Binder profile

3PE

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

Bound to: PA3676 — resistance-nodulation-cell division (RND) efflux transporter

Via homolog PDB 7m4p UniProt Q2FD94 C41H82NO8P
Mol. weight 748.08 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
3PE
PDB
7m4p
UniProt (similar protein)
Q2FD94
Target protein
PA3676

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 748.08 Da
LogP (Crippen) 12.06
H-bond donors 2
H-bond acceptors 8
TPSA 134.38 Ų
Rotatable bonds 41
Aromatic rings 0 / 0
Heavy atoms 51
Fraction sp³ C 0.95
Formula C41H82NO8P

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 Fail 2 violations
  • MW ≤ 500 Da 748.1
  • LogP ≤ 5 12.06
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 8
Veber's rules Fail
  • Rotatable bonds ≤ 10 41
  • TPSA ≤ 140 Ų 134.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCCCCCCCCCCCCCCCCC(=O)OC[C@H](COP(=O)(O)OCCN)OC(=O)CCCCCCCCCCCCCCCCC
InChI 
InChI=1S/C41H82NO8P/c1-3-5-7-9-11-13-15-17-19-21-23-25-27-29-31-33-40(43)47-37-39(38-49-51(45,46)48-36-35-42)50-41(44)34-32-30-28-26-24-22-20-18-16-14-12-10-8-6-4-2/h39H,3-38,42H2,1-2H3,(H,45,46)/t39-/m1/s1
InChIKey 
LVNGJLRDBYCPGB-LDLOPFEMSA-N

Provenance

Annotation context from LigQ_2 search.

Method
LigQ nearest_k
Source
PDB
Binding sites
PF00873

External resources

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

Other binders for this protein

Quick navigation to other ligands bound to PA3676.

PDB 32

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

Ligand PDB entry

ChEMBL 53

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)