Ligand profile

ORN

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

Bound to: KP13_15895 — Agmatinase

Via homolog PDB 6vst UniProt G7JFU5 Formula C₅H₁₂N₂O₂
Mol. weight 132.16 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ORN
PDB
6vst
UniProt (similar protein)
G7JFU5
Target protein
KP13_15895

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 132.16 Da
LogP (Crippen) -0.86
H-bond donors 3
H-bond acceptors 3
TPSA 89.34 Ų
Rotatable bonds 4
Aromatic rings 0 / 0
Heavy atoms 9
Fraction sp³ C 0.80
Formula C₅H₁₂N₂O₂

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 89.3
  • −1 ≤ LogP ≤ 5 -0.86
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 132.2
  • LogP ≤ 5 -0.86
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 3
Veber's rules Pass
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 89.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C(C[C@@H](C(=O)O)N)CN
InChI 
InChI=1S/C5H12N2O2/c6-3-1-2-4(7)5(8)9/h4H,1-3,6-7H2,(H,8,9)/t4-/m0/s1
InChIKey 
AHLPHDHHMVZTML-BYPYZUCNSA-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
PF00491

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 2

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)