Ligand profile

DOI

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

Bound to: VK055_2887 — adenylosuccinate synthase

Via homolog PDB 2gcq UniProt P0A7D4 Formula C₁₀H₁₄N₄O₁₀P₂
Mol. weight 412.19 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
DOI
PDB
2gcq
UniProt (similar protein)
P0A7D4
Target protein
VK055_2887

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 412.19 Da
LogP (Crippen) -0.94
H-bond donors 5
H-bond acceptors 10
TPSA 206.58 Ų
Rotatable bonds 6
Aromatic rings 2 / 3
Heavy atoms 26
Fraction sp³ C 0.50
Formula C₁₀H₁₄N₄O₁₀P₂

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 206.6
  • −1 ≤ LogP ≤ 5 -0.94
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 412.2
  • LogP ≤ 5 -0.94
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 10
Veber's rules Fail
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 206.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1nc2c(c(n1)OP(=O)(O)O)ncn2[C@H]3C[C@@H]([C@H](O3)COP(=O)(O)O)O
InChI 
InChI=1S/C10H14N4O10P2/c15-5-1-7(23-6(5)2-22-25(16,17)18)14-4-13-8-9(14)11-3-12-10(8)24-26(19,20)21/h3-7,15H,1-2H2,(H2,16,17,18)(H2,19,20,21)/t5-,6+,7+/m0/s1
InChIKey 
GEECATYOCBMMIR-RRKCRQDMSA-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)