Ligand profile

D7K

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 3fsj UniProt P20906 Formula C₂₀H₂₈N₄O₁₁P₃S⁺
Mol. weight 625.45 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
D7K
PDB
3fsj
UniProt (similar protein)
P20906
Target protein
VK055_4429

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 625.45 Da
LogP (Crippen) 1.87
H-bond donors 6
H-bond acceptors 11
TPSA 235.73 Ų
Rotatable bonds 12
Aromatic rings 3 / 3
Heavy atoms 39
Fraction sp³ C 0.35
Formula C₂₀H₂₈N₄O₁₁P₃S⁺

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 235.7
  • −1 ≤ LogP ≤ 5 1.87
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 625.5
  • LogP ≤ 5 1.87
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 11
Veber's rules Fail
  • Rotatable bonds ≤ 10 12
  • TPSA ≤ 140 Ų 235.7
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1c(sc([n+]1Cc2cnc(nc2N)C)[C@@](c3ccccc3)(O)[P@@](=O)(O)OC)CCO[P@@](=O)(O)OP(=O)(O)O
InChI 
InChI=1S/C20H27N4O11P3S/c1-13-17(9-10-34-38(31,32)35-37(28,29)30)39-19(24(13)12-15-11-22-14(2)23-18(15)21)20(25,36(26,27)33-3)16-7-5-4-6-8-16/h4-8,11,25H,9-10,12H2,1-3H3,(H5-,21,22,23,26,27,28,29,30,31,32)/p+1/t20-/m0/s1
InChIKey 
NEEQBMRCDKRNBV-FQEVSTJZSA-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)