Ligand profile

ZINC205997784

Virtual-screening candidate from ZINC.

Bound to: VK055_1726 — excinuclease ABC subunit B

Via homolog UniProt P56981 Formula C₂₄H₁₈N₄O₆
Tanimoto 0.72
Mol. weight 458.43 Da
Permeability Check
PAINS Alert

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC205997784
UniProt (similar protein)
P56981
Tanimoto
0.721
Target protein
VK055_1726

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 458.43 Da
LogP (Crippen) 4.10
H-bond donors 3
H-bond acceptors 7
TPSA 153.85 Ų
Rotatable bonds 5
Aromatic rings 3 / 5
Heavy atoms 34
Fraction sp³ C 0.17
Formula C₂₄H₁₈N₄O₆

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 153.9
  • −1 ≤ LogP ≤ 5 4.10
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 458.4
  • LogP ≤ 5 4.10
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 7
Veber's rules Fail
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 153.9
PAINS Alert

Matches PAINS filter: azo_A(324). May be a frequent false positive in HTS — review carefully.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
[N-]=[N+]=NCCCNC(=O)c1ccc2c(c1)C1(OC2=O)c2ccc(O)cc2Oc2cc(O)ccc21
InChI 
InChI=1S/C24H18N4O6/c25-28-27-9-1-8-26-22(31)13-2-5-16-19(10-13)24(34-23(16)32)17-6-3-14(29)11-20(17)33-21-12-15(30)4-7-18(21)24/h2-7,10-12,29-30H,1,8-9H2,(H,26,31)
InChIKey 
JQDJGCPZDAATOX-UHFFFAOYSA-N

Provenance

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

Method
LigQ nearest_k
Query
FLQ
Homolog
P56981

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_1726.

PDB 6

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)