Ligand profile

PSE

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

Bound to: KP13_00940 — Inner membrane protein

Via homolog PDB 6vdf UniProt P40709 Formula C₃H₁₀NO₅P
Mol. weight 171.09 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
PSE
PDB
6vdf
UniProt (similar protein)
P40709
Target protein
KP13_00940

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 171.09 Da
LogP (Crippen) -1.58
H-bond donors 4
H-bond acceptors 4
TPSA 113.01 Ų
Rotatable bonds 4
Aromatic rings 0 / 0
Heavy atoms 10
Fraction sp³ C 1.00
Formula C₃H₁₀NO₅P

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 113.0
  • −1 ≤ LogP ≤ 5 -1.58
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 171.1
  • LogP ≤ 5 -1.58
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 113.0
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C([C@H](COP(=O)(O)O)N)O
InChI 
InChI=1S/C3H10NO5P/c4-3(1-5)2-9-10(6,7)8/h3,5H,1-2,4H2,(H2,6,7,8)/t3-/m1/s1
InChIKey 
WDWYJNPKBKWDBL-GSVOUGTGSA-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
PF00884

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_00940.

PDB 1

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

Ligand PDB entry

ZINC 50

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)