Ligand profile

ZINC12656099

Virtual-screening candidate from ZINC.

Bound to: VK055_3605 — protein involved in utilization of DNA as a carbon source

Via homolog UniProt P37634 Formula C₁₃H₁₇N₅O₆
Tanimoto 0.60
Mol. weight 339.31 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC12656099
UniProt (similar protein)
P37634
Tanimoto
0.597
Target protein
VK055_3605

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 339.31 Da
LogP (Crippen) -1.68
H-bond donors 5
H-bond acceptors 10
TPSA 162.85 Ų
Rotatable bonds 6
Aromatic rings 2 / 3
Heavy atoms 24
Fraction sp³ C 0.54
Formula C₁₃H₁₇N₅O₆

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 162.8
  • −1 ≤ LogP ≤ 5 -1.68
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 339.3
  • LogP ≤ 5 -1.68
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 10
Veber's rules Fail
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 162.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
O=C(O)CCNc1ncnc2c1ncn2[C@@H]1O[C@H](CO)[C@@H](O)[C@H]1O
InChI 
InChI=1S/C13H17N5O6/c19-3-6-9(22)10(23)13(24-6)18-5-17-8-11(14-2-1-7(20)21)15-4-16-12(8)18/h4-6,9-10,13,19,22-23H,1-3H2,(H,20,21)(H,14,15,16)/t6-,9-,10-,13-/m1/s1
InChIKey 
QMTQDSJWWLCMNM-ZRFIDHNTSA-N

Provenance

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

Method
LigQ sequence
Query
HY8
Homolog
P37634

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_3605.

PDB 2

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)