Ligand profile

GNH

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

Bound to: VK055_2887 — adenylosuccinate synthase

Via homolog PDB 1hon UniProt P0A7D4 Formula C₁₀H₁₆N₆O₁₀P₂
Mol. weight 442.22 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
GNH
PDB
1hon
UniProt (similar protein)
P0A7D4
Target protein
VK055_2887

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 442.22 Da
LogP (Crippen) -2.49
H-bond donors 7
H-bond acceptors 12
TPSA 258.36 Ų
Rotatable bonds 6
Aromatic rings 2 / 3
Heavy atoms 28
Fraction sp³ C 0.50
Formula C₁₀H₁₆N₆O₁₀P₂

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 258.4
  • −1 ≤ LogP ≤ 5 -2.49
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 442.2
  • LogP ≤ 5 -2.49
  • H-bond donors ≤ 5 7
  • H-bond acceptors ≤ 10 12
Veber's rules Fail
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 258.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(N)O)O)O)N=C(NC2=O)N
InChI 
InChI=1S/C10H16N6O10P2/c11-10-14-7-4(8(19)15-10)13-2-16(7)9-6(18)5(17)3(25-9)1-24-28(22,23)26-27(12,20)21/h2-3,5-6,9,17-18H,1H2,(H,22,23)(H3,12,20,21)(H3,11,14,15,19)/t3-,5-,6-,9-/m1/s1
InChIKey 
ZGPDMUBRWRJAQQ-UUOKFMHZSA-N

Provenance

Annotation context from LigQ_2, the internal Target step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ sequence
Source
PDB
Binding sites
PF00709

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_2887.

PDB 14

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)