5V4Y | pdb_00005v4y

X-ray crystal structure of wild type HIV-1 protease in complex with GRL-09510

• PDB DOI: https://doi.org/10.2210/pdb5V4Y/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Human immunodeficiency virus 1
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2017-03-11 Released: 2017-09-13 
• Deposition Author(s): Yedidi, R.S., Delino, N.S., Das, D., Kaufman, J.D., Wingfield, P.T., Ghosh, A.K., Mitsuya, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.253 (Depositor), 0.285 (DCC) 
• R-Value Work: 
  0.206 (Depositor) 
• R-Value Observed: 
  0.210 (Depositor) 

Starting Model: experimental

Literature

GRL-09510, a Unique P2-Crown-Tetrahydrofuranylurethane -Containing HIV-1 Protease Inhibitor, Maintains Its Favorable Antiviral Activity against Highly-Drug-Resistant HIV-1 Variants in vitro.

Amano, M., Miguel Salcedo-Gomez, P., Yedidi, R.S., Delino, N.S., Nakata, H., Venkateswara Rao, K., Ghosh, A.K., Mitsuya, H.

(2017) Sci Rep 7: 12235-12235

• PubMed: 28947797 
• DOI: https://doi.org/10.1038/s41598-017-12052-9
• Primary Citation Related Structures: 
  5V4Y


• PubMed Abstract: 
  

  We report that GRL-09510, a novel HIV-1 protease inhibitor (PI) containing a newly-generated P2-crown-tetrahydrofuranylurethane (Crwn-THF), a P2'-methoxybenzene, and a sulfonamide isostere, is highly active against laboratory and primary clinical HIV-1 isolates (EC ₅₀ : 0.0014-0.0028 μM) with minimal cytotoxicity (CC ₅₀ : 39.0 μM). Similarly, GRL-09510 efficiently blocked the replication of HIV-1 _NL4-3 variants, which were capable of propagating at high-concentrations of atazanavir, lopinavir, and amprenavir (APV). GRL-09510 was also potent against multi-drug-resistant clinical HIV-1 variants and HIV-2 _ROD . Under the selection condition, where HIV-1 _NL4-3 rapidly acquired significant resistance to APV, an integrase inhibitor raltegravir, and a GRL-09510 congener (GRL-09610), no variants highly resistant against GRL-09510 emerged over long-term in vitro passage of the virus. Crystallographic analysis demonstrated that the Crwn-THF moiety of GRL-09510 forms strong hydrogen-bond-interactions with HIV-1 protease (PR) active-site amino acids and is bulkier with a larger contact surface, making greater van der Waals contacts with PR than the bis-THF moiety of darunavir. The present data demonstrate that GRL-09510 has favorable features for treating patients infected with wild-type and/or multi-drug-resistant HIV-1 variants, that the newly generated P2-Crwn-THF moiety confers highly desirable anti-HIV-1 potency. The use of the novel Crwn-THF moiety sheds lights in the design of novel PIs.

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Organizational Affiliation: 
• Departments of Infectious Diseases and Hematology, Kumamoto University School of Medicine, Kumamoto, 860-8556, Japan.
Experimental Retrovirology Section, HIV and AIDS Malignancy Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
Department of Biochemistry, Faculty of Medicine, University of Toronto, Toronto, ON, Canada.
Departments of Chemistry and Medicinal Chemistry, Purdue University, West Lafayette, IN, 47907, USA.
Departments of Infectious Diseases and Hematology, Kumamoto University School of Medicine, Kumamoto, 860-8556, Japan. [e-mail].
Experimental Retrovirology Section, HIV and AIDS Malignancy Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA. [e-mail].
National Center for Global Health and Medicine Research Institute, Tokyo, 162-8655, Japan. [e-mail].

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)

Macromolecule Content 

• Total Structure Weight: 11.31 kDa 
• Atom Count: 869 
• Modeled Residue Count: 99 
• Deposited Residue Count: 99 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protease	A	99	Human immunodeficiency virus 1	Mutation(s): 2
UniProt
Find proteins for Q72874 (Human immunodeficiency virus type 1) Explore Q72874  Go to UniProtKB:  Q72874

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
8FM	B [auth A]	(3S,3aR,5R,7aS,8S)-hexahydro-4H-3,5-methanofuro[2,3-b]pyran-8-yl [(2S,3R)-3-hydroxy-4-{[(4-methoxyphenyl)sulfonyl](2-methylpropyl)amino}-1-phenylbutan-2-yl]carbamate C30 H40 N2 O8 S JVINLJIUYCLBEU-JBQMQJJESA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.253 (Depositor), 0.285 (DCC) 
• R-Value Work:  0.206 (Depositor) 
• R-Value Observed: 0.210 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.473	α = 90
b = 62.473	β = 90
c = 82.929	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-09-13 
Deposition Author(s): Yedidi, R.S., Delino, N.S., Das, D., Kaufman, J.D., Wingfield, P.T., Ghosh, A.K., Mitsuya, H.

Revision History  

• Version 1.0: 2017-09-13
  Type: Initial release
  
• Version 1.1: 2017-10-04
  Changes: Database references
• Version 1.2: 2017-10-11
  Changes: Database references
• Version 1.3: 2023-10-04
  Changes: Data collection, Database references, Derived calculations, Refinement description