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: 11.41 kDa 
• Atom Count: 801 
• Modelled Residue Count: 99 
• Deposited Residue Count: 99 
• Unique protein chains: 1

2ZGA

HIV-1 protease in complex with a dimethylallyl decorated pyrrolidine based inhibitor (hexagonal space group)

• PDB DOI: 10.2210/pdb2ZGA/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Human immunodeficiency virus 1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-01-21 Released: 2009-02-03 
• Deposition Author(s): Boettcher, J., Blum, A., Heine, A., Diederich, W.E., Klebe, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.274 
• R-Value Work: 0.224 
• R-Value Observed: 0.225 

Literature

Two Solutions for the Same Problem: Multiple Binding Modes of Pyrrolidine-Based HIV-1 Protease Inhibitors

Blum, A., Bottcher, J., Dorr, S., Heine, A., Klebe, G., Diederich, W.E.

(2011) J Mol Biol 410: 745-755

• PubMed: 21762812 
• DOI: 10.1016/j.jmb.2011.04.052
• Primary Citation of Related Structures:  
  2ZGA, 3CKT


• PubMed Abstract: 
  

Structure-based drug design is an integral part of industrial and academic drug discovery projects. Initial lead structures are, in general, optimized in terms of affinity using iterative cycles comprising synthesis, biological evaluation, computational methods, and structural analysis. X-ray crystallography commonly suggests the existence of a single well-defined state, termed binding mode, which is generally assumed to be consistent in a series of similar ligands and therefore used for the following optimization process. During the further development of symmetrically disubstituted 3,4-amino-pyrrolidines as human immunodeficiency virus type 1 protease inhibitors, we discovered that, by modification of the P1/P1' moieties of our lead structure, the activity of the inhibitors towards the active-site mutation Ile84Val was altered, however, not being explainable with the initial underlying structure-activity relationship. The cocrystallization of the most potent derivative in complex with the human immunodeficiency virus type 1 protease surprisingly led to two different crystal forms (P2(1)2(1)2(1) and P6(1)22). Structural analysis revealed two completely different binding modes; the interaction of the pyrrolidine nitrogen atom with the catalytic aspartates remains as the only similarity. The study presented clearly demonstrates that structural biology has to escort the entire lead optimization process not to fail by an initially observed binding orientation.

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Organizational Affiliation: 

Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marburg, Germany.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protease	A	99	Human immunodeficiency virus 1	Mutation(s): 0  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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
YDP	B [auth A]	(3S,4S),-3,4-Bis-[(4-carbamoyl-benzensulfonyl)-(3-methyl-but-2-enyl)-amino]-pyrrolidine C28 H37 N5 O6 S2 SNNQNFFJBMXSFD-UIOOFZCWSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
YDP	PDBBind:  2ZGA	Ki: 480 (nM) from 1 assay(s)
	Binding MOAD:  2ZGA	Ki: 480 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.274 
• R-Value Work: 0.224 
• R-Value Observed: 0.225 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.625	α = 90
b = 62.625	β = 90
c = 82.303	γ = 120

Software Package:

Software Name	Purpose
SHELX	model building
SHELXL-97	refinement
MAR345dtb	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-01-21 
• Released Date: 2009-02-03 
Deposition Author(s): Boettcher, J., Blum, A., Heine, A., Diederich, W.E., Klebe, G.

Revision History  

• Version 1.0: 2009-02-03
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2011-08-10
  Changes: Database references, Structure summary