Ligand profile

AG2

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

Bound to: KP13_04463 — Putative ABC transporter periplasmic-binding protein

Via homolog PDB 6ye6 UniProt P31133 Formula C₅H₁₄N₄
Mol. weight 130.19 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
AG2
PDB
6ye6
UniProt (similar protein)
P31133
Target protein
KP13_04463

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 130.19 Da
LogP (Crippen) -0.79
H-bond donors 4
H-bond acceptors 2
TPSA 87.92 Ų
Rotatable bonds 4
Aromatic rings 0 / 0
Heavy atoms 9
Fraction sp³ C 0.80
Formula C₅H₁₄N₄

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 87.9
  • −1 ≤ LogP ≤ 5 -0.79
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 130.2
  • LogP ≤ 5 -0.79
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 2
Veber's rules Pass
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 87.9
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C(CCNC(=N)N)CN
InChI 
InChI=1S/C5H14N4/c6-3-1-2-4-9-5(7)8/h1-4,6H2,(H4,7,8,9)
InChIKey 
QYPPJABKJHAVHS-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
PF13416

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_04463.

PDB 10

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

Ligand PDB entry

ZINC 50

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

Compound Similarity (Tanimoto)