9CKY | pdb_00009cky

X-ray diffraction structure of papain co-crystallized with novel biosynthetic inhibitor amine-65

PDB DOI: https://doi.org/10.2210/pdb9CKY/pdb

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

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.40 ?
R-Value Free:
0.199 (Depositor), 0.199 (DCC)
R-Value Work:
0.158 (Depositor), 0.158 (DCC)
R-Value Observed:
0.160 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

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

DOI: https://doi.org/10.1038/s41589-025-01907-2

Macromolecule Content

Total Structure Weight: 23.86 kDa
Atom Count: 2,112
Modeled Residue Count: 212
Deposited Residue Count: 212
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00784
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1AXI (Subject of Investigation/LOI) Query on A1AXI Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	(3S)-4-({(1S)-2-[(8-aminooctyl)amino]-1-cyclobutyl-2-oxoethyl}amino)-3-hydroxy-4-oxobutanoic acid C₁₈ H₃₃ N₃ O₅ DGPBSMLADVAZDL-HOCLYGCPSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
MOH Query on MOH Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	METHANOL C H₄ O OKKJLVBELUTLKV-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.40 ?
R-Value Free: 0.199 (Depositor), 0.199 (DCC)
R-Value Work: 0.158 (Depositor), 0.158 (DCC)
R-Value Observed: 0.160 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( ? )	Angle ( ? )
a = 42.47	α = 90
b = 48.95	β = 90
c = 101.58	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-06-04

Deposition Author(s):

Rodriguez, J.A.

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

Revision History (Full details and data files)

Version 1.0: 2025-06-04
Type: Initial release

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.