Ligand profile

GPF

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

Bound to: VK055_1548 — 3-phosphoshikimate 1-carboxyvinyltransferase

Via homolog PDB 3fjz UniProt P0A6D3 Formula C₃H₈NO₅P
Mol. weight 169.07 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
GPF
PDB
3fjz
UniProt (similar protein)
P0A6D3
Target protein
VK055_1548

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 169.07 Da
LogP (Crippen) -1.20
H-bond donors 4
H-bond acceptors 3
TPSA 106.86 Ų
Rotatable bonds 4
Aromatic rings 0 / 0
Heavy atoms 10
Fraction sp³ C 0.67
Formula C₃H₈NO₅P

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 106.9
  • −1 ≤ LogP ≤ 5 -1.20
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 169.1
  • LogP ≤ 5 -1.20
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 3
Veber's rules Pass
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 106.9
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C(C(=O)O)NCP(=O)(O)O
InChI 
InChI=1S/C3H8NO5P/c5-3(6)1-4-2-10(7,8)9/h4H,1-2H2,(H,5,6)(H2,7,8,9)
InChIKey 
XDDAORKBJWWYJS-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
PF00275

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_1548.

PDB 9

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

Ligand PDB entry

ChEMBL 14

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)