Ligand profile

CHEMBL3706401

Bioactivity hit from ChEMBL on a similar protein.

Bound to: KP13_02726 — S-adenosylmethionine synthase

Via homolog UniProt P13444 Formula C₁₉H₃₃N₆O₁₄P₃S₂
pchembl 6.96 ~109.6 nM
Mol. weight 726.56 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
CHEMBL3706401
UniProt (similar protein)
P13444
pchembl
6.960 (~109.6 nM)
Target protein
KP13_02726

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 726.56 Da
LogP (Crippen) 0.16
H-bond donors 9
H-bond acceptors 16
TPSA 319.23 Ų
Rotatable bonds 18
Aromatic rings 2 / 3
Heavy atoms 44
Fraction sp³ C 0.68
Formula C₁₉H₃₃N₆O₁₄P₃S₂

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 319.2
  • −1 ≤ LogP ≤ 5 0.16
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 726.6
  • LogP ≤ 5 0.16
  • H-bond donors ≤ 5 9
  • H-bond acceptors ≤ 10 16
Veber's rules Fail
  • Rotatable bonds ≤ 10 18
  • TPSA ≤ 140 Ų 319.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCCCSc1ncnc2c1ncn2[C@@H]1O[C@H]([C@H](CSCC[C@H](N)C(=O)O)OP(=O)(O)OP(=O)(O)NP(=O)(O)O)[C@@H](O)[C@H]1O
InChI 
InChI=1S/C19H33N6O14P3S2/c1-2-3-5-44-17-12-16(21-8-22-17)25(9-23-12)18-14(27)13(26)15(37-18)11(7-43-6-4-10(20)19(28)29)38-42(35,36)39-41(33,34)24-40(30,31)32/h8-11,13-15,18,26-27H,2-7,20H2,1H3,(H,28,29)(H,35,36)(H4,24,30,31,32,33,34)/t10-,11-,13-,14+,15+,18+/m0/s1
InChIKey 
JSGYFHBIHPBINR-REWAFKANSA-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)