Ligand profile

JYN

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

Bound to: KP13_02430 — putative inorganic polyphosphate/ATP-NAD kinase

Via homolog PDB 6rbp UniProt Q8Y8D7 Formula C₉H₁₂N₈
Mol. weight 232.25 Da
Permeability Check
PAINS Alert

Identifiers

Database identifiers and provenance.

Ligand ID
JYN
PDB
6rbp
UniProt (similar protein)
Q8Y8D7
Target protein
KP13_02430

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 232.25 Da
LogP (Crippen) 1.50
H-bond donors 1
H-bond acceptors 6
TPSA 118.38 Ų
Rotatable bonds 5
Aromatic rings 2 / 2
Heavy atoms 17
Fraction sp³ C 0.44
Formula C₉H₁₂N₈

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 118.4
  • −1 ≤ LogP ≤ 5 1.50
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 232.3
  • LogP ≤ 5 1.50
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 118.4
PAINS Alert

Matches PAINS filter: azo_A(324). May be a frequent false positive in HTS — review carefully.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1nc(c2c(n1)n(cn2)CCCCN=[N+]=[N-])N
InChI 
InChI=1S/C9H12N8/c10-8-7-9(13-5-12-8)17(6-14-7)4-2-1-3-15-16-11/h5-6H,1-4H2,(H2,10,12,13)
InChIKey 
HVEKFLZTZQALAB-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
PF01513

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_02430.

PDB 51

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

Ligand PDB entry

ChEMBL 3

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)