4XX4 | pdb_00004xx4

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 (Depositor), 0.230 (DCC) 
  • R-Value Work: 
    0.210 (Depositor), 0.208 (DCC) 
  • R-Value Observed: 
    0.210 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 4XX4

Ligand Structure Quality Assessment 


This is version 1.6 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 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.

Macromolecule Content 

  • Total Structure Weight: 75.59 kDa 
  • Atom Count: 5,410 
  • Modeled Residue Count: 677 
  • Deposited Residue Count: 680 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P00797-1
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / 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
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
Binding Affinity Annotations 
IDSourceBinding Affinity
70Y 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 (Depositor), 0.230 (DCC) 
  • R-Value Work:  0.210 (Depositor), 0.208 (DCC) 
  • R-Value Observed: 0.210 (Depositor) 
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

View Full Validation Report



Ligand Structure Quality Assessment 


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
  • Version 1.6: 2024-10-09
    Changes: Structure summary