Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 45.44 kDa 
• Atom Count: 3203 
• Residue Count: 377 
• Unique protein chains: 1

2OHK

X-ray crystal structure of beta secretase complexed with 1-amino-isoquinoline

• DOI: 10.2210/pdb2OHK/pdb

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


• Deposited: 2007-01-10 Released: 2007-03-13 
• Deposition Author(s): Patel, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.279 
• R-Value Work: 0.221 
• R-Value Observed: 0.224 

Literature

Application of fragment screening by X-ray crystallography to beta-Secretase.

Murray, C.W., Callaghan, O., Chessari, G., Cleasby, A., Congreve, M., Frederickson, M., Hartshorn, M.J., McMenamin, R., Patel, S., Wallis, N.

(2007) J Med Chem 50: 1116-1123

• PubMed: 17315856 
• DOI: 10.1021/jm0611962
• Primary Citation of Related Structures:  
  2OF0, 2OHN, 2OHM, 2OHL, 2OHK


• PubMed Abstract: 
  

This paper describes an application of fragment screening to the aspartyl protease enzyme, beta-secretase (BACE-1), using high throughput X-ray crystallography. Three distinct chemotypes were identified by X-ray crystallography as binding to the catalytic aspartates either via an aminoheterocycle (such as 2-aminoquinoline), a piperidine, or an aliphatic hydroxyl group. The fragment hits were weak inhibitors of BACE-1 in the millimolar range but were of interest because most of them displayed relatively good ligand efficiencies. The aminoheterocycles exhibited a novel recognition motif that has not been seen before with aspartic proteases. Virtual screening around this motif identified an aminopyridine with increased potency and attractive growth points for further elaboration using structure-based drug design. The companion paper illustrates how sub-micromolar inhibitors were developed starting from this fragment.

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Organizational Affiliation: 

Astex Therapeutics Ltd., 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-secretase 1	A	402	Homo sapiens	Mutation(s): 2  Gene Names: BACE1, BACE, KIAA1149 EC: 3.4.23.46
Find proteins for P56817 (Homo sapiens) Explore P56817  Go to UniProtKB:  P56817
NIH Common Fund Data Resources
PHAROS  P56817 GTEx  ENSG00000186318

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1SQ	A	ISOQUINOLIN-1-AMINE C9 H8 N2 OSILBMSORKFRTB-UHFFFAOYSA-N
IOD	A	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M
DMS	A	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
1SQ	IC50:  2000000   nM  BindingDB
1SQ	IC50 :  2000000   nM  PDBBind

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.279 
• R-Value Work: 0.221 
• R-Value Observed: 0.224 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.895	α = 90
b = 102.895	β = 90
c = 168.312	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
MOSFLM	data reduction
CCP4	data scaling
C-SEARCH	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-01-10 
• Released Date: 2007-03-13 
Deposition Author(s): Patel, S.

Revision History 

• Version 1.0: 2007-03-13
  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: Advisory, Refinement description