Ligand profile

NC6

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

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

Via homolog PDB 1zd4 UniProt P34913 Formula C₁₃H₂₄N₂O₃
Mol. weight 256.35 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
NC6
PDB
1zd4
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) 2.26
H-bond donors 3
H-bond acceptors 2
TPSA 78.43 Ų
Rotatable bonds 7
Aromatic rings 0 / 1
Heavy atoms 18
Fraction sp³ C 0.85
Formula C₁₃H₂₄N₂O₃

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 78.4
  • −1 ≤ LogP ≤ 5 2.26
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 256.3
  • LogP ≤ 5 2.26
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 2
Veber's rules Pass
  • Rotatable bonds ≤ 10 7
  • TPSA ≤ 140 Ų 78.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C1CCC(CC1)NC(=O)NCCCCCC(=O)O
InChI 
InChI=1S/C13H24N2O3/c16-12(17)9-5-2-6-10-14-13(18)15-11-7-3-1-4-8-11/h11H,1-10H2,(H,16,17)(H2,14,15,18)
InChIKey 
KFTVEPYSUSWBRD-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)