Ligand profile

3PO

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

Bound to: KP13_02726 — S-adenosylmethionine synthase

Via homolog PDB 5t8s UniProt Q5FAC0 Formula H₅O₁₀P₃
Mol. weight 257.95 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
3PO
PDB
5t8s
UniProt (similar protein)
Q5FAC0
Target protein
KP13_02726

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 257.95 Da
LogP (Crippen) -0.69
H-bond donors 5
H-bond acceptors 5
TPSA 170.82 Ų
Rotatable bonds 4
Aromatic rings 0 / 0
Heavy atoms 13
Fraction sp³ C 0.00
Formula H₅O₁₀P₃

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 170.8
  • −1 ≤ LogP ≤ 5 -0.69
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 258.0
  • LogP ≤ 5 -0.69
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 5
Veber's rules Fail
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 170.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
OP(=O)(O)OP(=O)(O)OP(=O)(O)O
InChI 
InChI=1S/H5O10P3/c1-11(2,3)9-13(7,8)10-12(4,5)6/h(H,7,8)(H2,1,2,3)(H2,4,5,6)
InChIKey 
UNXRWKVEANCORM-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
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)