7YF6 | pdb_00007yf6

Crystal structure of HIV-1 protease in complex with macrocyclic peptide

• PDB DOI: https://doi.org/10.2210/pdb7YF6/pdb

• Classification: VIRAL PROTEIN/INHIBITOR
• Organism(s): Human immunodeficiency virus 1, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-07-07 Released: 2022-11-02 
• Deposition Author(s): Kusumoto, Y., Sato, S., Yamada, T., Kozono, I., Nakata, Z., Asada, N., Mitsuki, S., Wakasa-Morimoto, C., Tohru, M., Watanabe, A., Hayashi, K., Mikamiyama, H.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free: 
  0.234 (Depositor), 0.247 (DCC) 
• R-Value Work: 
  0.192 (Depositor), 0.197 (DCC) 
• R-Value Observed: 
  0.194 (Depositor) 

Starting Model: experimental

Literature

Highly Potent and Oral Macrocyclic Peptides as a HIV-1 Protease Inhibitor: mRNA Display-Derived Hit-to-Lead Optimization.

Kusumoto, Y., Hayashi, K., Sato, S., Yamada, T., Kozono, I., Nakata, Z., Asada, N., Mitsuki, S., Watanabe, A., Wakasa-Morimoto, C., Uemura, K., Arita, S., Miki, S., Mizutare, T., Mikamiyama, H.

(2022) ACS Med Chem Lett 13: 1634-1641

• PubMed: 36262395 
• DOI: https://doi.org/10.1021/acsmedchemlett.2c00310
• Primary Citation Related Structures: 
  7YF6


• PubMed Abstract: 
  

  Human immunodeficiency virus type-1 (HIV-1) protease is essential for viral propagation, and its inhibitors are key anti-HIV-1 drug candidates. In this study, we discovered a novel HIV-1 protease inhibitor (compound 16 ) with potent antiviral activity and oral bioavailability using a structure-based drug design approach via X-ray crystal structure analysis and improved metabolic stability, starting from hit macrocyclic peptides identified by mRNA display against HIV-1 protease. We found that the improvement of the proteolytic stability of macrocyclic peptides by introducing a methyl group to the α-position of amino acid is crucial to exhibit strong antiviral activity. In addition, macrocyclic peptides, which have moderate metabolic stability and solubility in solutions containing taurocholic acid, exhibited desirable plasma total clearance and oral bioavailability. These approaches may contribute to the successful discovery and development of orally bioavailable peptide drugs.

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Organizational Affiliation: 
• Shionogi Pharmaceutical Research Center, Shionogi & Co., Ltd. 1-1, Futaba-cho 3-chome, Toyonaka, Osaka 561-0825, Japan.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

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

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

Macromolecule Content 

• Total Structure Weight: 22.84 kDa 
• Atom Count: 1,645 
• Modeled Residue Count: 207 
• Deposited Residue Count: 207 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protease	A, B	99	Human immunodeficiency virus 1	Mutation(s): 0
UniProt
Find proteins for P12497 (Human immunodeficiency virus type 1 group M subtype B (isolate NY5)) Explore P12497  Go to UniProtKB:  P12497

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Macrocyclic Peptide	C	9	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG (Subject of Investigation/LOI)	D [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MEA	C	L-PEPTIDE LINKING	C10 H13 N O2		PHE

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free:  0.234 (Depositor), 0.247 (DCC) 
• R-Value Work:  0.192 (Depositor), 0.197 (DCC) 
• R-Value Observed: 0.194 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 31.877	α = 90
b = 49.325	β = 90
c = 122.078	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-11-02 
Deposition Author(s): Kusumoto, Y., Sato, S., Yamada, T., Kozono, I., Nakata, Z., Asada, N., Mitsuki, S., Wakasa-Morimoto, C., Tohru, M., Watanabe, A., Hayashi, K., Mikamiyama, H.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2022-11-02
  Type: Initial release
  
• Version 2.0: 2023-04-05
  Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Non-polymer description, Polymer sequence, Source and taxonomy, Structure summary
• Version 3.0: 2023-11-15
  Changes: Advisory, Atomic model, Data collection, Derived calculations
• Version 3.1: 2023-11-29
  Changes: Refinement description
• Version 3.2: 2024-11-13
  Changes: Structure summary