2PH6 | pdb_00002ph6

Crystal Structure of Human Beta Secretase Complexed with inhibitor

• PDB DOI: https://doi.org/10.2210/pdb2PH6/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2007-04-10 Released: 2007-06-05 
• Deposition Author(s): Munshi, S.

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Experimental Data Snapshot

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

Starting Model: experimental

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

• PubMed: 17482814 
• 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 45.76 kDa 
• Atom Count: 3,176 
• Modelled Residue Count: 371 
• Deposited Residue Count: 405 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-secretase 1	A	405	Homo sapiens	Mutation(s): 2  Gene Names: BACE1, BACE 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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
712	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
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Binding Affinity Annotations
ID	Source	Binding Affinity
712	BindingDB:  2PH6	IC50: min: 19, max: 163 (nM) from 3 assay(s)

Experimental Data & Validation

Experimental Data

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

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.795	α = 90
b = 127.13	β = 90
c = 76.205	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

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

Revision History  

• 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
• Version 1.5: 2024-10-30
  Changes: Structure summary