4J0T

CRYSTAL STRUCTURE OF BACE-1 IN COMPLEX WITH 5-Ethoxy-pyridine-2-carboxylic acid [3-((R)-2-amino-5,5-difluoro-4-methyl-5,6-dihydro-4H-[1,3]oxazin-4-yl)-4-fluoro-phenyl]-amide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.210
  • R-Value Work: 0.165

Literature

Macromolecules
Sequence Display for 4J0T

Classification: HYDROLASE / HYDROLASE INHIBITOR

Total Structure Weight: 46086.50

Macromolecule Entities
Molecule Chains Length Organism Details
Beta-secretase 1 A 409 Homo sapiens EC#: 3.4.23.46 IUBMB 4.3.1.23 IUBMB
Mutation: K307A
Gene Name(s): BACE1 Gene View BACE KIAA1149
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
6T9
Query on 6T9

A 5-Ethoxy-pyridine-2-carboxylic acid [3-((R)- 2-amino-5,5-difluoro-4-methyl-5,6-dihydro- 4H-[1,3]oxazin-4-yl)-4-fluoro-phenyl]-amide
C19 H19 F3 N4 O3
DWKGLYKXNUIYDM-GOSISDBHSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
DMS
Query on DMS

A DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

A SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
6T9 IC50: 184 - 480 nM (99) BindingDB

IC50: 148 nM  BindingMOAD
IC50: 184 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.210
  • R-Value Work: 0.165
  • Space Group: P 61 2 2

Unit Cell:

Length (Å) Angle (°)
a = 102.22 α = 90.00
b = 102.22 β = 90.00
c = 170.66 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2013-01-31
  • Released Date: 2013-05-01
  • Deposition author(s): Kuglstatter, A., Stihle, M.

Revision History

  • Version 1_0: 2013-05-01

    Type: Initial release

  • Version 1_1: 2013-06-19

    Type: Database references

  • Version 1_2: 2017-11-15

    Type: Refinement description