4XX3

Renin in complex with (S)-1-(3-(benzylcarbamoyl)benzyl)-4-isopropyl-4-methyl-6-oxotetrahydropyrimidin-2(1H)-iminium


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.208 

wwPDB Validation   3D Report Full Report


This is version 1.5 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: https://doi.org/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. In this letter we describe how we modified substitution around this pharmacophore to develop a potent, selective and orally active renin inhibitor.


  • Organizational Affiliation

    Discovery Chemistry, Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, NJ 07033, United States. Electronic address: brian.mckittrick@merck.com.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Renin
A, B
340Homo 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
GTEx:  ENSG00000143839 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00797
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
70X
Query on 70X

Download Ideal Coordinates CCD File 
D [auth A],
F [auth B]
N-benzyl-3-{[(2Z,4S)-2-imino-4-methyl-6-oxo-4-(propan-2-yl)tetrahydropyrimidin-1(2H)-yl]methyl}benzamide
C23 H28 N4 O2
OFTSPVADFMQIGQ-QHCPKHFHSA-N
NAG
Query on NAG

Download Ideal Coordinates CCD File 
C [auth A],
E [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
70X Binding MOAD:  4XX3 Ki: 56 (nM) from 1 assay(s)
BindingDB:  4XX3 Ki: 56 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.208 
  • Space Group: P 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 142.02α = 90
b = 142.02β = 90
c = 142.02γ = 90
Software Package:
Software NamePurpose
BUSTER-TNTrefinement
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
AMoREphasing
BUSTERrefinement

Structure Validation

View Full Validation Report



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
  • Version 1.5: 2023-09-27
    Changes: Data collection, Database references, Refinement description, Structure summary