Ligand profile

S6P

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

Bound to: HT085_RS00175 — 1-deoxy-D-xylulose-5-phosphate synthase

Via homolog PDB 4kxu UniProt P29401 Formula C₆H₁₅O₉P
Mol. weight 262.15 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
S6P
PDB
4kxu
UniProt (similar protein)
P29401
Target protein
HT085_RS00175

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 262.15 Da
LogP (Crippen) -3.47
H-bond donors 7
H-bond acceptors 7
TPSA 167.91 Ų
Rotatable bonds 7
Aromatic rings 0 / 0
Heavy atoms 16
Fraction sp³ C 1.00
Formula C₆H₁₅O₉P

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 167.9
  • −1 ≤ LogP ≤ 5 -3.47
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 262.2
  • LogP ≤ 5 -3.47
  • H-bond donors ≤ 5 7
  • H-bond acceptors ≤ 10 7
Veber's rules Fail
  • Rotatable bonds ≤ 10 7
  • TPSA ≤ 140 Ų 167.9
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C([C@@H]([C@H]([C@@H]([C@@H](COP(=O)(O)O)O)O)O)O)O
InChI 
InChI=1S/C6H15O9P/c7-1-3(8)5(10)6(11)4(9)2-15-16(12,13)14/h3-11H,1-2H2,(H2,12,13,14)/t3-,4+,5+,6+/m0/s1
InChIKey 
GACTWZZMVMUKNG-SLPGGIOYSA-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
PF00456' '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 HT085_RS00175.

PDB 9

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)