Ligand profile

5CN

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

Bound to: P10721

Via homolog PDB 2i1m UniProt P07333 Formula C₁₉H₂₁N₃O₃
Mol. weight 339.40 Da
Permeability High
PAINS Alert

Identifiers

Database identifiers and provenance.

Ligand ID
5CN
PDB
2i1m
UniProt (similar protein)
P07333
Target protein
P10721

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 339.40 Da
LogP (Crippen) 3.13
H-bond donors 2
H-bond acceptors 5
TPSA 89.50 Ų
Rotatable bonds 4
Aromatic rings 2 / 3
Heavy atoms 25
Fraction sp³ C 0.37
Formula C₁₉H₂₁N₃O₃

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 89.5
  • −1 ≤ LogP ≤ 5 3.13
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 339.4
  • LogP ≤ 5 3.13
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 89.5
PAINS Alert

Matches PAINS filter: anil_di_alk_D(198). May be a frequent false positive in HTS — review carefully.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC1CCN(CC1)c2ccc(cc2NC(=O)c3ccc(o3)C#N)CO
InChI 
InChI=1S/C19H21N3O3/c1-13-6-8-22(9-7-13)17-4-2-14(12-23)10-16(17)21-19(24)18-5-3-15(11-20)25-18/h2-5,10,13,23H,6-9,12H2,1H3,(H,21,24)
InChIKey 
NNPCFFIJVKYGHR-UHFFFAOYSA-N

Provenance

Annotation context from LigQ_2, the internal Target step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ domain
Source
PDB
Binding sites
PF07714

External resources

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

Other ligands for this protein

Quick navigation to other ligands bound to P10721.

PDB 232

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)