Ligand profile

6NF

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

Bound to: VK055_0681 — alpha/beta hydrolase fold family protein

Via homolog PDB 5aki UniProt P34913 Formula C₁₅H₂₀N₄
Mol. weight 256.35 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
6NF
PDB
5aki
UniProt (similar protein)
P34913
Target protein
VK055_0681

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 256.35 Da
LogP (Crippen) 3.46
H-bond donors 2
H-bond acceptors 3
TPSA 53.60 Ų
Rotatable bonds 4
Aromatic rings 2 / 3
Heavy atoms 19
Fraction sp³ C 0.47
Formula C₁₅H₂₀N₄

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 53.6
  • −1 ≤ LogP ≤ 5 3.46
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 256.4
  • LogP ≤ 5 3.46
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 3
Veber's rules Pass
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 53.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1cnccc1c2cc(n[nH]2)NCC3CCCCC3
InChI 
InChI=1S/C15H20N4/c1-2-4-12(5-3-1)11-17-15-10-14(18-19-15)13-6-8-16-9-7-13/h6-10,12H,1-5,11H2,(H2,17,18,19)
InChIKey 
PAVOZTULRSGNJC-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
PF00561

External resources

Open this ligand in third-party databases and cheminformatics tools.

Other ligands for this protein

Quick navigation to other ligands bound to VK055_0681.

PDB 98

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

Ligand PDB entry

ChEMBL 100

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)