Ligand profile

LHY

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

Bound to: VK055_3786 — peptide deformylase

Via homolog PDB 6jex UniProt B0VNL8 Formula C₁₀H₁₂N₂O₄
Mol. weight 224.22 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
LHY
PDB
6jex
UniProt (similar protein)
B0VNL8
Target protein
VK055_3786

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 224.22 Da
LogP (Crippen) 0.37
H-bond donors 4
H-bond acceptors 3
TPSA 98.66 Ų
Rotatable bonds 4
Aromatic rings 1 / 1
Heavy atoms 16
Fraction sp³ C 0.20
Formula C₁₀H₁₂N₂O₄

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 98.7
  • −1 ≤ LogP ≤ 5 0.37
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 224.2
  • LogP ≤ 5 0.37
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 3
Veber's rules Pass
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 98.7
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1ccc(cc1)C[C@@H](C(=O)O)NC(=O)NO
InChI 
InChI=1S/C10H12N2O4/c13-9(14)8(11-10(15)12-16)6-7-4-2-1-3-5-7/h1-5,8,16H,6H2,(H,13,14)(H2,11,12,15)/t8-/m0/s1
InChIKey 
IOFPEOPOAMOMBE-QMMMGPOBSA-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
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 11

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)