9HVP

Design, activity and 2.8 Angstroms crystal structure of a C2 symmetric inhibitor complexed to HIV-1 protease

• PDB DOI: https://doi.org/10.2210/pdb9HVP/pdb

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


• Deposited: 1990-11-06 Released: 1992-04-15 
• Deposition Author(s): Neidhart, D.J., Erickson, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Work: 0.177 

Literature

Design, activity, and 2.8 A crystal structure of a C2 symmetric inhibitor complexed to HIV-1 protease.

Erickson, J., Neidhart, D.J., VanDrie, J., Kempf, D.J., Wang, X.C., Norbeck, D.W., Plattner, J.J., Rittenhouse, J.W., Turon, M., Wideburg, N.

(1990) Science 249: 527-533

• PubMed: 2200122 
• DOI: https://doi.org/10.1126/science.2200122
• Primary Citation of Related Structures:  
  9HVP


• PubMed Abstract: 
  

  A two-fold (C2) symmetric inhibitor of the protease of human immunodeficiency virus type-1 (HIV-1) has been designed on the basis of the three-dimensional symmetry of the enzyme active site. The symmetric molecule inhibited both protease activity and acute HIV-1 infection in vitro, was at least 10,000-fold more potent against HIV-1 protease than against related enzymes, and appeared to be stable to degradative enzymes. The 2.8 angstrom crystal structure of the inhibitor-enzyme complex demonstrated that the inhibitor binds to the enzyme in a highly symmetric fashion.

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Organizational Affiliation: 

Department of Computer-Assisted Molecular Design, Abbott Laboratories, Abbott Park, IL 60064.

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: 22.4 kDa 
• Atom Count: 1,575 
• Modelled Residue Count: 198 
• Deposited Residue Count: 198 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HIV-1 Protease	A, B	99	Human immunodeficiency virus 1	Mutation(s): 0  Gene Names: pol
UniProt
Find proteins for P12497 (Human immunodeficiency virus type 1 group M subtype B (isolate NY5)) Explore P12497  Go to UniProtKB:  P12497

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
0E9	C [auth A]	benzyl [(1R,4S,6S,9R)-4,6-dibenzyl-5-hydroxy-1,9-bis(1-methylethyl)-2,8,11-trioxo-13-phenyl-12-oxa-3,7,10-triazatridec-1-yl]carbamate C43 H52 N4 O7 GEANBHANAKKWSL-ZQWQDMLBSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
0E9	BindingDB:  9HVP	Ki: 4.5 (nM) from 1 assay(s)
		IC50: 3 (nM) from 1 assay(s)

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000256 (0E9)	C [auth A]	benzyl [(1R,4S,6S,9R)-4,6-dibenzyl-5-hydroxy-1,9-bis(1-methylethyl)-2,8,11-trioxo-13-phenyl-12-oxa- 3,7,10-triazatridec-1-yl]carbamate	Peptide-like / Inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Work: 0.177 
• Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.3	α = 90
b = 63.3	β = 90
c = 83.6	γ = 120

Software Package:

Software Name	Purpose
X-PLOR	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 1992-04-15 
Deposition Author(s): Neidhart, D.J., Erickson, J.

Revision History  

• Version 1.0: 1992-04-15
  Type: Initial release
  
• Version 1.1: 2008-03-25
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
• Version 1.3: 2012-12-12
  Changes: Other
• Version 1.4: 2017-11-29
  Changes: Derived calculations, Other
• Version 1.5: 2024-02-14
  Changes: Data collection, Database references, Derived calculations, Source and taxonomy, Structure summary