9CKW | pdb_00009ckw

X-ray diffraction structure of papain co-crystallized with E-64D

• PDB DOI: https://doi.org/10.2210/pdb9CKW/pdb

• Classification: HYDROLASE
• Organism(s): Carica papaya
• Mutation(s): No 


• Deposited: 2024-07-10 Released: 2025-06-04 
• Deposition Author(s): Vlahakis, N.W., Rodriguez, J.A.
• Funding Organization(s): Howard Hughes Medical Institute (HHMI)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 
  0.175 (Depositor), 0.198 (DCC) 
• R-Value Work: 
  0.134 (Depositor) 
• R-Value Observed: 
  0.136 (Depositor) 

Starting Model: experimental

Literature

Enzymatic combinatorial synthesis of E-64 and related cysteine protease inhibitors.

Liu, M., Zang, X., Vlahakis, N.W., Rodriguez, J.A., Ohashi, M., Tang, Y.

(2025) Nat Chem Biol 21: 1783-1793

• PubMed: 40346252 
• DOI: https://doi.org/10.1038/s41589-025-01907-2
• Primary Citation Related Structures: 
  9CJN, 9CKT, 9CKW, 9CKY, 9CLH, 9EG7


• PubMed Abstract: 
  

  E-64 is an irreversible cysteine protease inhibitor prominently used in chemical biology and drug discovery. Here we uncover a nonribosomal peptide synthetase-independent biosynthetic pathway for E-64, which is widely conserved in fungi. The pathway starts with epoxidation of fumaric acid to the warhead (2S,3S)-trans-epoxysuccinic acid with an Fe(II)/α-ketoglutarate-dependent oxygenase, followed by successive condensation with an L-amino acid by an adenosine triphosphate grasp enzyme and with an amine by the fungal example of amide bond synthetase. Both amide bond-forming enzymes display notable biocatalytic potential, including scalability, stereoselectivity toward the warhead and broader substrate scopes in forming the amide bonds. Biocatalytic cascade with these amide bond-forming enzymes generated a library of cysteine protease inhibitors, leading to more potent cathepsin inhibitors. Additionally, one-pot reactions enabled the preparative synthesis of clinically relevant inhibitors. Our work highlights the importance of biosynthetic investigation for enzyme discovery and the potential of amide bond-forming enzymes in synthesizing small-molecule libraries.

---

Organizational Affiliation: 
• Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA, USA.
Department of Chemistry and Biochemistry, UCLA-DOE Institute for Genomics and Proteomics, STROBE, NSF Science and Technology Center, University of California, Los Angeles, Los Angeles, CA, USA.
Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA, USA. [e-mail].
Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA, USA. [e-mail].
Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, 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: 23.83 kDa 
• Atom Count: 2,168 
• Modeled Residue Count: 212 
• Deposited Residue Count: 212 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Papain	A	212	Carica papaya	Mutation(s): 0  EC: 3.4.22.2
UniProt
Find proteins for P00784 (Carica papaya) Explore P00784  Go to UniProtKB:  P00784

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
E6D (Subject of Investigation/LOI)	C [auth A]	ethyl (3S)-3-hydroxy-4-({(2S)-4-methyl-1-[(3-methylbutyl)amino]-1-oxopentan-2-yl}amino)-4-oxobutanoate C17 H32 N2 O5 FGRTVYZNNRCSAS-KBPBESRZSA-N
MOH	B [auth A]	METHANOL C H4 O OKKJLVBELUTLKV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free:  0.175 (Depositor), 0.198 (DCC) 
• R-Value Work:  0.134 (Depositor) 
• R-Value Observed: 0.136 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.88	α = 90
b = 49.3	β = 90
c = 90.69	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-06-04 
Deposition Author(s): Vlahakis, N.W., Rodriguez, J.A.

---

Funding Organization	Location	Grant Number
Howard Hughes Medical Institute (HHMI)	United States	--

Revision History  

• Version 1.0: 2025-06-04
  Type: Initial release
  
• Version 1.1: 2025-06-11
  Changes: Database references
• Version 1.2: 2025-11-05
  Changes: Database references