Ligand profile

9XN

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

Bound to: VK055_4003 — urease, alpha subunit

Via homolog PDB 5ol4 UniProt P41020 Formula H₄NO₂PS
Mol. weight 113.08 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
9XN
PDB
5ol4
UniProt (similar protein)
P41020
Target protein
VK055_4003

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 113.08 Da
LogP (Crippen) -0.85
H-bond donors 3
H-bond acceptors 1
TPSA 66.48 Ų
Rotatable bonds 0
Aromatic rings 0 / 0
Heavy atoms 5
Fraction sp³ C 0.00
Formula H₄NO₂PS

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 66.5
  • −1 ≤ LogP ≤ 5 -0.85
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 113.1
  • LogP ≤ 5 -0.85
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 1
Veber's rules Pass
  • Rotatable bonds ≤ 10 0
  • TPSA ≤ 140 Ų 66.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
NP(=S)(O)O
InChI 
InChI=1S/H4NO2PS/c1-4(2,3)5/h(H4,1,2,3,5)
InChIKey 
RJBIAAZJODIFHR-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)