Ligand profile

JY5

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

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

Via homolog PDB 6rc6 UniProt Q8Y8D7 Formula C₁₃H₁₅N₅O₂
Mol. weight 273.30 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
JY5
PDB
6rc6
UniProt (similar protein)
Q8Y8D7
Target protein
KP13_02430

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 273.30 Da
LogP (Crippen) 0.45
H-bond donors 2
H-bond acceptors 7
TPSA 99.08 Ų
Rotatable bonds 1
Aromatic rings 2 / 3
Heavy atoms 20
Fraction sp³ C 0.46
Formula C₁₃H₁₅N₅O₂

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 99.1
  • −1 ≤ LogP ≤ 5 0.45
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 273.3
  • LogP ≤ 5 0.45
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 7
Veber's rules Pass
  • Rotatable bonds ≤ 10 1
  • TPSA ≤ 140 Ų 99.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1nc(c2c(n1)n(c(n2)C#CCO)C3CCCCO3)N
InChI 
InChI=1S/C13H15N5O2/c14-12-11-13(16-8-15-12)18(9(17-11)4-3-6-19)10-5-1-2-7-20-10/h8,10,19H,1-2,5-7H2,(H2,14,15,16)
InChIKey 
AVGMEYBYAVAZNQ-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' 'PF20143

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)