2OHK

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

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 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history. 


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

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

  • 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 ...

    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.

    Organizational Affiliation: 

    Astex Therapeutics Ltd., 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom. c.murray@astex-therapeutics.com



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-secretase 1A402Homo sapiensMutation(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
GTEx:  ENSG00000186318 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP56817
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1SQ
Query on 1SQ
Download Ideal Coordinates CCD File 
F [auth A]ISOQUINOLIN-1-AMINE
C9 H8 N2
OSILBMSORKFRTB-UHFFFAOYSA-N		 Ligand Interaction
IOD
Query on IOD
Download Ideal Coordinates CCD File 
B [auth A],
C [auth A],
D [auth A]		IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M		 Ligand Interaction
DMS
Query on DMS
Download Ideal Coordinates CCD File 
E [auth A]DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
1SQ PDBBind:  2OHK IC50: 2.00e+6 (nM) from 1 assay(s)
BindingDB:  2OHK IC50: 2.00e+6 (nM) from 1 assay(s)
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 = 102.895α = 90
b = 102.895β = 90
c = 168.312γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
MOSFLMdata reduction
CCP4data scaling
C-SEARCHphasing

Structure Validation

View Full Validation Report



View more in-depth experimental data

Entry History 

Deposition Data

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

Revision History  (Full details and data files)

  • 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