3VSW

Human renin in complex with compound 8


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.309 
  • R-Value Work: 0.235 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Design and optimization of novel (2S,4S,5S)-5-amino-6-(2,2-dimethyl-5-oxo-4-phenylpiperazin-1-yl)-4-hydroxy-2-isopropylhexanamides as renin inhibitors

Nakamura, Y.Sugita, C.Meguro, M.Miyazaki, S.Tamaki, K.Takahashi, M.Nagai, Y.Nagayama, T.Kato, M.Suemune, H.Nishi, T.

(2012) Bioorg Med Chem Lett 22: 4561-4566

  • DOI: https://doi.org/10.1016/j.bmcl.2012.05.092
  • Primary Citation of Related Structures:  
    3VSW, 3VSX

  • PubMed Abstract: 

    Introduction of the 2,2-dimethyl-4-phenylpiperazin-5-one scaffold into the P(3)-P(1) portion of the (2S,4S,5S)-5-amino-6-dialkylamino-4-hydroxy-2-isopropylhexanamide backbone dramatically increased the renin inhibitory activity without using the interaction to the S(3)(sp) pocket. Compound 31 exhibited >10,000-fold selectivity over other human proteases, and 18.5% oral bioavailability in monkey.


  • Organizational Affiliation

    Lead Discovery & Optimization Research Laboratories I, Daiichi Sankyo Co., Ltd, 1-2-58 Hiromachi, Shinagawa-ku, Tokyo 140-8710, Japan.


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
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
R31
Query on R31

Download Ideal Coordinates CCD File 
D [auth A],
F [auth B]
(2S,4S,5S)-5-amino-N-(3-amino-2,2-dimethyl-3-oxopropyl)-4-hydroxy-6-{4-[2-(3-methoxypropoxy)phenyl]-3-oxopiperazin-1-yl}-2-(propan-2-yl)hexanamide
C28 H47 N5 O6
FOAHAYKWNMPVJI-FUDKSRODSA-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
R31 BindingDB:  3VSW IC50: min: 130, max: 2800 (nM) from 2 assay(s)
PDBBind:  3VSW IC50: 130 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.309 
  • R-Value Work: 0.235 
  • Space Group: P 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 140.762α = 90
b = 140.762β = 90
c = 140.762γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection
HKL-2000data scaling
CNXrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-07-25
    Type: Initial release
  • Version 1.1: 2017-11-22
    Changes: Refinement description
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.3: 2023-11-08
    Changes: Data collection, Database references, Refinement description, Structure summary