Ligand profile

GPX

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

Bound to: VK055_2887 — adenylosuccinate synthase

Via homolog PDB 1ch8 UniProt P0A7D4 Formula C₁₀H₁₄N₅O₁₃P₃
Mol. weight 505.17 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
GPX
PDB
1ch8
UniProt (similar protein)
P0A7D4
Target protein
VK055_2887

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 505.17 Da
LogP (Crippen) -1.29
H-bond donors 6
H-bond acceptors 13
TPSA 267.87 Ų
Rotatable bonds 6
Aromatic rings 2 / 4
Heavy atoms 31
Fraction sp³ C 0.50
Formula C₁₀H₁₄N₅O₁₃P₃

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 267.9
  • −1 ≤ LogP ≤ 5 -1.29
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 505.2
  • LogP ≤ 5 -1.29
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 13
Veber's rules Fail
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 267.9
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1nc2c(n1[C@H]3[C@H]4[C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O[P@@](=O)(O4)O)N=C(NC2=O)N
InChI 
InChI=1S/C10H14N5O13P3/c11-10-13-7-4(8(16)14-10)12-2-15(7)9-6-5(26-31(22,23)27-6)3(25-9)1-24-30(20,21)28-29(17,18)19/h2-3,5-6,9H,1H2,(H,20,21)(H,22,23)(H2,17,18,19)(H3,11,13,14,16)/t3-,5-,6-,9-/m1/s1
InChIKey 
NGYWTCOGOZELRS-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)