Ligand profile

HDJ

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

Bound to: VK055_1196 — tryptophan synthase, beta subunit

Via homolog PDB 6dwe UniProt P9WFX9 Formula C₁₈H₁₅F₃N₂
Mol. weight 316.33 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
HDJ
PDB
6dwe
UniProt (similar protein)
P9WFX9
Target protein
VK055_1196

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 316.33 Da
LogP (Crippen) 3.86
H-bond donors 1
H-bond acceptors 2
TPSA 35.82 Ų
Rotatable bonds 3
Aromatic rings 2 / 3
Heavy atoms 23
Fraction sp³ C 0.28
Formula C₁₈H₁₅F₃N₂

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 35.8
  • −1 ≤ LogP ≤ 5 3.86
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 316.3
  • LogP ≤ 5 3.86
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 2
Veber's rules Pass
  • Rotatable bonds ≤ 10 3
  • TPSA ≤ 140 Ų 35.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1cc(c(c(c1)F)c2ccc(cc2)C3C(NC3C#N)CF)F
InChI 
InChI=1S/C18H15F3N2/c1-10-6-13(20)17(14(21)7-10)11-2-4-12(5-3-11)18-15(8-19)23-16(18)9-22/h2-7,15-16,18,23H,8H2,1H3
InChIKey 
OZFKPHFHTNQIQS-UHFFFAOYSA-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
PF00290' '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_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)