Ligand profile

3C5

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

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

Via homolog PDB 4y2p UniProt P34913 Formula C₁₃H₁₄N₂
Mol. weight 198.27 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
3C5
PDB
4y2p
UniProt (similar protein)
P34913
Target protein
VK055_0681

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 198.27 Da
LogP (Crippen) 2.47
H-bond donors 1
H-bond acceptors 2
TPSA 24.92 Ų
Rotatable bonds 3
Aromatic rings 2 / 2
Heavy atoms 15
Fraction sp³ C 0.15
Formula C₁₃H₁₄N₂

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 24.9
  • −1 ≤ LogP ≤ 5 2.47
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 198.3
  • LogP ≤ 5 2.47
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 2
Veber's rules Pass
  • Rotatable bonds ≤ 10 3
  • TPSA ≤ 140 Ų 24.9
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CNCc1cccc(c1)c2cccnc2
InChI 
InChI=1S/C13H14N2/c1-14-9-11-4-2-5-12(8-11)13-6-3-7-15-10-13/h2-8,10,14H,9H2,1H3
InChIKey 
LZJRRTLTBULOHU-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)