Ligand profile

DBX

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

Bound to: VK055_4003 — urease, alpha subunit

Via homolog PDB 5fsd UniProt P41020 Formula C₆H₆O₅S
Mol. weight 190.18 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
DBX
PDB
5fsd
UniProt (similar protein)
P41020
Target protein
VK055_4003

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 190.18 Da
LogP (Crippen) 0.34
H-bond donors 3
H-bond acceptors 4
TPSA 94.83 Ų
Rotatable bonds 1
Aromatic rings 1 / 1
Heavy atoms 12
Fraction sp³ C 0.00
Formula C₆H₆O₅S

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 94.8
  • −1 ≤ LogP ≤ 5 0.34
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 190.2
  • LogP ≤ 5 0.34
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 1
  • TPSA ≤ 140 Ų 94.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1cc(c(cc1O)S(=O)(=O)O)O
InChI 
InChI=1S/C6H6O5S/c7-4-1-2-5(8)6(3-4)12(9,10)11/h1-3,7-8H,(H,9,10,11)
InChIKey 
IKQCSJBQLWJEPU-UHFFFAOYSA-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
PF01979

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_4003.

PDB 8

Ligands co-crystallized with this protein (structural evidence).

Ligand PDB entry

ZINC 50

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)