4XX4

Renin in complex with (4S)-4-isopropyl-4-methyl-6-oxo-1-(3-(2-oxo-4-phenylpyrrolidin-1-yl)benzyl)tetrahydropyrimidin-2(1H)-iminium

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.210 

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history. 


Literature

Iminopyrimidinones: a novel pharmacophore for the development of orally active renin inhibitors.

McKittrick, B.A., Caldwell, J.P., Bara, T., Boykow, G., Chintala, M., Clader, J., Czarniecki, M., Courneya, B., Duffy, R., Fleming, L., Giessert, R., Greenlee, W.J., Heap, C., Hong, L., Huang, Y., Iserloh, U., Josien, H., Khan, T., Korfmacher, W., Liang, X., Mazzola, R., Mitra, S., Moore, K., Orth, P., Rajagopalan, M., Roy, S., Sakwa, S., Strickland, C., Vaccaro, H., Voigt, J., Wang, H., Wong, J., Zhang, R., Zych, A.

(2015) Bioorg Med Chem Lett 25: 1592-1596

  • DOI: 10.1016/j.bmcl.2015.02.003
  • Primary Citation of Related Structures:  
    4S1G, 4XX3, 4XX4

  • PubMed Abstract: 

    • The development of renin inhibitors with favorable oral pharmacokinetic profiles has been a longstanding challenge for the pharmaceutical industry. As part of our work to identify inhibitors of BACE1, we have previously developed iminopyrimidinones as a novel pharmacophore for aspartyl protease inhibition ...

    The development of renin inhibitors with favorable oral pharmacokinetic profiles has been a longstanding challenge for the pharmaceutical industry. As part of our work to identify inhibitors of BACE1, we have previously developed iminopyrimidinones as a novel pharmacophore for aspartyl protease inhibition. In this letter we describe how we modified substitution around this pharmacophore to develop a potent, selective and orally active renin inhibitor.

    Organizational Affiliation: 

    Medicinal Chemistry Department, Albany Molecular Research, Inc., 26 Corporate Circle, Albany, NY 12203, United States.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ReninA, B340Homo sapiensMutation(s): 0 
Gene Names: REN
EC: 3.4.23.15
UniProt & NIH Common Fund Data Resources
Find proteins for P00797 (Homo sapiens)
Explore P00797 
Go to UniProtKB:  P00797
PHAROS:  P00797
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00797
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
70Y
Query on 70Y
Download Ideal Coordinates CCD File 
D [auth A],
E [auth B]		(2Z,6S)-2-imino-6-methyl-3-{3-[(4R)-2-oxo-4-phenylpyrrolidin-1-yl]benzyl}-6-(propan-2-yl)tetrahydropyrimidin-4(1H)-one
C25 H30 N4 O2
VBYHYTJHKFQNCE-CPJSRVTESA-N		 Ligand Interaction
NAG
Query on NAG
Download Ideal Coordinates CCD File 
C [auth A]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
70Y Binding MOAD:  4XX4 Ki: 44 (nM) from 1 assay(s)
BindingDB:  4XX4 Ki: 44 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.210 
  • Space Group: P 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 142.41α = 90
b = 142.41β = 90
c = 142.41γ = 90
Software Package:
Software NamePurpose
BUSTER-TNTrefinement
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
AMoREphasing
BUSTERrefinement

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

  • Released Date: 2015-02-18 
    • Deposition Author(s): Orth, P.

Revision History  (Full details and data files)

  • Version 1.0: 2015-02-18
    Type: Initial release
  • Version 1.1: 2016-03-16
    Changes: Data collection
  • Version 1.2: 2017-11-22
    Changes: Derived calculations, Refinement description
  • Version 1.3: 2018-04-18
    Changes: Data collection, Database references
  • Version 1.4: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary