Ligand profile

ZED

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

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

Via homolog PDB 2ewb UniProt P00727 Formula C₁₅H₁₉NO₃S₂
Mol. weight 325.46 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZED
PDB
2ewb
UniProt (similar protein)
P00727
Target protein
VK055_2794

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 325.46 Da
LogP (Crippen) 2.40
H-bond donors 2
H-bond acceptors 4
TPSA 57.61 Ų
Rotatable bonds 5
Aromatic rings 1 / 2
Heavy atoms 21
Fraction sp³ C 0.47
Formula C₁₅H₁₉NO₃S₂

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 57.6
  • −1 ≤ LogP ≤ 5 2.40
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 325.5
  • LogP ≤ 5 2.40
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 57.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C[C@H](CS)C(=O)N1C[C@H](C[C@H]1C(=O)O)Sc2ccccc2
InChI 
InChI=1S/C15H19NO3S2/c1-10(9-20)14(17)16-8-12(7-13(16)15(18)19)21-11-5-3-2-4-6-11/h2-6,10,12-13,20H,7-9H2,1H3,(H,18,19)/t10-,12+,13+/m1/s1
InChIKey 
UQWLOWFDKAFKAP-WXHSDQCUSA-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)