Ligand profile

ZINC12697899

Virtual-screening candidate from ZINC.

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

Via homolog UniProt P04995 Formula C₁₉H₁₉ClF₃N₃O₃
Tanimoto 0.51
Mol. weight 429.83 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC12697899
UniProt (similar protein)
P04995
Tanimoto
0.508
Target protein
VK055_5051

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 429.83 Da
LogP (Crippen) 3.88
H-bond donors 2
H-bond acceptors 4
TPSA 70.67 Ų
Rotatable bonds 7
Aromatic rings 2 / 2
Heavy atoms 29
Fraction sp³ C 0.26
Formula C₁₉H₁₉ClF₃N₃O₃

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 70.7
  • −1 ≤ LogP ≤ 5 3.88
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 429.8
  • LogP ≤ 5 3.88
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 7
  • TPSA ≤ 140 Ų 70.7
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
COc1ccc(NC(=O)CN(C)CC(=O)Nc2cc(C(F)(F)F)ccc2Cl)cc1
InChI 
InChI=1S/C19H19ClF3N3O3/c1-26(10-17(27)24-13-4-6-14(29-2)7-5-13)11-18(28)25-16-9-12(19(21,22)23)3-8-15(16)20/h3-9H,10-11H2,1-2H3,(H,24,27)(H,25,28)
InChIKey 
XKGRJOJNWZVQQK-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)