Ligand profile

GPE

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

Bound to: VK055_4403 — cysN

Via homolog PDB 6ra9 UniProt Q71V39 Formula C₅H₁₄NO₆P
Mol. weight 215.14 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
GPE
PDB
6ra9
UniProt (similar protein)
Q71V39
Target protein
VK055_4403

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 215.14 Da
LogP (Crippen) -1.57
H-bond donors 4
H-bond acceptors 6
TPSA 122.24 Ų
Rotatable bonds 7
Aromatic rings 0 / 0
Heavy atoms 13
Fraction sp³ C 1.00
Formula C₅H₁₄NO₆P

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 122.2
  • −1 ≤ LogP ≤ 5 -1.57
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 215.1
  • LogP ≤ 5 -1.57
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 7
  • TPSA ≤ 140 Ų 122.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C(CO[P@](=O)(O)OC[C@@H](CO)O)N
InChI 
InChI=1S/C5H14NO6P/c6-1-2-11-13(9,10)12-4-5(8)3-7/h5,7-8H,1-4,6H2,(H,9,10)/t5-/m1/s1
InChIKey 
JZNWSCPGTDBMEW-RXMQYKEDSA-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
PF03144' 'PF22594

External resources

Open this ligand in third-party databases and cheminformatics tools.

Other ligands for this protein

Quick navigation to other ligands bound to VK055_4403.

PDB 3

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

Ligand PDB entry

ChEMBL 1

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)