8Q10

Endothiapepsin in complex with ligand (3R,5R)-3-(2-(hydroxymethyl)thiazol-4-yl)-5-(3-(4-(trifluoromethyl)phenyl)-1,2,4-oxadiazol-5-yl)pyrrolidin-3-ol (CBWS-SE-125)

• PDB DOI: https://doi.org/10.2210/pdb8Q10/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: 1.27 Å
• R-Value Free: 0.165 
• R-Value Work: 0.144 
• R-Value Observed: 0.145 

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: 34.99 kDa 
• Atom Count: 2,744 
• 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 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IJY (Subject of Investigation/LOI)	B [auth A]	(3~{R},5~{R})-3-[2-(hydroxymethyl)-1,3-thiazol-4-yl]-5-[3-[4-(trifluoromethyl)phenyl]-1,2,4-oxadiazol-5-yl]pyrrolidin-3-ol C17 H15 F3 N4 O3 S CNTLIYFLZNNGNX-BDJLRTHQSA-N
PGE	K [auth A]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
MPD	J [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
PEG	G [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
DMS	C [auth A], D [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
ACT	E [auth A], F [auth A], H [auth A], I [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.27 Å
• R-Value Free: 0.165 
• R-Value Work: 0.144 
• R-Value Observed: 0.145 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.857	α = 90
b = 72.472	β = 109.17
c = 52.427	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