8Q14

Endothiapepsin in complex with ligand (3R,5R)-3-(2-((methyl(prop-2-yn-1-yl)amino)methyl)thiazol-4-yl)-5-(3-(2-nitro-4-(trifluoromethyl)phenyl)-1,2,4-oxadiazol-5-yl)pyrrolidin-3-ol (CBWS-SE-171)

• PDB DOI: https://doi.org/10.2210/pdb8Q14/pdb

• Classification: HYDROLASE
• Organism(s): Cryphonectria parasitica
• Mutation(s): No 


• Deposited: 2023-07-29 Released: 2024-08-07 
• Deposition Author(s): Mueller, J.M., Eckelt, S., Klebe, G., Glinca, S.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.13 Å
• R-Value Free: 0.178 
• R-Value Work: 0.159 
• R-Value Observed: 0.160 

Starting Model: experimental

Literature

Crystal structures of Endothiapepsin with ligands derived from merged fragment hits

Mueller, J.M.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 34.64 kDa 
• Atom Count: 2,787 
• Modelled Residue Count: 330 
• Deposited Residue Count: 330 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endothiapepsin	A	330	Cryphonectria parasitica	Mutation(s): 0  EC: 3.4.23.22
UniProt
Find proteins for P11838 (Cryphonectria parasitica) Explore P11838  Go to UniProtKB:  P11838

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IJS (Subject of Investigation/LOI)	E [auth A]	(3~{R},5~{R})-3-[2-[[methyl(prop-2-ynyl)amino]methyl]-1,3-thiazol-4-yl]-5-[3-[2-nitro-4-(trifluoromethyl)phenyl]-1,2,4-oxadiazol-5-yl]pyrrolidin-3-ol C21 H19 F3 N6 O4 S COBDFCAWUNRFOD-JLTOFOAXSA-N
MPD	B [auth A], C [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
DMS	D [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.13 Å
• R-Value Free: 0.178 
• R-Value Work: 0.159 
• R-Value Observed: 0.160 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.078	α = 90
b = 72.663	β = 109.41
c = 52.646	γ = 90

Software Package:

Software Name	Purpose
Coot	model building
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-08-07 
Deposition Author(s): Mueller, J.M., Eckelt, S., Klebe, G., Glinca, S.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-08-07
  Type: Initial release
  
• Version 1.1: 2024-10-16
  Changes: Structure summary