Ligand profile

GZ3

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

Bound to: VK055_4577 — 3-deoxy-7-phosphoheptulonate synthase

Via homolog PDB 4uma UniProt Q9K169 Formula C₄H₇O₅P
Mol. weight 166.07 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
GZ3
PDB
4uma
UniProt (similar protein)
Q9K169
Target protein
VK055_4577

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 166.07 Da
LogP (Crippen) 0.15
H-bond donors 3
H-bond acceptors 2
TPSA 94.83 Ų
Rotatable bonds 2
Aromatic rings 0 / 0
Heavy atoms 10
Fraction sp³ C 0.25
Formula C₄H₇O₅P

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 94.8
  • −1 ≤ LogP ≤ 5 0.15
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 166.1
  • LogP ≤ 5 0.15
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 2
Veber's rules Pass
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 94.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C/C(=C\P(=O)(O)O)/C(=O)O
InChI 
InChI=1S/C4H7O5P/c1-3(4(5)6)2-10(7,8)9/h2H,1H3,(H,5,6)(H2,7,8,9)/b3-2+
InChIKey 
XGDAHZFVQMTYCT-NSCUHMNNSA-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
PF00793

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_4577.

PDB 7

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)