Ligand profile

GD3

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

Bound to: VK055_4026 — ADP-ribose pyrophosphatase

Via homolog PDB 1ga7 UniProt Q93K97 Formula Gd³⁺
Mol. weight 157.25 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
GD3
PDB
1ga7
UniProt (similar protein)
Q93K97
Target protein
VK055_4026

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 157.25 Da
LogP (Crippen) 0.00
H-bond donors 0
H-bond acceptors 0
TPSA 0.00 Ų
Rotatable bonds 0
Aromatic rings 0 / 0
Heavy atoms 1
Fraction sp³ C 0.00
Formula Gd³⁺

Drug-likeness

Descriptor-based ADME screening flags from SMILES. These are not experimental toxicity results.

Permeability proxy High

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 0.0
  • −1 ≤ LogP ≤ 5 0.00
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 157.2
  • LogP ≤ 5 0.00
  • H-bond donors ≤ 5 0
  • H-bond acceptors ≤ 10 0
Veber's rules Pass
  • Rotatable bonds ≤ 10 0
  • TPSA ≤ 140 Ų 0.0
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
[Gd+3]
InChI 
InChI=1S/Gd/q+3
InChIKey 
RJOJUSXNYCILHH-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
PF00293

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_4026.

PDB 6

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)