Ligand profile

1Y7

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

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

Via homolog PDB 4kxx UniProt P29401 Formula C₇H₁₇O₁₀P
Mol. weight 292.18 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
1Y7
PDB
4kxx
UniProt (similar protein)
P29401
Target protein
HT085_RS00175

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 292.18 Da
LogP (Crippen) -4.11
H-bond donors 8
H-bond acceptors 8
TPSA 188.14 Ų
Rotatable bonds 8
Aromatic rings 0 / 0
Heavy atoms 18
Fraction sp³ C 1.00
Formula C₇H₁₇O₁₀P

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 188.1
  • −1 ≤ LogP ≤ 5 -4.11
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 292.2
  • LogP ≤ 5 -4.11
  • H-bond donors ≤ 5 8
  • H-bond acceptors ≤ 10 8
Veber's rules Fail
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 188.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C([C@@H]([C@H]([C@@H]([C@@H]([C@@H](COP(=O)(O)O)O)O)O)O)O)O
InChI 
InChI=1S/C7H17O10P/c8-1-3(9)5(11)7(13)6(12)4(10)2-17-18(14,15)16/h3-13H,1-2H2,(H2,14,15,16)/t3-,4+,5+,6+,7-/m0/s1
InChIKey 
RCCDYOCQCITNBH-CJZRUXIPSA-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)