ~100.0 nM
Mol. weight 397.48 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
CHEMBL4578643
UniProt (similar protein)
P31153
pchembl
7.000 (~100.0 nM)
Target protein
KP13_02726

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 397.48 Da
LogP (Crippen) 4.59
H-bond donors 2
H-bond acceptors 4
TPSA 70.39 Ų
Rotatable bonds 3
Aromatic rings 4 / 5
Heavy atoms 30
Fraction sp³ C 0.20
Formula C₂₅H₂₃N₃O₂

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 70.4
  • −1 ≤ LogP ≤ 5 4.59
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 397.5
  • LogP ≤ 5 4.59
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 3
  • TPSA ≤ 140 Ų 70.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1[nH]c2c(-c3ccccc3)c(-c3ccccc3)nn2c(=O)c1C1=CCC(O)CC1
InChI 
InChI=1S/C25H23N3O2/c1-16-21(18-12-14-20(29)15-13-18)25(30)28-24(26-16)22(17-8-4-2-5-9-17)23(27-28)19-10-6-3-7-11-19/h2-12,20,26,29H,13-15H2,1H3
InChIKey 
RSGUSLDUYFPARF-UHFFFAOYSA-N

Provenance

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

Method
LigQ nearest_k
Source
ChEMBL
Curation
pdb_similarity_tanimoto
Binding sites
PF00438' 'PF02772' 'PF02773

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_02726.

PDB 20

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

Ligand PDB entry

ChEMBL 99

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)