Ligand profile

ZINC16928956

Virtual-screening candidate from ZINC.

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

Via homolog UniProt Q5SIP1 Formula C₁₀H₁₄N₂O₄S
Tanimoto 0.81
Mol. weight 258.30 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC16928956
UniProt (similar protein)
Q5SIP1
Tanimoto
0.810
Target protein
VK055_2857

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 258.30 Da
LogP (Crippen) -0.14
H-bond donors 3
H-bond acceptors 6
TPSA 87.48 Ų
Rotatable bonds 2
Aromatic rings 1 / 2
Heavy atoms 17
Fraction sp³ C 0.60
Formula C₁₀H₁₄N₂O₄S

Drug-likeness

Descriptor-based ADME screening flags from SMILES. These are not experimental toxicity results.

Permeability proxy High

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 87.5
  • −1 ≤ LogP ≤ 5 -0.14
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 258.3
  • LogP ≤ 5 -0.14
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 87.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1cn([C@H]2C[C@@H](O)[C@@H](CO)O2)c(=O)[nH]c1=S
InChI 
InChI=1S/C10H14N2O4S/c1-5-3-12(10(15)11-9(5)17)8-2-6(14)7(4-13)16-8/h3,6-8,13-14H,2,4H2,1H3,(H,11,15,17)/t6-,7-,8-/m1/s1
InChIKey 
AVKSPBJBGGHUMW-BWZBUEFSSA-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)