Ligand profile

HJT

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

Bound to: VK055_2588 — phosphoserine phosphatase SerB

Via homolog PDB 6q6j UniProt P78330 Formula C₄H₉NO₅S
Mol. weight 183.18 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
HJT
PDB
6q6j
UniProt (similar protein)
P78330
Target protein
VK055_2588

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 183.18 Da
LogP (Crippen) -1.32
H-bond donors 3
H-bond acceptors 4
TPSA 117.69 Ų
Rotatable bonds 4
Aromatic rings 0 / 0
Heavy atoms 11
Fraction sp³ C 0.75
Formula C₄H₉NO₅S

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 117.7
  • −1 ≤ LogP ≤ 5 -1.32
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 183.2
  • LogP ≤ 5 -1.32
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 117.7
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C(CS(=O)(=O)O)[C@@H](C(=O)O)N
InChI 
InChI=1S/C4H9NO5S/c5-3(4(6)7)1-2-11(8,9)10/h3H,1-2,5H2,(H,6,7)(H,8,9,10)/t3-/m0/s1
InChIKey 
VBOQYPQEPHKASR-VKHMYHEASA-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
PF00702

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_2588.

PDB 6

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)