Ligand profile

S7M

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

Bound to: KP13_02726 — S-adenosylmethionine synthase

Via homolog PDB 5a1g UniProt P31153 Formula C₁₆H₂₅N₆O₅S⁺
Mol. weight 413.48 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
S7M
PDB
5a1g
UniProt (similar protein)
P31153
Target protein
KP13_02726

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 413.48 Da
LogP (Crippen) -1.53
H-bond donors 5
H-bond acceptors 10
TPSA 182.63 Ų
Rotatable bonds 8
Aromatic rings 2 / 3
Heavy atoms 28
Fraction sp³ C 0.62
Formula C₁₆H₂₅N₆O₅S⁺

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 182.6
  • −1 ≤ LogP ≤ 5 -1.53
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 413.5
  • LogP ≤ 5 -1.53
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 10
Veber's rules Fail
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 182.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC[S+](CC[C@@H](C(=O)O)N)C[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O
InChI 
InChI=1S/C16H24N6O5S/c1-2-28(4-3-8(17)16(25)26)5-9-11(23)12(24)15(27-9)22-7-21-10-13(18)19-6-20-14(10)22/h6-9,11-12,15,23-24H,2-5,17H2,1H3,(H2-,18,19,20,25,26)/p+1/t8-,9+,11+,12+,15+,28?/m0/s1
InChIKey 
UBQZUBPODLPCFG-PIBDHAAFSA-O

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
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 19

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

Ligand PDB entry

ChEMBL 100

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)