Ligand profile

3KH

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

Bound to: VK055_0984 — hypothetical protein

Via homolog PDB 4wcd UniProt O76290 Formula C₈H₆N₆S
Mol. weight 218.25 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
3KH
PDB
4wcd
UniProt (similar protein)
O76290
Target protein
VK055_0984

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 218.25 Da
LogP (Crippen) 1.06
H-bond donors 2
H-bond acceptors 6
TPSA 93.37 Ų
Rotatable bonds 1
Aromatic rings 3 / 3
Heavy atoms 15
Fraction sp³ C 0.00
Formula C₈H₆N₆S

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 93.4
  • −1 ≤ LogP ≤ 5 1.06
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 218.2
  • LogP ≤ 5 1.06
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 1
  • TPSA ≤ 140 Ų 93.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1cc2c(cc1c3nnc(s3)N)[nH]nn2
InChI 
InChI=1S/C8H6N6S/c9-8-13-12-7(15-8)4-1-2-5-6(3-4)11-14-10-5/h1-3H,(H2,9,13)(H,10,11,14)
InChIKey 
QEDRDOHUKCLXOP-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
PF13561

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_0984.

PDB 92

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

Ligand PDB entry

ChEMBL 35

Compounds with measured inhibitory activity on this target (higher pchembl = more potent).

Compound Potency (pchembl)

ZINC 50

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

Compound Similarity (Tanimoto)