2PH6

Crystal Structure of Human Beta Secretase Complexed with inhibitor

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.195 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history. 


Literature

Design, synthesis, and SAR of macrocyclic tertiary carbinamine BACE-1 inhibitors.

Lindsley, S.R., Moore, K.P., Rajapakse, H.A., Selnick, H.G., Young, M.B., Zhu, H., Munshi, S., Kuo, L., McGaughey, G.B., Colussi, D., Crouthamel, M.C., Lai, M.T., Pietrak, B., Price, E.A., Sankaranarayanan, S., Simon, A.J., Seabrook, G.R., Hazuda, D.J., Pudvah, N.T., Hochman, J.H., Graham, S.L., Vacca, J.P., Nantermet, P.G.

(2007) Bioorg Med Chem Lett 17: 4057-4061

  • DOI: https://doi.org/10.1016/j.bmcl.2007.04.072
  • Primary Citation of Related Structures:  
    2PH6

  • PubMed Abstract: 

    • This Letter describes the design and synthesis of tertiary carbinamine macrocyclic inhibitors of the beta-secretase (BACE-1) enzyme. These macrocyclic inhibitors, some of which incorporate novel P2 substituents, display a 2- to 100-fold increase in potency relative to the previously described acyclic analogs while affording greater stability ...

    This Letter describes the design and synthesis of tertiary carbinamine macrocyclic inhibitors of the beta-secretase (BACE-1) enzyme. These macrocyclic inhibitors, some of which incorporate novel P2 substituents, display a 2- to 100-fold increase in potency relative to the previously described acyclic analogs while affording greater stability.

    Organizational Affiliation: 

    Department of Medicinal Chemistry, Merck Research Laboratories, PO Box 4, West Point, PA 19486, USA.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-secretase 1405Homo sapiensMutation(s): 2 
Gene Names: BACE1, BACE, KIAA1149
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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP56817
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
712
Query on 712
Download Ideal Coordinates CCD File 
C [auth A]3-({[(1R)-1-(4-FLUOROPHENYL)ETHYL]AMINO}CARBONYL)-5-[METHYL(METHYLSULFONYL)AMINO]BENZYL ALPHA-METHYL-D-PHENYLALANINATE
C28 H32 F N3 O5 S
PTQRJCCBUDSHTQ-WHLCRQNOSA-N		 Ligand Interaction
SO4
Query on SO4
Download Ideal Coordinates CCD File 
B [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
712 BindingDB:  2PH6 IC50: min: 19, max: 163 (nM) from 3 assay(s)
Binding MOAD:  2PH6 IC50: 27 (nM) from 1 assay(s)
PDBBind:  2PH6 IC50: 27 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.195 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.795α = 90
b = 127.13β = 90
c = 76.205γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History 

Deposition Data

  • Released Date: 2007-06-05 
    • Deposition Author(s): Munshi, S.

Revision History  (Full details and data files)

  • Version 1.0: 2007-06-05
    Type: Initial release
  • Version 1.1: 2007-10-10
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2021-10-20
    Changes: Database references, Derived calculations
  • Version 1.4: 2023-08-30
    Changes: Data collection, Refinement description