Ligand profile

CHEMBL419878

Bioactivity hit from ChEMBL on a similar protein.

Bound to: VK055_3786 — peptide deformylase

Via homolog UniProt Q9JN24 Formula C₁₈H₃₃N₃O₄
pchembl 8.00 ~10.0 nM
Mol. weight 355.48 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
CHEMBL419878
UniProt (similar protein)
Q9JN24
pchembl
8.000 (~10.0 nM)
Target protein
VK055_3786

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 355.48 Da
LogP (Crippen) 1.79
H-bond donors 2
H-bond acceptors 4
TPSA 89.95 Ų
Rotatable bonds 9
Aromatic rings 0 / 1
Heavy atoms 25
Fraction sp³ C 0.83
Formula C₁₈H₃₃N₃O₄

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 90.0
  • −1 ≤ LogP ≤ 5 1.79
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 355.5
  • LogP ≤ 5 1.79
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 9
  • TPSA ≤ 140 Ų 90.0
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCCC[C@H](CN(O)C=O)C(=O)N[C@H](C(=O)N1CCCC1)C(C)(C)C
InChI 
InChI=1S/C18H33N3O4/c1-5-6-9-14(12-21(25)13-22)16(23)19-15(18(2,3)4)17(24)20-10-7-8-11-20/h13-15,25H,5-12H2,1-4H3,(H,19,23)/t14-,15-/m1/s1
InChIKey 
NIEXBMNRVYIVII-HUUCEWRRSA-N

Provenance

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

Method
LigQ nearest_k
Source
ChEMBL
Binding sites
PF01327

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_3786.

PDB 12

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

Ligand PDB entry

ChEMBL 99

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)