4XRY

Human Cytochrome P450 2D6 BACE1 Inhibitor 5 Complex

  • Classification: OXIDOREDUCTASE
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli
  • Mutation(s): No 
  • Membrane Protein: Yes  OPM

  • Deposited: 2015-01-21 Released: 2015-05-20 
  • Deposition Author(s): Johnson, E.F., Fan, Y.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.210 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Utilizing Structures of CYP2D6 and BACE1 Complexes To Reduce Risk of Drug-Drug Interactions with a Novel Series of Centrally Efficacious BACE1 Inhibitors.

Brodney, M.A.Beck, E.M.Butler, C.R.Barreiro, G.Johnson, E.F.Riddell, D.Parris, K.Nolan, C.E.Fan, Y.Atchison, K.Gonzales, C.Robshaw, A.E.Doran, S.D.Bundesmann, M.W.Buzon, L.Dutra, J.Henegar, K.LaChapelle, E.Hou, X.Rogers, B.N.Pandit, J.Lira, R.Martinez-Alsina, L.Mikochik, P.Murray, J.C.Ogilvie, K.Price, L.Sakya, S.M.Yu, A.Zhang, Y.O'Neill, B.T.

(2015) J Med Chem 58: 3223-3252

  • DOI: 10.1021/acs.jmedchem.5b00191
  • Primary Citation of Related Structures:  
    4XRY, 4XRZ, 4XXS

  • PubMed Abstract: 
  • In recent years, the first generation of β-secretase (BACE1) inhibitors advanced into clinical development for the treatment of Alzheimer's disease (AD). However, the alignment of drug-like properties and selectivity remains a major challenge. Herein, we describe the discovery of a novel class of potent, low clearance, CNS penetrant BACE1 inhibitors represented by thioamidine 5 ...

    In recent years, the first generation of β-secretase (BACE1) inhibitors advanced into clinical development for the treatment of Alzheimer's disease (AD). However, the alignment of drug-like properties and selectivity remains a major challenge. Herein, we describe the discovery of a novel class of potent, low clearance, CNS penetrant BACE1 inhibitors represented by thioamidine 5. Further profiling suggested that a high fraction of the metabolism (>95%) was due to CYP2D6, increasing the potential risk for victim-based drug-drug interactions (DDI) and variable exposure in the clinic due to the polymorphic nature of this enzyme. To guide future design, we solved crystal structures of CYP2D6 complexes with substrate 5 and its corresponding metabolic product pyrazole 6, which provided insight into the binding mode and movements between substrate/inhibitor complexes. Guided by the BACE1 and CYP2D6 crystal structures, we designed and synthesized analogues with reduced risk for DDI, central efficacy, and improved hERG therapeutic margins.


    Organizational Affiliation

    ∇WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome P450 2D6A, B, C, D479Homo sapiensMutation(s): 0 
Gene Names: CYP2D6CYP2DL1
EC: 1.14.14.1 (PDB Primary Data), 1.14.14 (UniProt)
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P10635 (Homo sapiens)
Explore P10635 
Go to UniProtKB:  P10635
PHAROS:  P10635
GTEx:  ENSG00000100197 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP10635
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
E [auth A],
K [auth B],
P [auth C],
W [auth D]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
SI5
Query on SI5

Download Ideal Coordinates CCD File 
F [auth A],
L [auth B],
Q [auth C],
X [auth D]
(4aR,6R,8aS)-8a-(2,4-difluorophenyl)-6-(1-methyl-1H-pyrazol-4-yl)-4,4a,5,6,8,8a-hexahydropyrano[3,4-d][1,3]thiazin-2-amine
C17 H18 F2 N4 O S
JYDYMWJEZLKIBS-CXMBCZLWSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
AA [auth D],
BA [auth D],
CA [auth D],
G [auth A],
H [auth A],
AA [auth D],
BA [auth D],
CA [auth D],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
M [auth B],
N [auth B],
O [auth B],
R [auth C],
S [auth C],
T [auth C],
U [auth C],
V [auth C],
Y [auth D],
Z [auth D]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
SI5 BindingDB:  4XRY IC50: 1.39e+4 (nM) from 1 assay(s)
Binding MOAD:  4XRY IC50: 1.39e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.210 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.064α = 90
b = 192.341β = 90
c = 247.304γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2015-01-21 
  • Released Date: 2015-05-20 
  • Deposition Author(s): Johnson, E.F., Fan, Y.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM031001

Revision History  (Full details and data files)

  • Version 1.0: 2015-05-20
    Type: Initial release
  • Version 1.1: 2017-09-27
    Changes: Author supporting evidence, Database references, Derived calculations, Source and taxonomy, Structure summary
  • Version 1.2: 2019-12-25
    Changes: Author supporting evidence