Biological Assembly 1  

 3D View: Structure | 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: 22.89 kDa 
• Atom Count: 1625 
• Residue Count: 198 
• Unique protein chains: 1

1HPS

RATIONAL DESIGN, SYNTHESIS AND CRYSTALLOGRAPHIC ANALYSIS OF A HYDROXYETHYLENE-BASED HIV-1 PROTEASE INHIBITOR CONTAINING A HETEROCYCLIC P1'-P2' AMIDE BOND ISOSTERE

• DOI: 10.2210/pdb1HPS/pdb

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


• Deposited: 1994-05-24 Released: 1994-08-31 
• Deposition Author(s): Abdel-Meguid, S., Zhao, B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Observed: 0.194 

Literature

Rational design, synthesis, and crystallographic analysis of a hydroxyethylene-based HIV-1 protease inhibitor containing a heterocyclic P1'--P2' amide bond isostere.

Thompson, S.K., Murthy, K.H., Zhao, B., Winborne, E., Green, D.W., Fisher, S.M., DesJarlais, R.L., Tomaszek Jr., T.A., Meek, T.D., Gleason, J.G., Abdel-Meguid, S.S.

(1994) J Med Chem 37: 3100-3107

• PubMed: 7932533 
• DOI: 10.1021/jm00045a015
• Primary Citation of Related Structures:  
  1HPS


• PubMed Abstract: 
  

The rational design and synthesis of a highly potent inhibitor of HIV-1 protease have been accomplished. The inhibitor, SB 206343, is based on a model derived from the structure of the MVT-101/HIV-1 protease complex and contains a 4(5)-acylimidazole ring as an isosteric replacement for the P1'--P2' amide bond. It is a competitive inhibitor with an apparent inhibition constant of 0.6 nM at pH 6.0. The three-dimensional structure of SB 206343 bound in the active site of HIV-1 protease has been determined at 2.3 A resolution by X-ray diffraction techniques and refined to a crystallographic discrepancy factor, R (= sigma parallel Fo magnitude of/Fc parallel/sigma magnitude of), of 0.194. The inhibitor is held in the enzyme by a set of hydrophobic and polar interactions. N-3 of the imidazole ring participates in a novel hydrogen-bonding interaction with the bound water molecule, demonstrating the effectiveness of the imidazole ring as an isosteric replacement for the P1'--P2' amide bond in hydroxyethylene-based HIV-1 protease inhibitors. Also present are hydrogen-bonding interactions between N-1 of the imidazole ring and the carbonyl of Gly-127 as well as between the imidazole acyl carbonyl oxygen and the amide nitrogen of Asp-129, exemplifying the peptidomimetic nature of the 4(5)-acylimidazole isostere. All of these interactions are in qualitative agreement with those predicted by the model.

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Organizational Affiliation: 

Department of Medicinal Chemistry, SmithKline Beecham Pharmaceuticals, King of Prussia, Pennsylvania 19406.

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)
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B (isolate BH10)) Explore P03366  Go to UniProtKB:  P03366

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
RUN	B	2-[(1R,3S,4S)-1-BENZYL-4-[N-(BENZYLOXYCARBONYL)-L-VALYL]AMINO-3-PHENYLPENTYL]-4(5)-(2-METHYLPROPIONYL)IMIDAZOLE C38 H46 N4 O5 RQAVEWKEUKIFLD-LVPKLHHISA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
RUN	Ki :  0.6000000238418579   nM  PDBBind
RUN	Ki:  0.6000000238418579   nM  BindingDB
RUN	Ki:  0.6000000238418579   nM  Binding MOAD

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Observed: 0.194 
• Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63	α = 90
b = 63	β = 90
c = 83.3	γ = 120

Software Package:

Software Name	Purpose
X-PLOR	model building
PROLSQ	refinement
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1994-05-24 
• Released Date: 1994-08-31 
Deposition Author(s): Abdel-Meguid, S., Zhao, B.

Revision History 

• Version 1.0: 1994-08-31
  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: 2012-02-22
  Changes: Database references
• Version 1.4: 2017-11-29
  Changes: Derived calculations, Other