Ligand profile

PGS

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

Bound to: VK055_2887 — adenylosuccinate synthase

Via homolog PDB 1ksz UniProt P0A7D4 Formula C₁₀H₁₅N₄O₁₀P₂S⁺
Mol. weight 445.26 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
PGS
PDB
1ksz
UniProt (similar protein)
P0A7D4
Target protein
VK055_2887

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 445.26 Da
LogP (Crippen) -1.84
H-bond donors 6
H-bond acceptors 10
TPSA 218.83 Ų
Rotatable bonds 6
Aromatic rings 2 / 3
Heavy atoms 27
Fraction sp³ C 0.50
Formula C₁₀H₁₅N₄O₁₀P₂S⁺

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 218.8
  • −1 ≤ LogP ≤ 5 -1.84
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 445.3
  • LogP ≤ 5 -1.84
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 10
Veber's rules Fail
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 218.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1[nH+]c(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)O)SP(=O)(O)O
InChI 
InChI=1S/C10H14N4O10P2S/c15-6-4(1-23-25(17,18)19)24-10(7(6)16)14-3-13-5-8(14)11-2-12-9(5)27-26(20,21)22/h2-4,6-7,10,15-16H,1H2,(H2,17,18,19)(H2,20,21,22)/p+1/t4-,6-,7-,10-/m1/s1
InChIKey 
NYBPOGVUIOPXHI-KQYNXXCUSA-O

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)