Ligand profile

1EF

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

Bound to: VK055_4295 — peptidase M16 inactive domain protein

Via homolog PDB 4ifh UniProt P14735 Formula C₂₅H₂₅N₅O₃
Mol. weight 443.51 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
1EF
PDB
4ifh
UniProt (similar protein)
P14735
Target protein
VK055_4295

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 443.51 Da
LogP (Crippen) 3.35
H-bond donors 3
H-bond acceptors 6
TPSA 109.14 Ų
Rotatable bonds 8
Aromatic rings 4 / 4
Heavy atoms 33
Fraction sp³ C 0.20
Formula C₂₅H₂₅N₅O₃

Drug-likeness

Descriptor-based ADME screening flags from SMILES. These are not experimental toxicity results.

Permeability proxy Check

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 109.1
  • −1 ≤ LogP ≤ 5 3.35
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 443.5
  • LogP ≤ 5 3.35
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 109.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1ccc(cc1)C(=O)NCc2cn(nn2)[C@H](Cc3ccc4ccccc4c3)CC(=O)NO
InChI 
InChI=1S/C25H25N5O3/c1-17-6-9-20(10-7-17)25(32)26-15-22-16-30(29-27-22)23(14-24(31)28-33)13-18-8-11-19-4-2-3-5-21(19)12-18/h2-12,16,23,33H,13-15H2,1H3,(H,26,32)(H,28,31)/t23-/m1/s1
InChIKey 
QIIHKUBWBJHTFJ-HSZRJFAPSA-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
PF00675' 'PF05193

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_4295.

PDB 15

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

Ligand PDB entry

ChEMBL 12

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)