8J3T | pdb_00008j3t

Complex structure of human cytomegalovirus protease and a non-covalent small-molecule ligand

• PDB DOI: https://doi.org/10.2210/pdb8J3T/pdb

• Classification: HYDROLASE
• Organism(s): Human betaherpesvirus 5
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2023-04-18 Released: 2023-11-08 
• Deposition Author(s): Yoshida, S., Sako, Y., Nikaido, E., Ueda, T., Kozono, I., Ichihashi, Y., Nakahashi, A., Onishi, M., Yamatsu, Y., Kato, T., Nishikawa, J., Tachibana, Y.
• Funding Organization(s): Not funded

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 
  0.309 (Depositor), 0.307 (DCC) 
• R-Value Work: 
  0.224 (Depositor), 0.228 (DCC) 
• R-Value Observed: 
  0.229 (Depositor) 

Literature

Peptide-to-Small Molecule: Discovery of Non-Covalent, Active-Site Inhibitors of beta-Herpesvirus Proteases.

Yoshida, S., Sako, Y., Nikaido, E., Ueda, T., Kozono, I., Ichihashi, Y., Nakahashi, A., Onishi, M., Yamatsu, Y., Kato, T., Nishikawa, J., Tachibana, Y.

(2023) ACS Med Chem Lett 14: 1558-1566

• PubMed: 37974946 
• DOI: https://doi.org/10.1021/acsmedchemlett.3c00359
• Primary Citation Related Structures: 
  8J3S, 8J3T


• PubMed Abstract: 
  

  Viral proteases, the key enzymes that regulate viral replication and assembly, are promising targets for antiviral drug discovery. Herpesvirus proteases are enzymes with no crystallographically confirmed noncovalent active-site binders, owing to their shallow and polar substrate-binding pockets. Here, we applied our previously reported "Peptide-to-Small Molecule" strategy to generate novel inhibitors of β-herpesvirus proteases. Rapid selection with a display technology was used to identify macrocyclic peptide 1 bound to the active site of human cytomegalovirus protease (HCMV ^Pro ) with high affinity, and pharmacophore queries were defined based on the results of subsequent intermolecular interaction analyses. Membrane-permeable small molecule 19 , designed de novo according to this hypothesis, exhibited enzyme inhibitory activity (IC ₅₀ = 10 ^-6 to 10 ^-7 M) against β-herpesvirus proteases, and the design concept was proved by X-ray cocrystal analysis.

---

Organizational Affiliation: 
• Pharmaceutical Research Division, Shionogi Pharmaceutical Research Center, 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan.
PeptiDream Inc., 3-25-23 Tonomachi, Kawasaki-ku, Kawasaki, Kanagawa 210-0821, Japan.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 59.64 kDa 
• Atom Count: 3,185 
• Modeled Residue Count: 414 
• Deposited Residue Count: 526 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Assemblin	A, B	263	Human betaherpesvirus 5	Mutation(s): 1  Gene Names: UL80 EC: 3.4.21.97
UniProt
Find proteins for P16753 (Human cytomegalovirus (strain AD169)) Explore P16753  Go to UniProtKB:  P16753

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
T1F (Subject of Investigation/LOI)	C [auth A], D [auth B]	(4R)-1-[1-[(S)-[1-cyclopentyl-3-(2-methylphenyl)pyrazol-4-yl]-(4-methylphenyl)methyl]-2-oxidanylidene-pyridin-3-yl]-3-methyl-2-oxidanylidene-N-(3-oxidanylidene-2-azabicyclo[2.2.2]octan-4-yl)imidazolidine-4-carboxamide C40 H45 N7 O4 GUMPNBZZBQKOPS-KFTXPEDNSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free:  0.309 (Depositor), 0.307 (DCC) 
• R-Value Work:  0.224 (Depositor), 0.228 (DCC) 
• R-Value Observed: 0.229 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.364	α = 90
b = 76.364	β = 90
c = 215.03	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data scaling
XDS	data reduction
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-11-08 
Deposition Author(s): Yoshida, S., Sako, Y., Nikaido, E., Ueda, T., Kozono, I., Ichihashi, Y., Nakahashi, A., Onishi, M., Yamatsu, Y., Kato, T., Nishikawa, J., Tachibana, Y.

---

Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2023-11-08
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Database references