Ligand profile

THY

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

Bound to: VK055_2182 — 1-deoxy-D-xylulose-5-phosphate synthase

Via homolog PDB 2bev UniProt P21953 Formula C₁₇H₂₈N₄O₈P₂S
Mol. weight 510.45 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
THY
PDB
2bev
UniProt (similar protein)
P21953
Target protein
VK055_2182

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 510.45 Da
LogP (Crippen) 2.14
H-bond donors 5
H-bond acceptors 9
TPSA 189.20 Ų
Rotatable bonds 11
Aromatic rings 2 / 2
Heavy atoms 32
Fraction sp³ C 0.53
Formula C₁₇H₂₈N₄O₈P₂S

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 189.2
  • −1 ≤ LogP ≤ 5 2.14
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 510.4
  • LogP ≤ 5 2.14
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 9
Veber's rules Fail
  • Rotatable bonds ≤ 10 11
  • TPSA ≤ 140 Ų 189.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC[C@H](C)[C-](c1[n+](c(c(s1)CCO[P@](=O)(O)OP(=O)(O)O)C)Cc2cnc(nc2N)C)O
InChI 
InChI=1S/C17H28N4O8P2S/c1-5-10(2)15(22)17-21(9-13-8-19-12(4)20-16(13)18)11(3)14(32-17)6-7-28-31(26,27)29-30(23,24)25/h8,10,22H,5-7,9H2,1-4H3,(H,26,27)(H2,18,19,20)(H2,23,24,25)/t10-/m0/s1
InChIKey 
MZVVOGXJVCPANP-JTQLQIEISA-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
PF00676' 'PF02779

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_2182.

PDB 12

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

Ligand PDB entry

ChEMBL 30

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)