Ligand profile

TBN

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

Bound to: VK055_2591 — purine nucleoside phosphorylase

Via homolog PDB 1pr5 UniProt P0ABP9 Formula C₁₁H₁₄N₄O₄
Mol. weight 266.26 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
TBN
PDB
1pr5
UniProt (similar protein)
P0ABP9
Target protein
VK055_2591

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 266.26 Da
LogP (Crippen) -1.38
H-bond donors 4
H-bond acceptors 8
TPSA 126.65 Ų
Rotatable bonds 2
Aromatic rings 2 / 3
Heavy atoms 19
Fraction sp³ C 0.45
Formula C₁₁H₁₄N₄O₄

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 126.7
  • −1 ≤ LogP ≤ 5 -1.38
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 266.3
  • LogP ≤ 5 -1.38
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 8
Veber's rules Pass
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 126.7
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1cn(c2c1c(ncn2)N)[C@H]3[C@@H]([C@@H]([C@H](O3)CO)O)O
InChI 
InChI=1S/C11H14N4O4/c12-9-5-1-2-15(10(5)14-4-13-9)11-8(18)7(17)6(3-16)19-11/h1-2,4,6-8,11,16-18H,3H2,(H2,12,13,14)/t6-,7-,8-,11-/m1/s1
InChIKey 
HDZZVAMISRMYHH-KCGFPETGSA-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
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)