Biological Assembly 1  

 3D View: Structure | 1D-3D View | 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: 22.52 kDa 
• Atom Count: 1701 
• Modelled Residue Count: 202 
• Deposited Residue Count: 202 
• Unique protein chains: 2

1HTE

X-RAY CRYSTALLOGRAPHIC STUDIES OF A SERIES OF PENICILLIN-DERIVED ASYMMETRIC INHIBITORS OF HIV-1 PROTEASE

• PDB DOI: 10.2210/pdb1HTE/pdb

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


• Deposited: 1994-04-29 Released: 1994-07-31 
• Deposition Author(s): Jhoti, H., Wonacott, A., Murray-Rust, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Observed: 0.161 

Literature

X-ray crystallographic studies of a series of penicillin-derived asymmetric inhibitors of HIV-1 protease.

Jhoti, H., Singh, O.M., Weir, M.P., Cooke, R., Murray-Rust, P., Wonacott, A.

(1994) Biochemistry 33: 8417-8427

• PubMed: 8031777 
• DOI: 10.1021/bi00194a005
• Primary Citation of Related Structures:  
  1HTE, 1HTF, 1HTG


• PubMed Abstract: 
  

In the development of a treatment for AIDS, the HIV-1 protease has been identified as a good target enzyme for inhibitor design. We previously reported a series of dimeric penicillin-derived C2-symmetric HIV-1 protease inhibitors [Humber, D., et al. (1993) J. Med. Chem. 36, 3120-3128]. In an attempt to reduce the size and optimize the binding of these C2-symmetric inhibitors, molecular modeling studies led to a novel series of monomeric penicillin-derived inhibitors of HIV-1 protease. The binding modes of these monomeric inhibitors have been characterized by X-ray crystallographic and NMR studies. Crystal structures of HIV-1 protease complexed to three inhibitors (GR123976, GR126045, and GR137615) from this series identify the molecular details of the interactions. The binding of GR123976 (IC50 = 2.3 microM) exhibits good hydrophobic contacts but few electrostatic interactions. A strategy of structure-based design and chemical synthesis led to the elaboration of GR123976 to optimize interactions with the protein. Crystallographic analysis of HIV-1 protease complexed to GR126045 and GR137615 identified these interactions with the catalytic aspartates and the protein binding pockets. The crystal structures of the three complexes confirm the presence of the major interactions modeled in order to optimize potency and reveal details of the molecular recognition by HIV-1 protease of this novel series of nonpeptidic inhibitors.

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Related Citations: 

• A Series of Penicillin-Derived C2-Symmetric Inhibitors of HIV-1 Proteinase: Structural and Modeling Studies
  Wonacott, A., Cooke, R., Hayes, F.R., Hayes, M.M., Jhoti, H., Mcmeekin, P., Mistry, A., Murray-Rust, P., Singh, O.M.P., Weir, M.P.
  (1993) J Med Chem 36: 3113

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Organizational Affiliation: 

Department of Biomolecular Structure, Glaxo Research & Development Limited, Greenford, Middlesex, England.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HIV-1 PROTEASE	A, B	99	Human immunodeficiency virus 1	Mutation(s): 0  EC: 3.4.23.16 (UniProt), 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 P03366 (Human immunodeficiency virus type 1 group M subtype B (isolate BH10)) Explore P03366  Go to UniProtKB:  P03366

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HIV-1 PROTEASE	C	4	N/A	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
G23	D [auth A]	(2R,4S)-2-[(R)-BENZYLCARBAMOYL-PHENYLACETYL-METHYL]-5,5-DIMETHYL-THIAZOLIDINE-4-CARBOXYLIC ACID C23 H27 N3 O4 S UDMBRVGTYILYDX-SVFBPWRDSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
G23	PDBBind:  1HTE	IC50: 2265 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Observed: 0.161 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.3	α = 90
b = 87.3	β = 90
c = 46.4	γ = 90

Software Package:

Software Name	Purpose
PROLSQ	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1994-04-29 
• Released Date: 1994-07-31 
Deposition Author(s): Jhoti, H., Wonacott, A., Murray-Rust, P.

Revision History  

• Version 1.0: 1994-07-31
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-11-29
  Changes: Advisory, Derived calculations, Other