5HE5

BACE-1 in complex with (7aR)-7a-(5-cyanothiophen-2-yl)-6-(5-fluoro-4-methyl-6-(methylamino)pyrimidin-2-yl)-3-methyl-4-oxooctahydro-2H-pyrrolo[3,4-d]pyrimidin-2-iminium

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.186 

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Ligand Structure Quality Assessment 


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Literature

Structure-Based Design of an Iminoheterocyclic beta-Site Amyloid Precursor Protein Cleaving Enzyme (BACE) Inhibitor that Lowers Central A beta in Nonhuman Primates.

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

(2016) J Med Chem 59: 3231-3248

  • DOI: 10.1021/acs.jmedchem.5b01995
  • Primary Citation of Related Structures:  
    5HD0, 5HDU, 5HDV, 5HDX, 5HDZ, 5HE4, 5HE5, 5HE7

  • PubMed Abstract: 

    • We describe successful efforts to optimize the in vivo profile and address off-target liabilities of a series of BACE1 inhibitors represented by 6 that embodies the recently validated fused pyrrolidine iminopyrimidinone scaffold. Employing structure-based design, truncation of the cyanophenyl group of 6 that binds in the S3 pocket of BACE1 followed by modification of the thienyl group in S1 was pursued ...

    We describe successful efforts to optimize the in vivo profile and address off-target liabilities of a series of BACE1 inhibitors represented by 6 that embodies the recently validated fused pyrrolidine iminopyrimidinone scaffold. Employing structure-based design, truncation of the cyanophenyl group of 6 that binds in the S3 pocket of BACE1 followed by modification of the thienyl group in S1 was pursued. Optimization of the pyrimidine substituent that binds in the S2'-S2″ pocket of BACE1 remediated time-dependent CYP3A4 inhibition of earlier analogues in this series and imparted high BACE1 affinity. These efforts resulted in the discovery of difluorophenyl analogue 9 (MBi-4), which robustly lowered CSF and cortex Aβ40 in both rats and cynomolgus monkeys following a single oral dose. Compound 9 represents a unique molecular shape among BACE inhibitors reported to potently lower central Aβ in nonrodent preclinical species.

    Organizational Affiliation: 

    Department of Global Chemistry, ‡Department of Neuroscience, §Department of Safety Assessment and Laboratory Animal Research, ∥Department of Discovery Pharmaceutical Sciences, and ⊥Department of Pharmacokinetics, Pharmacodynamics, and Drug Metabolism, Merck Research Laboratories , 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-secretase 1A, B414Homo 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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
60S
Query on 60S
Download Ideal Coordinates CCD File 
D [auth A],
F [auth B]		5-{(2E,4aR,7aR)-6-[5-fluoro-4-methyl-6-(methylamino)pyrimidin-2-yl]-2-imino-3-methyl-4-oxooctahydro-7aH-pyrrolo[3,4-d]pyrimidin-7a-yl}thiophene-2-carbonitrile
C18 H19 F N8 O S
ZGUINBOSNMEMBB-VOJFVSQTSA-N		 Ligand Interaction
TLA
Query on TLA
Download Ideal Coordinates CCD File 
C [auth A],
E [auth B]		L(+)-TARTARIC ACID
C4 H6 O6
FEWJPZIEWOKRBE-JCYAYHJZSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
60S BindingDB:  5HE5 Ki: 336 (nM) from 1 assay(s)
IC50: 157 (nM) from 1 assay(s)
Binding MOAD:  5HE5 Ki: 336 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.186 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.458α = 90
b = 89.308β = 90
c = 131.437γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
DENZOdata reduction
BUSTERrefinement
AMoREphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

  • Deposited Date: 2016-01-05 
  • Released Date: 2016-03-16 
    • Deposition Author(s): Orth, P.

Revision History  (Full details and data files)

  • Version 1.0: 2016-03-16
    Type: Initial release
  • Version 1.1: 2016-04-27
    Changes: Database references