Ligand profile

PPK

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

Bound to: KP13_02726 — S-adenosylmethionine synthase

Via homolog PDB 1p7l UniProt P0A817 Formula H₆NO₉P₃
Mol. weight 256.97 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
PPK
PDB
1p7l
UniProt (similar protein)
P0A817
Target protein
KP13_02726

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 256.97 Da
LogP (Crippen) -1.12
H-bond donors 6
H-bond acceptors 4
TPSA 173.62 Ų
Rotatable bonds 4
Aromatic rings 0 / 0
Heavy atoms 13
Fraction sp³ C 0.00
Formula H₆NO₉P₃

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 173.6
  • −1 ≤ LogP ≤ 5 -1.12
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 257.0
  • LogP ≤ 5 -1.12
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 4
Veber's rules Fail
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 173.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
N(P(=O)(O)O)[P@](=O)(O)OP(=O)(O)O
InChI 
InChI=1S/H6NO9P3/c2-11(3,4)1-12(5,6)10-13(7,8)9/h(H2,7,8,9)(H4,1,2,3,4,5,6)
InChIKey 
PELPUMGXMYVGSQ-UHFFFAOYSA-N

Provenance

Annotation context from LigQ_2, the internal Target step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ sequence
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)