1EPP | pdb_00001epp

ENDOTHIA ASPARTIC PROTEINASE (ENDOTHIAPEPSIN) COMPLEXED WITH PD-130,693 (MAS PHE LYS+MTF STA MBA)

• PDB DOI: https://doi.org/10.2210/pdb1EPP/pdb

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


• Deposited: 1994-07-27 Released: 1994-12-20 
• Deposition Author(s): Wallace, B.A., Cooper, J.B., Blundell, T.L.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Observed: 
  0.160 (Depositor) 

Literature

Analyses of ligand binding in five endothiapepsin crystal complexes and their use in the design and evaluation of novel renin inhibitors.

Lunney, E.A., Hamilton, H.W., Hodges, J.C., Kaltenbronn, J.S., Repine, J.T., Badasso, M., Cooper, J.B., Dealwis, C., Wallace, B.A., Lowther, W.T.

(1993) J Med Chem 36: 3809-3820

• PubMed: 8254610 
• DOI: https://doi.org/10.1021/jm00076a008
• Primary Citation of Related Structures:  
  1EPP, 1EPQ


• PubMed Abstract: 
  

  Five renin inhibitors were cocrystallized with endothiapepsin, a fungal enzyme homologous to renin. Crystal structures of inhibitor-bound complexes have provided invaluable insight regarding the three-dimensional structure of the aspartic proteinase family of enzymes, as well as the steric and polar interactions that occur between the proteins and the bound ligands. Beyond this, subtleties of binding have been revealed, including multiple subsite binding modes and subsite interdependencies. This information has been applied in the design of novel potent renin inhibitors and in the understanding of structure-activity relationships and enzyme selectivities.

---

Organizational Affiliation: 

Parke-Davis Pharmaceutical Research, Division of Warner-Lambert Company, Ann Arbor, Michigan 48105-2430.

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: 34.71 kDa 
• Atom Count: 2,706 
• 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 [auth E]	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1Z1	D [auth E]	N-(dimethylsulfamoyl)-L-phenylalanyl-N-[(1S,2S)-2-hydroxy-4-{[(2S)-2-methylbutyl]amino}-1-(2-methylpropyl)-4-oxobutyl]-N~6~-(methylcarbamothioyl)-L-lysinamide C32 H57 N7 O6 S2 GBPRCFWBWHGSJH-BLVAWXTGSA-N
SO4	B [auth E], C [auth E]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000392 (1Z1)	D [auth E]	N-(dimethylsulfamoyl)-L-phenylalanyl-N-[(1R,2R)-2-hydroxy-4-{[(2S)-2-methylbutyl]amino}-1-(2-methylpropyl)-4-oxobutyl]-6-[(methylcarbamothioyl)ammonio]-L-norleucinamide	Peptide-like / Inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Observed: 0.160 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.1	α = 90
b = 75.6	β = 97.2
c = 42.9	γ = 90

Software Package:

Software Name	Purpose
RESTRAIN	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 1994-12-20 
Deposition Author(s): Wallace, B.A., Cooper, J.B., Blundell, T.L.

Revision History  

• Version 1.0: 1994-12-20
  Type: Initial release
  
• Version 1.1: 2008-03-10
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
• Version 1.3: 2012-12-12
  Changes: Other
• Version 1.4: 2017-11-29
  Changes: Derived calculations, Other
• Version 1.5: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary