Ligand profile

2FD

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

Bound to: VK055_2591 — purine nucleoside phosphorylase

Via homolog PDB 1pke UniProt P0ABP9 Formula C₁₀H₁₂FN₅O₃
Mol. weight 269.24 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
2FD
PDB
1pke
UniProt (similar protein)
P0ABP9
Target protein
VK055_2591

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 269.24 Da
LogP (Crippen) -0.81
H-bond donors 3
H-bond acceptors 8
TPSA 119.31 Ų
Rotatable bonds 2
Aromatic rings 2 / 3
Heavy atoms 19
Fraction sp³ C 0.50
Formula C₁₀H₁₂FN₅O₃

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 119.3
  • −1 ≤ LogP ≤ 5 -0.81
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 269.2
  • LogP ≤ 5 -0.81
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 8
Veber's rules Pass
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 119.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1nc2c(nc(nc2n1[C@H]3C[C@@H]([C@H](O3)CO)O)F)N
InChI 
InChI=1S/C10H12FN5O3/c11-10-14-8(12)7-9(15-10)16(3-13-7)6-1-4(18)5(2-17)19-6/h3-6,17-18H,1-2H2,(H2,12,14,15)/t4-,5+,6+/m0/s1
InChIKey 
ZWPYUXAXLRFWQC-KVQBGUIXSA-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)