Ligand profile

POP

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

Bound to: HT085_RS00375 — 4-hydroxy-3-methylbut-2-enyl diphosphate reductase

Via homolog PDB 3f7t UniProt P62623 Formula H₂O₇P₂²⁻
Mol. weight 175.96 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
POP
PDB
3f7t
UniProt (similar protein)
P62623
Target protein
HT085_RS00375

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 175.96 Da
LogP (Crippen) -2.08
H-bond donors 2
H-bond acceptors 5
TPSA 129.95 Ų
Rotatable bonds 2
Aromatic rings 0 / 0
Heavy atoms 9
Fraction sp³ C 0.00
Formula H₂O₇P₂²⁻

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 129.9
  • −1 ≤ LogP ≤ 5 -2.08
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 176.0
  • LogP ≤ 5 -2.08
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 129.9
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
O[P@@](=O)([O-])O[P@@](=O)(O)[O-]
InChI 
InChI=1S/H4O7P2/c1-8(2,3)7-9(4,5)6/h(H2,1,2,3)(H2,4,5,6)/p-2
InChIKey 
XPPKVPWEQAFLFU-UHFFFAOYSA-L

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
PF02401

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_RS00375.

PDB 16

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

Ligand PDB entry

ChEMBL 1

Compounds with measured inhibitory activity on this target (higher pchembl = more potent).

Compound Potency (pchembl)

ZINC 12

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)