Ligand profile

3D1

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

Bound to: VK055_2857 — 2',3'-cyclic-nucleotide 2'-phosphodiesterase

Via homolog PDB 4q7f UniProt Q2G1L5 Formula C₁₀H₁₃N₅O₃
Mol. weight 251.25 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
3D1
PDB
4q7f
UniProt (similar protein)
Q2G1L5
Target protein
VK055_2857

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 251.25 Da
LogP (Crippen) -0.95
H-bond donors 3
H-bond acceptors 8
TPSA 119.31 Ų
Rotatable bonds 2
Aromatic rings 2 / 3
Heavy atoms 18
Fraction sp³ C 0.50
Formula C₁₀H₁₃N₅O₃

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 -0.95
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 251.2
  • LogP ≤ 5 -0.95
  • 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 
c1nc(c2c(n1)n(cn2)[C@H]3C[C@@H]([C@H](O3)CO)O)N
InChI 
InChI=1S/C10H13N5O3/c11-9-8-10(13-3-12-9)15(4-14-8)7-1-5(17)6(2-16)18-7/h3-7,16-17H,1-2H2,(H2,11,12,13)/t5-,6+,7+/m0/s1
InChIKey 
OLXZPDWKRNYJJZ-RRKCRQDMSA-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
PF00149' 'PF02872

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_2857.

PDB 8

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)