Ligand profile

CHEMBL4870597

Bioactivity hit from ChEMBL on a similar protein.

Bound to: KP13_02726 — S-adenosylmethionine synthase

Via homolog UniProt P31153 Formula C₂₅H₂₄N₄O₃
pchembl 8.10 ~7.9 nM
Mol. weight 428.49 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
CHEMBL4870597
UniProt (similar protein)
P31153
pchembl
8.100 (~7.9 nM)
Target protein
KP13_02726

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 428.49 Da
LogP (Crippen) 4.38
H-bond donors 1
H-bond acceptors 6
TPSA 71.86 Ų
Rotatable bonds 3
Aromatic rings 4 / 6
Heavy atoms 32
Fraction sp³ C 0.28
Formula C₂₅H₂₄N₄O₃

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 71.9
  • −1 ≤ LogP ≤ 5 4.38
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 428.5
  • LogP ≤ 5 4.38
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 3
  • TPSA ≤ 140 Ų 71.9
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1[nH]c2c(N3CCCCC3)c(-c3ccccc3)nn2c(=O)c1-c1ccc2c(c1)OCO2
InChI 
InChI=1S/C25H24N4O3/c1-16-21(18-10-11-19-20(14-18)32-15-31-19)25(30)29-24(26-16)23(28-12-6-3-7-13-28)22(27-29)17-8-4-2-5-9-17/h2,4-5,8-11,14,26H,3,6-7,12-13,15H2,1H3
InChIKey 
NURMTFFWMUILBS-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)