Ligand profile

A3N

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

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

Via homolog PDB 3v7y UniProt Q8Y8D7 Formula C₁₃H₁₆N₆O₃
Mol. weight 304.31 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
A3N
PDB
3v7y
UniProt (similar protein)
Q8Y8D7
Target protein
KP13_02430

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 304.31 Da
LogP (Crippen) -1.75
H-bond donors 4
H-bond acceptors 9
TPSA 131.34 Ų
Rotatable bonds 4
Aromatic rings 2 / 3
Heavy atoms 22
Fraction sp³ C 0.46
Formula C₁₃H₁₆N₆O₃

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 131.3
  • −1 ≤ LogP ≤ 5 -1.75
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 304.3
  • LogP ≤ 5 -1.75
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 9
Veber's rules Pass
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 131.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C#CCNCC1C(C(C(O1)n2cnc3c2ncnc3N)O)O
InChI 
InChI=1S/C13H16N6O3/c1-2-3-15-4-7-9(20)10(21)13(22-7)19-6-18-8-11(14)16-5-17-12(8)19/h1,5-7,9-10,13,15,20-21H,3-4H2,(H2,14,16,17)
InChIKey 
WYZJLWUBEMXBJJ-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)