Ligand profile

DIH

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

Bound to: VK055_2591 — purine nucleoside phosphorylase

Via homolog PDB 3occ UniProt B1JL34 Formula C₁₂H₁₇N₄O₃⁺
Mol. weight 265.29 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
DIH
PDB
3occ
UniProt (similar protein)
B1JL34
Target protein
VK055_2591

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 265.29 Da
LogP (Crippen) -2.38
H-bond donors 5
H-bond acceptors 4
TPSA 106.44 Ų
Rotatable bonds 3
Aromatic rings 2 / 3
Heavy atoms 19
Fraction sp³ C 0.50
Formula C₁₂H₁₇N₄O₃⁺

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 106.4
  • −1 ≤ LogP ≤ 5 -2.38
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 265.3
  • LogP ≤ 5 -2.38
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 3
  • TPSA ≤ 140 Ų 106.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1c(c2c([nH]1)C(=O)NC=N2)C[NH+]3C[C@@H]([C@H](C3)O)CO
InChI 
InChI=1S/C12H16N4O3/c17-5-8-3-16(4-9(8)18)2-7-1-13-11-10(7)14-6-15-12(11)19/h1,6,8-9,13,17-18H,2-5H2,(H,14,15,19)/p+1/t8-,9+/m1/s1
InChIKey 
AFNHHLILYQEHKK-BDAKNGLRSA-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
PF01048

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_2591.

PDB 25

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)