3E16

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

• PDB DOI: https://doi.org/10.2210/pdb3E16/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2008-08-01 Released: 2008-09-09 
• Deposition Author(s): Spraggon, G., Hornsby, M., Shipway, A., Harris, J.L., Lesley, S.A.

---

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 

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

• PubMed: 18752942 
• 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. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 30.45 kDa 
• Atom Count: 2,161 
• Modelled Residue Count: 247 
• Deposited Residue Count: 271 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Prostasin	A [auth B]	271	Homo sapiens	Mutation(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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
B4C	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	B	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
DMS	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 = 53.253	α = 90
b = 55.009	β = 90
c = 82.799	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
ADSC	data collection
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-09-09 
Deposition Author(s): Spraggon, G., Hornsby, M., Shipway, A., Harris, J.L., Lesley, S.A.

Revision History  

• 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