Ligand profile

NC3

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

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

Via homolog PDB 1zd2 UniProt P34913 Formula C₉H₁₆N₂O₃
Mol. weight 200.24 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
NC3
PDB
1zd2
UniProt (similar protein)
P34913
Target protein
VK055_0681

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 200.24 Da
LogP (Crippen) 0.70
H-bond donors 3
H-bond acceptors 2
TPSA 78.43 Ų
Rotatable bonds 3
Aromatic rings 0 / 1
Heavy atoms 14
Fraction sp³ C 0.78
Formula C₉H₁₆N₂O₃

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 0.70
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 200.2
  • LogP ≤ 5 0.70
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 2
Veber's rules Pass
  • Rotatable bonds ≤ 10 3
  • TPSA ≤ 140 Ų 78.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C1CCC(CC1)NC(=O)NCC(=O)O
InChI 
InChI=1S/C9H16N2O3/c12-8(13)6-10-9(14)11-7-4-2-1-3-5-7/h7H,1-6H2,(H,12,13)(H2,10,11,14)
InChIKey 
NVORCMBCUHQRDL-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)