4HA5

Structure of BACE Bound to (S)-3-(5-(2-imino-1,4-dimethyl-6-oxohexahydropyrimidin-4-yl)thiophen-3-yl)benzonitrile


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.189 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Design and Validation of Bicyclic Iminopyrimidinones As Beta Amyloid Cleaving Enzyme-1 (BACE1) Inhibitors: Conformational Constraint to Favor a Bioactive Conformation.

Mandal, M.Zhu, Z.Cumming, J.N.Liu, X.Strickland, C.Mazzola, R.D.Caldwell, J.P.Leach, P.Grzelak, M.Hyde, L.Zhang, Q.Terracina, G.Zhang, L.Chen, X.Kuvelkar, R.Kennedy, M.E.Favreau, L.Cox, K.Orth, P.Buevich, A.Voigt, J.Wang, H.Kazakevich, I.McKittrick, B.A.Greenlee, W.Parker, E.M.Stamford, A.W.

(2012) J Med Chem 55: 9331-9345

  • DOI: 10.1021/jm301039c
  • Primary Citation of Related Structures:  
    4H1E, 4H3F, 4H3G, 4H3I, 4H3J, 4HA5

  • PubMed Abstract: 
  • On the basis of our observation that the biaryl substituent of iminopyrimidinone 7 must be in a pseudoaxial conformation to occupy the contiguous S1-S3 subsites of BACE1, we have designed a novel fused bicyclic iminopyrimidinone scaffold intended to favor this bioactive conformation ...

    On the basis of our observation that the biaryl substituent of iminopyrimidinone 7 must be in a pseudoaxial conformation to occupy the contiguous S1-S3 subsites of BACE1, we have designed a novel fused bicyclic iminopyrimidinone scaffold intended to favor this bioactive conformation. Strategic incorporation of a nitrogen atom in the new constrained ring allowed us to develop SAR around the S2' binding pocket and ultimately resulted in analogues with low nanomolar potency for BACE1. In particular, optimization of the prime side substituent led to major improvements in potency by displacement of two conserved water molecules from a region near S2'. Further optimization of the pharmacokinetic properties of this fused pyrrolidine series, in conjunction with facile access to a rat pharmacodynamic model, led to identification of compound 43, which is an orally active, brain penetrant inhibitor that reduces Aβ(40) in the plasma, CSF, and cortex of rats in a dose-dependent manner.


    Organizational Affiliation

    Department of Medicinal Chemistry, Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States. mihirbaran.mandal@merck.com



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-secretase 1A, B414Homo sapiensMutation(s): 0 
Gene Names: BACEBACE1KIAA1149
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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
13W (Subject of Investigation/LOI)
Query on 13W

Download Ideal Coordinates CCD File 
D [auth A], G [auth B]3-{5-[(2E,4S)-2-imino-1,4-dimethyl-6-oxohexahydropyrimidin-4-yl]thiophen-3-yl}benzonitrile
C17 H16 N4 O S
MLNWGLXMDFUREO-KRWDZBQOSA-N
 Ligand Interaction
TLA
Query on TLA

Download Ideal Coordinates CCD File 
C [auth A], E [auth B], F [auth B]L(+)-TARTARIC ACID
C4 H6 O6
FEWJPZIEWOKRBE-JCYAYHJZSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
13W PDBBind:  4HA5 Ki: 58 (nM) from 1 assay(s)
Binding MOAD:  4HA5 Ki: 56 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.189 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.442α = 90
b = 89.616β = 90
c = 131.098γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection
DENZOdata reduction
CNSphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-10-17
    Type: Initial release
  • Version 1.1: 2012-11-21
    Changes: Database references