3UDY | pdb_00003udy

Crystal Structure of BACE with Compound 11


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.308 (Depositor), 0.310 (DCC) 
  • R-Value Work: 
    0.225 (Depositor), 0.229 (DCC) 
  • R-Value Observed: 
    0.230 (Depositor) 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Discovery and optimization of a novel spiropyrrolidine inhibitor of {beta}-secretase (BACE1) through fragment-based drug design.

Efremov, I.V.Vajdos, F.F.Borzilleri, K.A.Capetta, S.Chen, H.Dorff, P.H.Dutra, J.K.Goldstein, S.W.Mansour, M.McColl, A.Noell, S.Oborski, C.E.O'Connell, T.N.O'Sullivan, T.J.Pandit, J.Wang, H.Wei, B.Withka, J.M.

(2012) J Med Chem 55: 9069-9088

  • DOI: https://doi.org/10.1021/jm201715d
  • Primary Citation Related Structures: 
    3UDH, 3UDJ, 3UDK, 3UDM, 3UDN, 3UDP, 3UDQ, 3UDR, 3UDY

  • PubMed Abstract: 

    The aspartyl protease β-secretase, or BACE, has been demonstrated to be a key factor in the proteolytic formation of Aβ-peptide, a major component of plaques in the brains of Alzheimer's disease (AD) patients, and inhibition of this enzyme has emerged as a major strategy for pharmacologic intervention in AD. An X-ray-based fragment screen of Pfizer's proprietary fragment collection has resulted in the identification of a novel BACE binder featuring spiropyrrolidine framework. Although exhibiting only weak inhibitory activity against the BACE enzyme, the small compound was verified by biophysical and NMR-based methods as a bona fide BACE inhibitor. Subsequent optimization of the lead compound, relying heavily on structure-based drug design and computational prediction of physiochemical properties, resulted in a nearly 1000-fold improvement in potency while maintaining ligand efficiency and properties predictive of good permeability and low P-gp liability.


  • Organizational Affiliation
    • Pfizer Worldwide Research, Groton Laboratories, Eastern Point Road, Groton, Connecticut 06340, United States. ivan.efremov@pfizer.com

Macromolecule Content 

  • Total Structure Weight: 46 kDa 
  • Atom Count: 3,492 
  • Modeled Residue Count: 394 
  • Deposited Residue Count: 404 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Beta-secretase 1404Homo sapiensMutation(s): 0 
Gene Names: BACE1BACEKIAA1149
EC: 3.4.23.46
UniProt & NIH Common Fund Data Resources
Find proteins for P56817 (Homo sapiens)
Explore P56817 
Go to UniProtKB:  P56817
PHAROS:  P56817
GTEx:  ENSG00000186318 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP56817
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
09G

Query on 09G



Download:Ideal Coordinates CCD File
B [auth A]3-bromo-4-cyanobenzyl (3S,5'R)-2-oxo-1,2-dihydrospiro[indole-3,3'-pyrrolidine]-5'-carboxylate
C20 H16 Br N3 O3
DJYALAFSFGHFLN-YLJYHZDGSA-N
PEG

Query on PEG



Download:Ideal Coordinates CCD File
E [auth A]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
F [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
C [auth A],
D [auth A],
G [auth A],
H [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.308 (Depositor), 0.310 (DCC) 
  • R-Value Work:  0.225 (Depositor), 0.229 (DCC) 
  • R-Value Observed: 0.230 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.69α = 90
b = 103.964β = 90
c = 99.406γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
autoBUSTERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2012-04-18
    Type: Initial release
  • Version 1.1: 2013-06-19
    Changes: Database references
  • Version 1.2: 2018-04-04
    Changes: Data collection, Refinement description
  • Version 1.3: 2024-11-20
    Changes: Data collection, Database references, Derived calculations, Structure summary