3OK9

Crystal structure of wild-type HIV-1 protease with new oxatricyclic designed inhibitor GRL-0519A

• PDB DOI: https://doi.org/10.2210/pdb3OK9/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Human immunodeficiency virus 1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2010-08-24 Released: 2010-09-22 
• Deposition Author(s): Wang, Y.-F., Agniswamy, J., Weber, I.T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.27 Å
• R-Value Free: 0.189 
• R-Value Work: 0.145 
• R-Value Observed: 0.145 

Starting Model: experimental

Literature

Probing Multidrug-Resistance and Protein-Ligand Interactions with Oxatricyclic Designed Ligands in HIV-1 Protease Inhibitors.

Ghosh, A.K., Xu, C.X., Rao, K.V., Baldridge, A., Agniswamy, J., Wang, Y.F., Weber, I.T., Aoki, M., Miguel, S.G., Amano, M., Mitsuya, H.

(2010) ChemMedChem 5: 1850-1854

• PubMed: 20827746 
• DOI: https://doi.org/10.1002/cmdc.201000318
• Primary Citation of Related Structures:  
  3OK9

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Organizational Affiliation: 

Department of Chemistry and Medicinal Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN 47907, USA. [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: 22.53 kDa 
• Atom Count: 2,071 
• Modelled Residue Count: 198 
• Deposited Residue Count: 198 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protease	A, B	99	Human immunodeficiency virus 1	Mutation(s): 5  Gene Names: pol EC: 3.4.23.16
UniProt
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B (isolate BH10)) Explore P03366  Go to UniProtKB:  P03366

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
G52	C [auth A]	(3R,3aS,3bR,6aS,7aS)-octahydrodifuro[2,3-b:3',2'-d]furan-3-yl [(1S,2R)-1-benzyl-2-hydroxy-3-{[(4-methoxyphenyl)sulfonyl](2-methylpropyl)amino}propyl]carbamate C30 H40 N2 O9 S QWMNYFXRFHGYGS-DDGGWZRMSA-N
GOL	G [auth A], M [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	E [auth A], F [auth A], I [auth B], J [auth B], K [auth B], L [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	D [auth A], H [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
G52	PDBBind:  3OK9	Ki: 5.90e-3 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.27 Å
• R-Value Free: 0.189 
• R-Value Work: 0.145 
• R-Value Observed: 0.145 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.546	α = 90
b = 86.212	β = 90
c = 45.635	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
SHELXL-97	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-09-22 
Deposition Author(s): Wang, Y.-F., Agniswamy, J., Weber, I.T.

Revision History  

• Version 1.0: 2010-09-22
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-08-23
  Changes: Data collection
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description