Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 45.72 kDa 
• Atom Count: 3166 
• Modelled Residue Count: 377 
• Deposited Residue Count: 402 
• Unique protein chains: 1

2OHU

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

• PDB DOI: 10.2210/pdb2OHU/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: 2.35 Å
• R-Value Free: 0.248 
• R-Value Work: 0.195 
• R-Value Observed: 0.198 

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:  
  2OHP, 2OHQ, 2OHR, 2OHS, 2OHT, 2OHU


• 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

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
UniProt & NIH Common Fund Data Resources
Find proteins for P56817 (Homo sapiens) Explore P56817  Go to UniProtKB:  P56817
PHAROS:  P56817

Small Molecules

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

Binding Affinity Annotations
ID	Source	Binding Affinity
IP7	Binding MOAD:  2OHU	IC50: 4200 (nM) from 1 assay(s)
	PDBBind:  2OHU	IC50: 4200 (nM) from 1 assay(s)
	BindingDB:  2OHU	IC50: 4200 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.248 
• R-Value Work: 0.195 
• R-Value Observed: 0.198 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.162	α = 90
b = 102.162	β = 90
c = 168.385	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	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
• Version 1.4: 2021-10-20
  Changes: Advisory, Database references, Derived calculations