Ligand profile

ZINC5833727

Virtual-screening candidate from ZINC.

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

Via homolog UniProt Q5SIP1 Formula C₁₁H₁₇N₃O₄
Tanimoto 0.79
Mol. weight 255.27 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC5833727
UniProt (similar protein)
Q5SIP1
Tanimoto
0.791
Target protein
VK055_2857

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 255.27 Da
LogP (Crippen) -1.29
H-bond donors 3
H-bond acceptors 6
TPSA 96.35 Ų
Rotatable bonds 3
Aromatic rings 1 / 2
Heavy atoms 18
Fraction sp³ C 0.64
Formula C₁₁H₁₇N₃O₄

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 96.4
  • −1 ≤ LogP ≤ 5 -1.29
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 255.3
  • LogP ≤ 5 -1.29
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 3
  • TPSA ≤ 140 Ų 96.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CN[C@H]1C[C@H](n2cc(C)c(=O)[nH]c2=O)O[C@H]1CO
InChI 
InChI=1S/C11H17N3O4/c1-6-4-14(11(17)13-10(6)16)9-3-7(12-2)8(5-15)18-9/h4,7-9,12,15H,3,5H2,1-2H3,(H,13,16,17)/t7-,8-,9+/m0/s1
InChIKey 
LDZKBUFNIZADPS-XHNCKOQMSA-N

Provenance

Annotation context from LigQ_2, the internal Target step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ nearest_k
Query
THM
Homolog
Q5SIP1

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 9

Ligands co-crystallized with this protein (structural evidence).

Ligand PDB entry

ZINC 49

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)