2BB9 | pdb_00002bb9

Structure of HIV1 protease and AKC4p_133a complex.

• PDB DOI: https://doi.org/10.2210/pdb2BB9/pdb

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


• Deposited: 2005-10-17 Released: 2005-11-15 
• Deposition Author(s): Smith III, A.B., Charnley, A.K., Kuo, L.C., Munshi, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free: 
  0.261 (Depositor) 
• R-Value Work: 
  0.237 (Depositor) 

Starting Model: experimental

Literature

Design, synthesis, and biological evaluation of monopyrrolinone-based HIV-1 protease inhibitors possessing augmented P2' side chains

Smith III, A.B., Charnley, A.K., Harada, H., Beiger, J.J., Cantin, L.D., Kenesky, C.S., Hirschmann, R., Munshi, S., Olsen, D.B., Stahlhut, M.W., Schleif, W.A., Kuo, L.C.

(2006) Bioorg Med Chem Lett 16: 859-863

• PubMed: 16298527 
• DOI: https://doi.org/10.1016/j.bmcl.2005.11.011
• Primary Citation Related Structures: 
  2BB9, 2BBB


• PubMed Abstract: 
  

  A series of monopyrrolinone-based HIV-1 protease inhibitors possessing rationally designed P2' side chains have been synthesized and evaluated for activity against wild-type HIV-1 protease. The most potent inhibitor displays subnanomolar potency in vitro for the wild-type HIV-1 protease. Additionally, the monopyrrolinone inhibitors retain potency in cellular assays against clinically significant mutant forms of the virus. X-ray structures of these inhibitors bound in the wild-type enzyme reveal important insights into the observed biological activity.

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Organizational Affiliation: 
• Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA. [e-mail]

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: 22.23 kDa 
• Atom Count: 1,866 
• Modeled Residue Count: 198 
• Deposited Residue Count: 198 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protease	A, B	99	Human immunodeficiency virus 1	Mutation(s): 0  Gene Names: GAG EC: 3.4.23.16
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
AKC	C [auth A]	2-ETHOXYETHYL (1S,2S)-3-{(2S)-4-[(3AS,8S,8AR)-2-OXO-3,3A,8,8A-TETRAHYDRO-2H-INDENO[1,2-D][1,3]OXAZOL-8-YL]-2-BENZYL-3-OXO-2,3-DIHYDRO-1H-PYRROL-2-YL}-1-BENZYL-2-HYDROXYPROPYLCARBAMATE C36 H39 N3 O7 CGBRFCVAMLJVEA-ZGURCIGKSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free:  0.261 (Depositor) 
• R-Value Work:  0.237 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.238	α = 90
b = 86.18	β = 90
c = 46.533	γ = 90

Software Package:

Software Name	Purpose
CNX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
CNX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-11-15 
Deposition Author(s): Smith III, A.B., Charnley, A.K., Kuo, L.C., Munshi, S.

Revision History  

• Version 1.0: 2005-11-15
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-08-23
  Changes: Data collection, Database references, Derived calculations, Refinement description