Ligand profile

CHEMBL3706628

Bioactivity hit from ChEMBL on a similar protein.

Bound to: VK055_3786 — peptide deformylase

Via homolog UniProt Q9JN24 Formula C₂₃H₃₅N₃O₄
pchembl 8.05 ~8.9 nM
Mol. weight 417.55 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
CHEMBL3706628
UniProt (similar protein)
Q9JN24
pchembl
8.050 (~8.9 nM)
Target protein
VK055_3786

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 417.55 Da
LogP (Crippen) 3.15
H-bond donors 2
H-bond acceptors 4
TPSA 89.95 Ų
Rotatable bonds 9
Aromatic rings 1 / 2
Heavy atoms 30
Fraction sp³ C 0.61
Formula C₂₃H₃₅N₃O₄

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 3.15
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 417.6
  • LogP ≤ 5 3.15
  • 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)N1CCCc2ccccc21)C(C)(C)C
InChI 
InChI=1S/C23H35N3O4/c1-5-6-10-18(15-25(30)16-27)21(28)24-20(23(2,3)4)22(29)26-14-9-12-17-11-7-8-13-19(17)26/h7-8,11,13,16,18,20,30H,5-6,9-10,12,14-15H2,1-4H3,(H,24,28)/t18-,20-/m1/s1
InChIKey 
XBEBZFZSXGPETD-UYAOXDASSA-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)