Binder profile

2DE

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

Bound to: PA4569 — octaprenyl-diphosphate synthase

Via homolog PDB 3aqc UniProt O66129 C14H26O7P2
Mol. weight 368.30 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
2DE
PDB
3aqc
UniProt (similar protein)
O66129
Target protein
PA4569

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 368.30 Da
LogP (Crippen) 4.24
H-bond donors 3
H-bond acceptors 4
TPSA 113.29 Ų
Rotatable bonds 11
Aromatic rings 0 / 0
Heavy atoms 23
Fraction sp³ C 0.57
Formula C14H26O7P2

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.

Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 368.3
  • LogP ≤ 5 4.24
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 4
Veber's rules Fail
  • Rotatable bonds ≤ 10 11
  • TPSA ≤ 140 Ų 113.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC(=CCC/C(=C/CC/C=C/CO[P@](=O)(O)OP(=O)(O)O)/C)C
InChI 
InChI=1S/C14H26O7P2/c1-13(2)9-8-11-14(3)10-6-4-5-7-12-20-23(18,19)21-22(15,16)17/h5,7,9-10H,4,6,8,11-12H2,1-3H3,(H,18,19)(H2,15,16,17)/b7-5+,14-10+
InChIKey 
AFSHNJXUHHFZPQ-XOBXVUKQSA-N

Provenance

Annotation context from LigQ_2, the internal TPW step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ nearest_k
Source
PDB
Binding sites
PF00348' 'PF22538

External resources

Open this ligand in third-party databases and cheminformatics tools.

Other binders for this protein

Quick navigation to other ligands bound to PA4569.

PDB 4

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

Ligand PDB entry

ChEMBL 3

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)