Ligand profile

U4P

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

Bound to: KP13_02726 — S-adenosylmethionine synthase

Via homolog PDB 6wkb UniProt P31153 Formula C₉H₁₂N₂O₅
Mol. weight 228.20 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
U4P
PDB
6wkb
UniProt (similar protein)
P31153
Target protein
KP13_02726

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 228.20 Da
LogP (Crippen) -1.82
H-bond donors 3
H-bond acceptors 6
TPSA 104.55 Ų
Rotatable bonds 1
Aromatic rings 1 / 2
Heavy atoms 16
Fraction sp³ C 0.56
Formula C₉H₁₂N₂O₅

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 104.6
  • −1 ≤ LogP ≤ 5 -1.82
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 228.2
  • LogP ≤ 5 -1.82
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 1
  • TPSA ≤ 140 Ų 104.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C[C@@H]1[C@H]([C@H]([C@@H](O1)N2C=CC(=O)NC2=O)O)O
InChI 
InChI=1S/C9H12N2O5/c1-4-6(13)7(14)8(16-4)11-3-2-5(12)10-9(11)15/h2-4,6-8,13-14H,1H3,(H,10,12,15)/t4-,6-,7-,8-/m1/s1
InChIKey 
WUBAOANSQGKRHF-XVFCMESISA-N

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

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)