Ligand profile

CHEMBL345440

Bioactivity hit from ChEMBL on a similar protein.

Bound to: VK055_3786 — peptide deformylase

Via homolog UniProt Q9JN24 Formula C₂₈H₄₂F₂N₄O₅
pchembl 8.70 ~2.0 nM
Mol. weight 552.66 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
CHEMBL345440
UniProt (similar protein)
Q9JN24
pchembl
8.700 (~2.0 nM)
Target protein
VK055_3786

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 552.66 Da
LogP (Crippen) 2.84
H-bond donors 3
H-bond acceptors 7
TPSA 113.42 Ų
Rotatable bonds 12
Aromatic rings 1 / 3
Heavy atoms 39
Fraction sp³ C 0.68
Formula C₂₈H₄₂F₂N₄O₅

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 113.4
  • −1 ≤ LogP ≤ 5 2.84
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 552.7
  • LogP ≤ 5 2.84
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 7
Veber's rules Fail
  • Rotatable bonds ≤ 10 12
  • TPSA ≤ 140 Ų 113.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC(C)(C)[C@H](NC(=O)[C@H](CC1CCCC1)CN(O)C=O)C(=O)c1cc(F)c(F)cc1N1CCN(CCO)CC1
InChI 
InChI=1S/C28H42F2N4O5/c1-28(2,3)26(31-27(38)20(17-34(39)18-36)14-19-6-4-5-7-19)25(37)21-15-22(29)23(30)16-24(21)33-10-8-32(9-11-33)12-13-35/h15-16,18-20,26,35,39H,4-14,17H2,1-3H3,(H,31,38)/t20-,26-/m1/s1
InChIKey 
GNMHZXHBDNRMPA-FQRUVTKNSA-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)