4I12

Design and synthesis of thiophene dihydroisoquinolins as novel BACE-1 inhibitors


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.231 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Design and synthesis of thiophene dihydroisoquinolines as novel BACE1 inhibitors.

Xu, Y.Z.Yuan, S.Bowers, S.Hom, R.K.Chan, W.Sham, H.L.Zhu, Y.L.Beroza, P.Pan, H.Brecht, E.Yao, N.Lougheed, J.Yan, J.Tam, D.Ren, Z.Ruslim, L.Bova, M.P.Artis, D.R.

(2013) Bioorg Med Chem Lett 23: 3075-3080

  • DOI: 10.1016/j.bmcl.2013.03.009
  • Primary Citation of Related Structures:  
    4I0D, 4I0E, 4I0F, 4I12, 4I1C

  • PubMed Abstract: 
  • Utilizing a structure based design approach, combined with extensive medicinal chemistry execution, highly selective, potent and novel BACE1 inhibitor 8 (BACE1 Alpha assay IC50=8nM) was made from a weak μM potency hit in an extremely efficient way. The detailed SAR and general design approaches will be discussed ...

    Utilizing a structure based design approach, combined with extensive medicinal chemistry execution, highly selective, potent and novel BACE1 inhibitor 8 (BACE1 Alpha assay IC50=8nM) was made from a weak μM potency hit in an extremely efficient way. The detailed SAR and general design approaches will be discussed.


    Organizational Affiliation

    Department of Chemical Sciences, Elan Pharmaceuticals, 180 Oyster Point Boulevard, South San Francisco, CA 94080, USA. ying_zi_xu@yahoo.com



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-secretase 1A406Homo sapiensMutation(s): 0 
Gene Names: BACE1BACEKIAA1149
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1BC (Subject of Investigation/LOI)
Query on 1BC

Download Ideal Coordinates CCD File 
B [auth A]2-{(1S)-1-{[(1Z)-6-chloro-3,3-dimethyl-3,4-dihydroisoquinolin-1(2H)-ylidene]amino}-2-[2-propyl-4-(1H-pyrazol-4-yl)thiophen-3-yl]ethyl}pyrimidin-4(5H)-one
C27 H29 Cl N6 O S
SHQGADSMADPNBQ-QFIPXVFZSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A], D [auth A], E [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
F [auth A], G [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
1BC PDBBind:  4I12 IC50: 406 (nM) from 1 assay(s)
Binding MOAD:  4I12 IC50: 4.00e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.231 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.458α = 90
b = 103.122β = 90
c = 98.835γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
REFMACrefinement
CrystalCleardata reduction
CrystalCleardata scaling
REFMACphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-03-06
    Type: Initial release
  • Version 1.1: 2013-07-03
    Changes: Database references
  • Version 1.2: 2018-01-24
    Changes: Structure summary