Ligand profile

16D

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

Bound to: KP13_15895 — Agmatinase

Via homolog PDB 3nip UniProt Q9I6K2 Formula C₆H₁₆N₂
Mol. weight 116.21 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
16D
PDB
3nip
UniProt (similar protein)
Q9I6K2
Target protein
KP13_15895

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 116.21 Da
LogP (Crippen) 0.46
H-bond donors 2
H-bond acceptors 2
TPSA 52.04 Ų
Rotatable bonds 5
Aromatic rings 0 / 0
Heavy atoms 8
Fraction sp³ C 1.00
Formula C₆H₁₆N₂

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 52.0
  • −1 ≤ LogP ≤ 5 0.46
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 116.2
  • LogP ≤ 5 0.46
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 2
Veber's rules Pass
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 52.0
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C(CCCN)CCN
InChI 
InChI=1S/C6H16N2/c7-5-3-1-2-4-6-8/h1-8H2
InChIKey 
NAQMVNRVTILPCV-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
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)