Ligand profile

DHI

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

Bound to: VK055_3290 — D-tyrosyl-tRNA(Tyr) deacylase

Via homolog PDB 3koc UniProt Q8IIS0 Formula C₆H₁₀N₃O₂⁺
Mol. weight 156.16 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
DHI
PDB
3koc
UniProt (similar protein)
Q8IIS0
Target protein
VK055_3290

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 156.16 Da
LogP (Crippen) -1.22
H-bond donors 3
H-bond acceptors 2
TPSA 93.25 Ų
Rotatable bonds 3
Aromatic rings 1 / 1
Heavy atoms 11
Fraction sp³ C 0.33
Formula C₆H₁₀N₃O₂⁺

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 93.2
  • −1 ≤ LogP ≤ 5 -1.22
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 156.2
  • LogP ≤ 5 -1.22
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 2
Veber's rules Pass
  • Rotatable bonds ≤ 10 3
  • TPSA ≤ 140 Ų 93.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1c([nH+]c[nH]1)C[C@H](C(=O)O)N
InChI 
InChI=1S/C6H9N3O2/c7-5(6(10)11)1-4-2-8-3-9-4/h2-3,5H,1,7H2,(H,8,9)(H,10,11)/p+1/t5-/m1/s1
InChIKey 
HNDVDQJCIGZPNO-RXMQYKEDSA-O

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
PF02580

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_3290.

PDB 3

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)