Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 45721.73 
• Atom Count: 3005 
• Residue Count: 402 
• Unique protein chains: 1

2OHU

X-ray crystal structure of beta secretase complexed with compound 8b

• DOI: 10.2210/pdb2OHU/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): 2 


• 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: 2.35 Å
• R-Value Free: 0.248 
• R-Value Work: 0.195 

Literature

Application of fragment screening by X-ray crystallography to the discovery of aminopyridines as inhibitors of beta-secretase.

Congreve, M., Aharony, D., Albert, J., Callaghan, O., Campbell, J., Carr, R.A., Chessari, G., Cowan, S., Edwards, P.D., Frederickson, M., McMenamin, R., Murray, C.W., Patel, S., Wallis, N.

(2007) J.Med.Chem. 50: 1124-1132

• PubMed: 17315857 
• DOI: 10.1021/jm061197u
• Primary Citation of Related Structures:  
  2OHT, 2OHS, 2OHR, 2OHQ, 2OHP


• PubMed Abstract: 
  

Fragment-based lead discovery has been successfully applied to the aspartyl protease enzyme beta-secretase (BACE-1). Fragment hits that contained an aminopyridine motif binding to the two catalytic aspartic acid residues in the active site of the enzyme were the chemical starting points. Structure-based design approaches have led to identification of low micromolar lead compounds that retain these interactions and additionally occupy adjacent hydrophobic pockets of the active site. These leads form two subseries, for which compounds 4 (IC50 = 25 microM) and 6c (IC50 = 24 microM) are representative. In the latter series, further optimization has led to 8a (IC50 = 690 nM).

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Organizational Affiliation: 

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

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
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) Go to Gene View: BACE1 Go to UniProtKB:  P56817

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
IOD	A	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M
IP7	A	N~3~-[5-(1H-INDOL-6-YL)-2-(PYRIDIN-2-YLMETHOXY)BENZYL]PYRIDINE-2,3-DIAMINE C26 H23 N5 O KMBPJSHPAXOXBT-UHFFFAOYSA-N
DMS	A	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
IP7	IC50: 4200 nM (99) BINDINGDB
IP7	IC50: 4200 nM BINDINGMOAD
IP7	IC50: 4200 nM PDBBIND

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.248 
• R-Value Work: 0.195 
• Space Group: P 6₁ 2 2

Unit Cell:

Length (Å)	Angle (°)
a = 102.162	α = 90.00
b = 102.162	β = 90.00
c = 168.385	γ = 120.00

Software Package:

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

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
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance
• Version 1.3: 2017-10-18
  Type: Advisory, Refinement description