Ligand profile

DT3

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

Bound to: VK055_3698 — phosphoenolpyruvate carboxykinase

Via homolog PDB 1ylh UniProt A6VKV4 Formula C₄H₉O₅S₂⁻
Mol. weight 201.25 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
DT3
PDB
1ylh
UniProt (similar protein)
A6VKV4
Target protein
VK055_3698

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 201.25 Da
LogP (Crippen) -1.82
H-bond donors 3
H-bond acceptors 6
TPSA 97.66 Ų
Rotatable bonds 4
Aromatic rings 0 / 0
Heavy atoms 11
Fraction sp³ C 1.00
Formula C₄H₉O₅S₂⁻

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 97.7
  • −1 ≤ LogP ≤ 5 -1.82
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 201.2
  • LogP ≤ 5 -1.82
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 97.7
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C([C@H]([C@@H](CS(=O)(=O)[O-])O)O)S
InChI 
InChI=1S/C4H10O5S2/c5-3(1-10)4(6)2-11(7,8)9/h3-6,10H,1-2H2,(H,7,8,9)/p-1/t3-,4-/m1/s1
InChIKey 
BJXWUWDPCVAQDI-QWWZWVQMSA-M

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
PF01293

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_3698.

PDB 9

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

Ligand PDB entry

ZINC 6

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

Compound Similarity (Tanimoto)