Ligand profile

KD8

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

Bound to: KP13_03284 — Endonuclease 8 bifunctional protein

Via homolog PDB 6rp7 UniProt P42371 Formula C₈H₈N₄OS
Mol. weight 208.25 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
KD8
PDB
6rp7
UniProt (similar protein)
P42371
Target protein
KP13_03284

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 208.25 Da
LogP (Crippen) 0.99
H-bond donors 2
H-bond acceptors 4
TPSA 74.43 Ų
Rotatable bonds 0
Aromatic rings 2 / 2
Heavy atoms 14
Fraction sp³ C 0.25
Formula C₈H₈N₄OS

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 74.4
  • −1 ≤ LogP ≤ 5 0.99
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 208.2
  • LogP ≤ 5 0.99
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 0
  • TPSA ≤ 140 Ų 74.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1c(nc2c(n1)C(=O)NC(=S)N2)C
InChI 
InChI=1S/C8H8N4OS/c1-3-4(2)10-6-5(9-3)7(13)12-8(14)11-6/h1-2H3,(H2,10,11,12,13,14)
InChIKey 
FMPVXDGAZOSEMT-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
PF06827' 'PF06831

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)