5F00

CRYSTAL STRUCTURE OF BACE-1 IN COMPLEX WITH 5-[3-[(3-chloro-8-quinolyl)amino]phenyl]-5-methyl-2,6-dihydro-1,4-oxazin-3-amine

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.223 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history. 


Literature

A Real-World Perspective on Molecular Design.

Kuhn, B., Guba, W., Hert, J., Banner, D., Bissantz, C., Ceccarelli, S., Haap, W., Korner, M., Kuglstatter, A., Lerner, C., Mattei, P., Neidhart, W., Pinard, E., Rudolph, M.G., Schulz-Gasch, T., Woltering, T., Stahl, M.

(2016) J Med Chem 59: 4087-4102

  • DOI: 10.1021/acs.jmedchem.5b01875
  • Primary Citation of Related Structures:  
    5EDB, 5EDC, 5EDE, 5EDG, 5EDH, 5EDI, 5EZX, 5EZZ, 5F00, 5F01, 5F02, 5F03, 5I2R

  • PubMed Abstract: 

    • We present a series of small molecule drug discovery case studies where computational methods were prospectively employed to impact Roche research projects, with the aim of highlighting those methods that provide real added value. Our brief accounts encompass a broad range of methods and techniques applied to a variety of enzymes and receptors ...

    We present a series of small molecule drug discovery case studies where computational methods were prospectively employed to impact Roche research projects, with the aim of highlighting those methods that provide real added value. Our brief accounts encompass a broad range of methods and techniques applied to a variety of enzymes and receptors. Most of these are based on judicious application of knowledge about molecular conformations and interactions: filling of lipophilic pockets to gain affinity or selectivity, addition of polar substituents, scaffold hopping, transfer of SAR, conformation analysis, and molecular overlays. A case study of sequence-driven focused screening is presented to illustrate how appropriate preprocessing of information enables effective exploitation of prior knowledge. We conclude that qualitative statements enabling chemists to focus on promising regions of chemical space are often more impactful than quantitative prediction.

    Organizational Affiliation: 

    Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd. , Grenzacherstrasse 124, 4070 Basel, Switzerland.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-secretase 1A390Homo sapiensMutation(s): 0 
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
5T8
Query on 5T8
Download Ideal Coordinates CCD File 
E [auth A](5~{R})-5-[3-[(3-chloranylquinolin-8-yl)amino]phenyl]-5-methyl-2,6-dihydro-1,4-oxazin-3-amine
C20 H19 Cl N4 O
MISZEAYFRRVHET-FQEVSTJZSA-N		 Ligand Interaction
DMS
Query on DMS
Download Ideal Coordinates CCD File 
D [auth A]DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N		 Ligand Interaction
NA
Query on NA
Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]		SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
5T8 BindingDB:  5F00 IC50: 250 (nM) from 1 assay(s)
Binding MOAD:  5F00 IC50: 250 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.223 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.504α = 90
b = 103.504β = 90
c = 169.212γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XPREPdata scaling
REFMACphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-02-24
    Type: Initial release
  • Version 1.1: 2016-05-25
    Changes: Database references
  • Version 1.2: 2017-11-29
    Changes: Database references