Ligand profile

8PA

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

Bound to: VK055_4429 — thiamine pyrophosphate enzyme, C-terminal TPP binding domain protein

Via homolog PDB 3f6b UniProt P20906 Formula C₂₀H₂₆N₅O₈P₂S⁺
Mol. weight 558.47 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
8PA
PDB
3f6b
UniProt (similar protein)
P20906
Target protein
VK055_4429

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 558.47 Da
LogP (Crippen) 1.98
H-bond donors 5
H-bond acceptors 10
TPSA 202.09 Ų
Rotatable bonds 11
Aromatic rings 3 / 3
Heavy atoms 36
Fraction sp³ C 0.30
Formula C₂₀H₂₆N₅O₈P₂S⁺

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 202.1
  • −1 ≤ LogP ≤ 5 1.98
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 558.5
  • LogP ≤ 5 1.98
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 10
Veber's rules Fail
  • Rotatable bonds ≤ 10 11
  • TPSA ≤ 140 Ų 202.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1c(sc([n+]1Cc2cnc(nc2N)C)[C@H](\C=C\c3cccnc3)O)CCO[P@](=O)(O)OP(=O)(O)O
InChI 
InChI=1S/C20H25N5O8P2S/c1-13-18(7-9-32-35(30,31)33-34(27,28)29)36-20(17(26)6-5-15-4-3-8-22-10-15)25(13)12-16-11-23-14(2)24-19(16)21/h3-6,8,10-11,17,26H,7,9,12H2,1-2H3,(H4-,21,23,24,27,28,29,30,31)/p+1/b6-5+/t17-/m0/s1
InChIKey 
HUCLASQGRJZNFE-RTRPANQVSA-O

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
PF00205' 'PF02775' 'PF02776

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_4429.

PDB 33

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

Ligand PDB entry

ChEMBL 5

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)