Ligand profile

PTK

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

Bound to: VK055_0078 — pyruvate kinase

Via homolog PDB 3is4 UniProt Q27686 Formula C₁₆H₁₀O₁₂S₄
Mol. weight 522.51 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
PTK
PDB
3is4
UniProt (similar protein)
Q27686
Target protein
VK055_0078

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 522.51 Da
LogP (Crippen) 1.57
H-bond donors 4
H-bond acceptors 8
TPSA 217.48 Ų
Rotatable bonds 4
Aromatic rings 4 / 4
Heavy atoms 32
Fraction sp³ C 0.00
Formula C₁₆H₁₀O₁₂S₄

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 217.5
  • −1 ≤ LogP ≤ 5 1.57
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 522.5
  • LogP ≤ 5 1.57
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 8
Veber's rules Fail
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 217.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1cc2c(cc(c3c2c4c1c(cc(c4cc3)S(=O)(=O)O)S(=O)(=O)O)S(=O)(=O)O)S(=O)(=O)O
InChI 
InChI=1S/C16H10O12S4/c17-29(18,19)11-5-13(31(23,24)25)9-3-4-10-14(32(26,27)28)6-12(30(20,21)22)8-2-1-7(11)15(9)16(8)10/h1-6H,(H,17,18,19)(H,20,21,22)(H,23,24,25)(H,26,27,28)
InChIKey 
CZLSHVQVNDDHDQ-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
PF00224

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_0078.

PDB 9

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

Ligand PDB entry

ChEMBL 54

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)