Ligand profile

ZINC5113209

Virtual-screening candidate from ZINC.

Bound to: KP13_15895 — Agmatinase

Via homolog UniProt G7JFU5 Formula C₁₂H₂₅N₃O₄
Tanimoto 0.58
Mol. weight 275.35 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC5113209
UniProt (similar protein)
G7JFU5
Tanimoto
0.577
Target protein
KP13_15895

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 275.35 Da
LogP (Crippen) -0.26
H-bond donors 5
H-bond acceptors 5
TPSA 138.67 Ų
Rotatable bonds 12
Aromatic rings 0 / 0
Heavy atoms 19
Fraction sp³ C 0.83
Formula C₁₂H₂₅N₃O₄

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 138.7
  • −1 ≤ LogP ≤ 5 -0.26
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 275.3
  • LogP ≤ 5 -0.26
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 5
Veber's rules Fail
  • Rotatable bonds ≤ 10 12
  • TPSA ≤ 140 Ų 138.7
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
N[C@@H](CCCCNCCCC[C@H](N)C(=O)O)C(=O)O
InChI 
InChI=1S/C12H25N3O4/c13-9(11(16)17)5-1-3-7-15-8-4-2-6-10(14)12(18)19/h9-10,15H,1-8,13-14H2,(H,16,17)(H,18,19)/t9-,10-/m0/s1
InChIKey 
HYLBTMZBXLEVCL-UWVGGRQHSA-N

Provenance

Annotation context from LigQ_2, the internal Target step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ nearest_k
Query
ORN
Homolog
G7JFU5

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_15895.

PDB 3

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

Ligand PDB entry

ZINC 49

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

Compound Similarity (Tanimoto)