Ligand profile

ZINC4878189

Virtual-screening candidate from ZINC.

Bound to: VK055_3123 — biotin operon repressor

Via homolog UniProt O57883 Formula C₉H₁₄N₄O₅
Tanimoto 0.60
Mol. weight 258.23 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC4878189
UniProt (similar protein)
O57883
Tanimoto
0.596
Target protein
VK055_3123

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 258.23 Da
LogP (Crippen) -2.82
H-bond donors 5
H-bond acceptors 8
TPSA 156.85 Ų
Rotatable bonds 3
Aromatic rings 1 / 2
Heavy atoms 18
Fraction sp³ C 0.56
Formula C₉H₁₄N₄O₅

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 156.8
  • −1 ≤ LogP ≤ 5 -2.82
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 258.2
  • LogP ≤ 5 -2.82
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 8
Veber's rules Fail
  • Rotatable bonds ≤ 10 3
  • TPSA ≤ 140 Ų 156.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
NC(=O)c1c(N)ncn1[C@H]1O[C@@H](CO)[C@@H](O)[C@H]1O
InChI 
InChI=1S/C9H14N4O5/c10-7-4(8(11)17)13(2-12-7)9-6(16)5(15)3(1-14)18-9/h2-3,5-6,9,14-16H,1,10H2,(H2,11,17)/t3-,5+,6+,9-/m0/s1
InChIKey 
LGCWEVVMUUZXHY-PXMDKTAGSA-N

Provenance

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

Method
LigQ nearest_k
Query
ADN
Homolog
O57883

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_3123.

PDB 5

Ligands co-crystallized with this protein (structural evidence).

Ligand PDB entry

ChEMBL 2

Compounds with measured inhibitory activity on this target (higher pchembl = more potent).

Compound Potency (pchembl)

ZINC 49

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)