Ligand profile

ZINC3869414

Virtual-screening candidate from ZINC.

Bound to: VK055_2187 — 6,7-dimethyl-8-ribityllumazine synthase

Via homolog UniProt O66529 Formula C₉H₁₆N₄O₆
Tanimoto 0.67
Mol. weight 276.25 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC3869414
UniProt (similar protein)
O66529
Tanimoto
0.667
Target protein
VK055_2187

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 276.25 Da
LogP (Crippen) -3.87
H-bond donors 8
H-bond acceptors 8
TPSA 184.69 Ų
Rotatable bonds 6
Aromatic rings 1 / 1
Heavy atoms 19
Fraction sp³ C 0.56
Formula C₉H₁₆N₄O₆

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 184.7
  • −1 ≤ LogP ≤ 5 -3.87
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 276.2
  • LogP ≤ 5 -3.87
  • H-bond donors ≤ 5 8
  • H-bond acceptors ≤ 10 8
Veber's rules Fail
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 184.7
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Nc1c(NC[C@H](O)[C@H](O)[C@H](O)CO)[nH]c(=O)[nH]c1=O
InChI 
InChI=1S/C9H16N4O6/c10-5-7(12-9(19)13-8(5)18)11-1-3(15)6(17)4(16)2-14/h3-4,6,14-17H,1-2,10H2,(H3,11,12,13,18,19)/t3-,4+,6-/m0/s1
InChIKey 
XKQZIXVJVUPORE-RPDRRWSUSA-N

Provenance

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

Method
LigQ nearest_k
Query
LMZ
Homolog
O66529

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_2187.

PDB 8

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)