2HM1 | pdb_00002hm1

Crystal Structure of human beta-secretase (BACE) in the presence of an inhibitor (2)

• PDB DOI: https://doi.org/10.2210/pdb2HM1/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2006-07-10 Released: 2007-01-23 
• Deposition Author(s): Benson, T.E., Prince, D.B., Tomasselli, A.G., Emmons, T.L., Paddock, D.J.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.251 (Depositor), 0.242 (DCC) 
• R-Value Work: 
  0.204 (Depositor), 0.200 (DCC) 

Literature

Design of potent inhibitors of human beta-secretase. Part 2.

Freskos, J.N., Fobian, Y.M., Benson, T.E., Moon, J.B., Bienkowski, M.J., Brown, D.L., Emmons, T.L., Heintz, R., Laborde, A., McDonald, J.J., Mischke, B.V., Molyneaux, J.M., Mullins, P.B., Bryan Prince, D., Paddock, D.J., Tomasselli, A.G., Winterrowd, G.

(2007) Bioorg Med Chem Lett 17: 78-81

• PubMed: 17049233 
• DOI: https://doi.org/10.1016/j.bmcl.2006.09.091
• Primary Citation Related Structures: 
  2HM1


• PubMed Abstract: 
  

  We describe an optimized series of acyclic hydroxyethylamine transition state isosteres of beta-secretase that incorporates a variety of P(2) side chains that yield potent inhibitors with excellent cellular activity. A 2.2A crystal structure of compound 13 is shown.

---

Organizational Affiliation: 
• Pfizer Inc., 700N. Chesterfield Pkwy., St. Louis, MO 63198, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 46.09 kDa 
• Atom Count: 3,165 
• Modeled Residue Count: 375 
• Deposited Residue Count: 406 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-secretase 1	A	406	Homo sapiens	Mutation(s): 0  Gene Names: 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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LIQ	B [auth A]	N-{(1S)-2-({(1S,2R)-1-(3,5-DIFLUOROBENZYL)-3-[(3-ETHYLBENZYL)AMINO]-2-HYDROXYPROPYL}AMINO)-2-OXO-1-[(PENTYLSULFONYL)METHYL]ETHYL}NICOTINAMIDE C33 H42 F2 N4 O5 S IOTPZWJUHSYLHJ-OJDZSJEKSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.251 (Depositor), 0.242 (DCC) 
• R-Value Work:  0.204 (Depositor), 0.200 (DCC) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.99	α = 90
b = 104.88	β = 94.99
c = 50.06	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-01-23 
Deposition Author(s): Benson, T.E., Prince, D.B., Tomasselli, A.G., Emmons, T.L., Paddock, D.J.

Revision History  

• Version 1.0: 2007-01-23
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2024-10-30
  Changes: Data collection, Database references, Structure summary