3E16

X-ray structure of human prostasin in complex with Benzoxazole warhead peptidomimic, lysine in P3

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.188 

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This is version 1.3 of the entry. See complete history. 


Literature

Discovery of inhibitors of the channel-activating protease prostasin (CAP1/PRSS8) utilizing structure-based design.

Tully, D.C., Vidal, A., Chatterjee, A.K., Williams, J.A., Roberts, M.J., Petrassi, H.M., Spraggon, G., Bursulaya, B., Pacoma, R., Shipway, A., Schumacher, A.M., Danahay, H., Harris, J.L.

(2008) Bioorg Med Chem Lett 18: 5895-5899

  • DOI: https://doi.org/10.1016/j.bmcl.2008.08.029
  • Primary Citation of Related Structures:  
    3E0P, 3E16

  • PubMed Abstract: 

    Structure-based design was utilized to guide the early stage optimization of a substrate-like inhibitor to afford potent peptidomimetic inhibitors of the channel-activating protease prostasin. The first X-ray crystal structures of prostasin with small molecule inhibitors bound to the active site are also reported.

    • Organizational Affiliation: 

    Genomics Institute of the Novartis Research Foundation, 10675 John J. Hopkins Dr., San Diego, CA 92121, USA. dtully@gnf.org


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ProstasinA [auth B]271Homo sapiensMutation(s): 3 
Gene Names: PRSS8
EC: 3.4.21
UniProt & NIH Common Fund Data Resources
Find proteins for Q16651 (Homo sapiens)
Explore Q16651 
Go to UniProtKB:  Q16651
PHAROS:  Q16651
GTEx:  ENSG00000052344 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ16651
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
B4C
Query on B4C
Download Ideal Coordinates CCD File 
C [auth B]benzyl [(1S)-5-amino-1-{[(1S)-1-({(1S)-5-amino-1-[(S)-1,3-benzoxazol-2-yl(hydroxy)methyl]pentyl}carbamoyl)-3-phenylpropyl]carbamoyl}pentyl]carbamate
C37 H48 N6 O6
HJDPWVALYXRQIB-QUUJSONZSA-N
GOL
Query on GOL
Download Ideal Coordinates CCD File 
B
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
DMS
Query on DMS
Download Ideal Coordinates CCD File 
D [auth B]DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.188 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.253α = 90
b = 55.009β = 90
c = 82.799γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
ADSCdata collection
HKL-2000data reduction
HKL-2000data scaling

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: 2008-09-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.2: 2021-07-28
    Changes: Database references, Derived calculations, Refinement description
  • Version 1.3: 2021-10-20
    Changes: Database references