Ligand profile

ZINC13320508

Virtual-screening candidate from ZINC.

Bound to: VK055_5051 — exonuclease I, 3' -- 5' specific deoxyribophosphodiesterase

Via homolog UniProt P04995 Formula C₂₁H₂₃ClF₃N₃O₃
Tanimoto 0.52
Mol. weight 457.88 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC13320508
UniProt (similar protein)
P04995
Tanimoto
0.516
Target protein
VK055_5051

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 457.88 Da
LogP (Crippen) 4.73
H-bond donors 1
H-bond acceptors 4
TPSA 54.04 Ų
Rotatable bonds 5
Aromatic rings 2 / 3
Heavy atoms 31
Fraction sp³ C 0.38
Formula C₂₁H₂₃ClF₃N₃O₃

Drug-likeness

Descriptor-based ADME screening flags from SMILES. These are not experimental toxicity results.

Permeability proxy High

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 54.0
  • −1 ≤ LogP ≤ 5 4.73
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 457.9
  • LogP ≤ 5 4.73
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 54.0
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
COc1ccc(OC)c(CN2CCN(C(=O)Nc3cc(C(F)(F)F)ccc3Cl)CC2)c1
InChI 
InChI=1S/C21H23ClF3N3O3/c1-30-16-4-6-19(31-2)14(11-16)13-27-7-9-28(10-8-27)20(29)26-18-12-15(21(23,24)25)3-5-17(18)22/h3-6,11-12H,7-10,13H2,1-2H3,(H,26,29)
InChIKey 
CLRZPOLHPNZDRS-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
CF1
Homolog
P04995

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_5051.

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)