Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 22.46 kDa 
• Atom Count: 1779 
• Modelled Residue Count: 198 
• Deposited Residue Count: 198 
• Unique protein chains: 1

3VFB

Crystal Structure of HIV-1 Protease Mutant N88D with novel P1'-Ligands GRL-02031

• PDB DOI: 10.2210/pdb3VFB/pdb

• Classification: hydrolase/hydrolase inhibitor
• Organism(s): Human immunodeficiency virus type 1 (BRU ISOLATE)
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2012-01-09 Released: 2012-11-21 
• Deposition Author(s): Yu, X.X., Wang, Y.F., Chang, Y.C.E., Weber, I.T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.216 
• R-Value Observed: 0.158 

Literature

Potent antiviral HIV-1 protease inhibitor GRL-02031 adapts to the structures of drug resistant mutants with its P1'-pyrrolidinone ring.

Chang, Y.C., Yu, X., Zhang, Y., Tie, Y., Wang, Y.F., Yashchuk, S., Ghosh, A.K., Harrison, R.W., Weber, I.T.

(2012) J Med Chem 55: 3387-3397

• PubMed: 22401672 
• DOI: 10.1021/jm300072d
• Primary Citation of Related Structures:  
  3VF5, 3VF7, 3VFA, 3VFB


• PubMed Abstract: 
  

GRL-02031 (1) is an HIV-1 protease (PR) inhibitor containing a novel P1' (R)-aminomethyl-2-pyrrolidinone group. Crystal structures at resolutions of 1.25-1.55 Å were analyzed for complexes of 1 with the PR containing major drug resistant mutations, PR(I47V), PR(L76V), PR(V82A), and PR(N88D). Mutations of I47V and V82A alter residues in the inhibitor-binding site, while L76V and N88D are distal mutations having no direct contact with the inhibitor. Substitution of a smaller amino acid in PR(I47V) and PR(L76V) and the altered charge of PR(N88D) are associated with significant local structural changes compared to the wild-type PR(WT), while substitution of alanine in PR(V82A) increases the size of the S1' subsite. The P1' pyrrolidinone group of 1 accommodates to these local changes by assuming two different conformations. Overall, the conformation and interactions of 1 with PR mutants resemble those of PR(WT) with similar inhibition constants in good agreement with the antiviral potency on multidrug resistant HIV-1.

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Organizational Affiliation: 

Department of Biology, Molecular Basis of Disease Program, Georgia State University, P.O. Box 4010, Atlanta, Georgia 30302-4010, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
protease	A, B	99	Human immunodeficiency virus type 1 (BRU ISOLATE)	Mutation(s): 6  Gene Names: gag-pol EC: 3.4.23.16 (PDB Primary Data), 2.7.7.49 (UniProt), 2.7.7.7 (UniProt), 3.1.26.13 (UniProt), 3.1.13.2 (UniProt), 2.7.7 (UniProt), 3.1 (UniProt)
UniProt
Find proteins for P03367 (Human immunodeficiency virus type 1 group M subtype B (isolate BRU/LAI)) Explore P03367  Go to UniProtKB:  P03367

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
031	C [auth A]	(3aS,5R,6aR)-hexahydro-2H-cyclopenta[b]furan-5-yl [(1S,2R)-1-benzyl-2-hydroxy-3-([(4-methoxyphenyl)sulfonyl]{[(2R)-5-oxopyrrolidin-2-yl]methyl}amino)propyl]carbamate C30 H39 N3 O8 S RPIALZPTIFOQGC-CXLNPQPMSA-N
GOL	E [auth A], F [auth A], G [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	D [auth A], I [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	H [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
031	BindingDB:  3VFB	Ki: min: 0.1, max: 0.44 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.216 
• R-Value Observed: 0.158 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.255	α = 90
b = 86.386	β = 90
c = 46.068	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-01-09 
• Released Date: 2012-11-21 
Deposition Author(s): Yu, X.X., Wang, Y.F., Chang, Y.C.E., Weber, I.T.

Revision History  

• Version 1.0: 2012-11-21
  Type: Initial release
  
• Version 1.1: 2012-11-28
  Changes: Data collection
• Version 1.2: 2015-03-25
  Changes: Database references