3VSW | pdb_00003vsw

Human renin in complex with compound 8

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 
    0.309 (Depositor), 0.304 (DCC) 
  • R-Value Work: 
    0.235 (Depositor), 0.233 (DCC) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.4 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 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.

Macromolecule Content 

  • Total Structure Weight: 76.08 kDa 
  • Atom Count: 5,348 
  • Modeled Residue Count: 680 
  • 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: 1
Go to GlyGen: P00797-1
Sequence Annotations
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Reference Sequence

Small Molecules

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free:  0.309 (Depositor), 0.304 (DCC) 
  • R-Value Work:  0.235 (Depositor), 0.233 (DCC) 
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

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Ligand Structure Quality Assessment 


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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
  • Version 1.4: 2024-10-09
    Changes: Structure summary