Ligand profile

223

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

Bound to: VK055_2591 — purine nucleoside phosphorylase

Via homolog PDB 2isc UniProt A2E7Y6 Formula C₁₂H₁₇N₅O₂
Mol. weight 263.30 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
223
PDB
2isc
UniProt (similar protein)
A2E7Y6
Target protein
VK055_2591

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 263.30 Da
LogP (Crippen) -0.67
H-bond donors 4
H-bond acceptors 6
TPSA 111.29 Ų
Rotatable bonds 3
Aromatic rings 2 / 3
Heavy atoms 19
Fraction sp³ C 0.50
Formula C₁₂H₁₇N₅O₂

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 111.3
  • −1 ≤ LogP ≤ 5 -0.67
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 263.3
  • LogP ≤ 5 -0.67
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 3
  • TPSA ≤ 140 Ų 111.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1c(c2c([nH]1)c(ncn2)N)C[N@@]3C[C@@H]([C@H](C3)O)CO
InChI 
InChI=1S/C12H17N5O2/c13-12-11-10(15-6-16-12)7(1-14-11)2-17-3-8(5-18)9(19)4-17/h1,6,8-9,14,18-19H,2-5H2,(H2,13,15,16)/t8-,9+/m1/s1
InChIKey 
HYYXEHQHMXTTFP-BDAKNGLRSA-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
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)