Ligand profile

TOD

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

Bound to: VK055_2794 — pepA Transcriptional Repressor, Aminopeptidase A/I

Via homolog PDB 4x2t UniProt Q8IL11 Formula C₁₆H₂₂N₂O₆
Mol. weight 338.36 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
TOD
PDB
4x2t
UniProt (similar protein)
Q8IL11
Target protein
VK055_2794

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 338.36 Da
LogP (Crippen) 0.46
H-bond donors 5
H-bond acceptors 5
TPSA 135.96 Ų
Rotatable bonds 8
Aromatic rings 1 / 1
Heavy atoms 24
Fraction sp³ C 0.44
Formula C₁₆H₂₂N₂O₆

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 136.0
  • −1 ≤ LogP ≤ 5 0.46
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 338.4
  • LogP ≤ 5 0.46
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 136.0
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC(C)C[C@H]([C@@H](C(=O)NO)O)C(=O)N[C@@H](c1ccccc1)C(=O)O
InChI 
InChI=1S/C16H22N2O6/c1-9(2)8-11(13(19)15(21)18-24)14(20)17-12(16(22)23)10-6-4-3-5-7-10/h3-7,9,11-13,19,24H,8H2,1-2H3,(H,17,20)(H,18,21)(H,22,23)/t11-,12+,13+/m1/s1
InChIKey 
FIVIXKOBUJPPEI-AGIUHOORSA-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
PF00883

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_2794.

PDB 9

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)