Ligand profile

JY2

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

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

Via homolog PDB 6rc2 UniProt Q8Y8D7 Formula C₁₁H₁₃N₅
Mol. weight 215.26 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
JY2
PDB
6rc2
UniProt (similar protein)
Q8Y8D7
Target protein
KP13_02430

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 215.26 Da
LogP (Crippen) 1.13
H-bond donors 1
H-bond acceptors 5
TPSA 69.62 Ų
Rotatable bonds 3
Aromatic rings 2 / 2
Heavy atoms 16
Fraction sp³ C 0.36
Formula C₁₁H₁₃N₅

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 69.6
  • −1 ≤ LogP ≤ 5 1.13
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 215.3
  • LogP ≤ 5 1.13
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 3
  • TPSA ≤ 140 Ų 69.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1nc2c(ncnc2n1CCCC#C)N
InChI 
InChI=1S/C11H13N5/c1-3-4-5-6-16-8(2)15-9-10(12)13-7-14-11(9)16/h1,7H,4-6H2,2H3,(H2,12,13,14)
InChIKey 
XNRGOKLMAXATIA-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)