1XS7

Crystal Structure of a cycloamide-urethane-derived novel inhibitor bound to human brain memapsin 2 (beta-secretase).

• PDB DOI: https://doi.org/10.2210/pdb1XS7/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2004-10-18 Released: 2004-12-21 
• Deposition Author(s): Ghosh, A., Devasamudram, T., Hong, L., DeZutter, C., Xu, X., Weerasena, V., Koelsch, G., Bilcer, G., Tang, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å

Starting Model: experimental

Literature

Structure-based design of cycloamide-urethane-derived novel inhibitors of human brain memapsin 2 (beta-secretase).

Ghosh, A.K., Devasamudram, T., Hong, L., Dezutter, C., Xu, X., Weerasena, V., Koelsch, G., Bilcer, G., Tang, J.

(2005) Bioorg Med Chem Lett 15: 15-20

• PubMed: 15582402 
• DOI: https://doi.org/10.1016/j.bmcl.2004.10.084
• Primary Citation of Related Structures:  
  1XS7


• PubMed Abstract: 
  

  A series of novel macrocyclic amide-urethanes was designed and synthesized based upon the X-ray crystal structure of our lead inhibitor (1, OM99-2 with eight residues) bound to memapsin 2. Ring size and substituent effects have been investigated. Cycloamide-urethanes containing 14- to 16-membered rings exhibited low nanomolar inhibitory potencies against human brain memapsin 2 (beta-secretase).

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Organizational Affiliation: 

Department of Chemistry, University of Illinois at Chicago, 845 West Taylor Street, Chicago, IL 60607, USA. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 44.04 kDa 
• Atom Count: 3,105 
• Modelled Residue Count: 389 
• Deposited Residue Count: 389 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-secretase 1	A [auth D]	389	Homo sapiens	Mutation(s): 0  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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MMI	B [auth D]	N-[(4S,5S,7R)-8-({(S)-1-[(BENZYLAMINO)OXOMETHYL]-2-METHYLPROPYL}AMINO)-5-HYDROXY-2,7-DIMETHYL-8-OXO-OCT-4-YL]-(4S,7S)-4 -ISOPROPYL-2,5,9-TRIOXO-1-OXA-3,6,10-TRIAZACYCLOHEXADECANE-7-CARBOXAMIDE C38 H62 N6 O8 QJAPFAZHNSZLJE-CWURXVSKSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
MMI	PDBBind:  1XS7	Ki: 25.1 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.839	α = 90
b = 87.807	β = 89.81
c = 130.644	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-12-21 
Deposition Author(s): Ghosh, A., Devasamudram, T., Hong, L., DeZutter, C., Xu, X., Weerasena, V., Koelsch, G., Bilcer, G., Tang, J.

Revision History  

• Version 1.0: 2004-12-21
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-08-23
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary