Ligand profile

KBN

Ligand co-crystallized with a similar protein (Protein Data Bank).

Bound to: KP13_03284 — Endonuclease 8 bifunctional protein

Via homolog PDB 6rnr UniProt P42371 Formula C₆H₃F₃N₄S
Mol. weight 220.18 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
KBN
PDB
6rnr
UniProt (similar protein)
P42371
Target protein
KP13_03284

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 220.18 Da
LogP (Crippen) 1.66
H-bond donors 2
H-bond acceptors 4
TPSA 54.46 Ų
Rotatable bonds 0
Aromatic rings 2 / 2
Heavy atoms 14
Fraction sp³ C 0.17
Formula C₆H₃F₃N₄S

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 54.5
  • −1 ≤ LogP ≤ 5 1.66
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 220.2
  • LogP ≤ 5 1.66
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 0
  • TPSA ≤ 140 Ų 54.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1[nH]c2c(n1)c(nc(n2)C(F)(F)F)S
InChI 
InChI=1S/C6H3F3N4S/c7-6(8,9)5-12-3-2(4(14)13-5)10-1-11-3/h1H,(H2,10,11,12,13,14)
InChIKey 
NVRHELPZQYUXMX-UHFFFAOYSA-N

Provenance

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

Method
LigQ nearest_k
Source
PDB
Binding sites
PF01149' 'PF06827

External resources

Open this ligand in third-party databases and cheminformatics tools.

Other ligands for this protein

Quick navigation to other ligands bound to KP13_03284.

PDB 6

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

Ligand PDB entry

ZINC 50

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

Compound Similarity (Tanimoto)