Ligand profile

HE1

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

Bound to: VK055_1196 — tryptophan synthase, beta subunit

Via homolog PDB 1c29 UniProt P0A2K1 Formula C₁₀H₁₃O₄PS
Mol. weight 260.25 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
HE1
PDB
1c29
UniProt (similar protein)
P0A2K1
Target protein
VK055_1196

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 260.25 Da
LogP (Crippen) 2.57
H-bond donors 3
H-bond acceptors 3
TPSA 77.76 Ų
Rotatable bonds 5
Aromatic rings 1 / 1
Heavy atoms 16
Fraction sp³ C 0.20
Formula C₁₀H₁₃O₄PS

Drug-likeness

Descriptor-based ADME screening flags from SMILES. These are not experimental toxicity results.

Permeability proxy High

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 77.8
  • −1 ≤ LogP ≤ 5 2.57
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 260.3
  • LogP ≤ 5 2.57
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 3
Veber's rules Pass
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 77.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1ccc(c(c1)O)SCC\C=C\P(=O)(O)O
InChI 
InChI=1S/C10H13O4PS/c11-9-5-1-2-6-10(9)16-8-4-3-7-15(12,13)14/h1-3,5-7,11H,4,8H2,(H2,12,13,14)/b7-3+
InChIKey 
GHNIEXOPSISMGX-XVNBXDOJSA-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
PF00290

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_1196.

PDB 40

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)