Ligand profile

LJS

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

Bound to: VK055_2570 — threonine synthase

Via homolog PDB 6nmx UniProt A8HUA2 Formula C₁₃H₁₈N₂O₁₀P₂
Mol. weight 424.24 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
LJS
PDB
6nmx
UniProt (similar protein)
A8HUA2
Target protein
VK055_2570

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 424.24 Da
LogP (Crippen) 0.52
H-bond donors 7
H-bond acceptors 7
TPSA 206.21 Ų
Rotatable bonds 8
Aromatic rings 0 / 1
Heavy atoms 27
Fraction sp³ C 0.23
Formula C₁₃H₁₈N₂O₁₀P₂

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 206.2
  • −1 ≤ LogP ≤ 5 0.52
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 424.2
  • LogP ≤ 5 0.52
  • H-bond donors ≤ 5 7
  • H-bond acceptors ≤ 10 7
Veber's rules Fail
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 206.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC1=C(/C(=C\N=C(/C=C\CP(=O)(O)O)\C(=O)O)/C(=CN1)COP(=O)(O)O)O
InChI 
InChI=1S/C13H18N2O10P2/c1-8-12(16)10(9(5-14-8)7-25-27(22,23)24)6-15-11(13(17)18)3-2-4-26(19,20)21/h2-3,5-6,14,16H,4,7H2,1H3,(H,17,18)(H2,19,20,21)(H2,22,23,24)/b3-2-,10-6-,15-11+
InChIKey 
XGSUDZJIHIXLDE-NTUDHWJFSA-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
PF00291

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_2570.

PDB 4

Ligands co-crystallized with this protein (structural evidence).

Ligand PDB entry

ZINC 20

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)