Ligand profile

ZINC5080460

Virtual-screening candidate from ZINC.

Bound to: VK055_0020 — diguanylate cyclase domain protein

Via homolog UniProt Q9X2A8 Formula C₁₃H₁₇N₅O₅
Tanimoto 0.66
Mol. weight 323.31 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC5080460
UniProt (similar protein)
Q9X2A8
Tanimoto
0.656
Target protein
VK055_0020

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 323.31 Da
LogP (Crippen) -0.89
H-bond donors 3
H-bond acceptors 9
TPSA 137.51 Ų
Rotatable bonds 1
Aromatic rings 2 / 4
Heavy atoms 23
Fraction sp³ C 0.62
Formula C₁₃H₁₇N₅O₅

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 137.5
  • −1 ≤ LogP ≤ 5 -0.89
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 323.3
  • LogP ≤ 5 -0.89
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 9
Veber's rules Pass
  • Rotatable bonds ≤ 10 1
  • TPSA ≤ 140 Ų 137.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC1(C)OC[C@@H]2O[C@@H](n3cnc4c(=O)[nH]c(N)nc43)[C@@H](O)[C@@H]2O1
InChI 
InChI=1S/C13H17N5O5/c1-13(2)21-3-5-8(23-13)7(19)11(22-5)18-4-15-6-9(18)16-12(14)17-10(6)20/h4-5,7-8,11,19H,3H2,1-2H3,(H3,14,16,17,20)/t5-,7-,8+,11+/m0/s1
InChIKey 
VDVHAPVSQCJZHA-WOIOKPISSA-N

Provenance

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

Method
LigQ nearest_k
Query
C2E
Homolog
Q9X2A8

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_0020.

PDB 4

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)