Ligand profile

GA2

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

Bound to: VK055_2591 — purine nucleoside phosphorylase

Via homolog PDB 4da6 UniProt O34925 Formula C₉H₁₃N₅O₄
Mol. weight 255.23 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
GA2
PDB
4da6
UniProt (similar protein)
O34925
Target protein
VK055_2591

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 255.23 Da
LogP (Crippen) -1.97
H-bond donors 4
H-bond acceptors 8
TPSA 139.28 Ų
Rotatable bonds 5
Aromatic rings 2 / 2
Heavy atoms 18
Fraction sp³ C 0.44
Formula C₉H₁₃N₅O₄

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 139.3
  • −1 ≤ LogP ≤ 5 -1.97
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 255.2
  • LogP ≤ 5 -1.97
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 8
Veber's rules Pass
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 139.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1nc2c(n1COC(CO)CO)N=C(NC2=O)N
InChI 
InChI=1S/C9H13N5O4/c10-9-12-7-6(8(17)13-9)11-3-14(7)4-18-5(1-15)2-16/h3,5,15-16H,1-2,4H2,(H3,10,12,13,17)
InChIKey 
IRSCQMHQWWYFCW-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
PF01048

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_2591.

PDB 25

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)