Ligand profile

ZINC38580931

Virtual-screening candidate from ZINC.

Bound to: VK055_0020 — diguanylate cyclase domain protein

Via homolog UniProt Q9X2A8 Formula C₁₀H₁₂N₅O₇P
Tanimoto 0.65
Mol. weight 345.21 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC38580931
UniProt (similar protein)
Q9X2A8
Tanimoto
0.651
Target protein
VK055_0020

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 345.21 Da
LogP (Crippen) -1.58
H-bond donors 3
H-bond acceptors 10
TPSA 168.89 Ų
Rotatable bonds 1
Aromatic rings 2 / 4
Heavy atoms 23
Fraction sp³ C 0.50
Formula C₁₀H₁₂N₅O₇P

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 168.9
  • −1 ≤ LogP ≤ 5 -1.58
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 345.2
  • LogP ≤ 5 -1.58
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 10
Veber's rules Fail
  • Rotatable bonds ≤ 10 1
  • TPSA ≤ 140 Ų 168.9
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Nc1c2ncn([C@@H]3O[C@@H]4CO[P@](=O)(O)O[C@H]4[C@H]3O)c2nc[n+]1[O-]
InChI 
InChI=1S/C10H12N5O7P/c11-8-5-9(13-3-15(8)17)14(2-12-5)10-6(16)7-4(21-10)1-20-23(18,19)22-7/h2-4,6-7,10,16H,1,11H2,(H,18,19)/t4-,6-,7-,10-/m1/s1
InChIKey 
BDQMQFQUJOMWAB-KQYNXXCUSA-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)