1AJV

HIV-1 PROTEASE IN COMPLEX WITH THE CYCLIC SULFAMIDE INHIBITOR AHA006

• PDB DOI: https://doi.org/10.2210/pdb1AJV/pdb

• Classification: ASPARTYL PROTEASE
• Organism(s): Human immunodeficiency virus 1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 1997-05-11 Released: 1997-08-20 
• Deposition Author(s): Backbro, K., Unge, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.247 
• R-Value Work: 0.187 
• R-Value Observed: 0.187 

Starting Model: experimental

Literature

Unexpected binding mode of a cyclic sulfamide HIV-1 protease inhibitor.

Backbro, K., Lowgren, S., Osterlund, K., Atepo, J., Unge, T., Hulten, J., Bonham, N.M., Schaal, W., Karlen, A., Hallberg, A.

(1997) J Med Chem 40: 898-902

• PubMed: 9083478 
• DOI: https://doi.org/10.1021/jm960588d
• Primary Citation of Related Structures:  
  1AJV, 1AJX


• PubMed Abstract: 
  

  Two cyclic, C2-symmetric HIV-1 protease inhibitors, one sulfamide and one urea derivative, both comprising phenyl ether groups in the P1/P1' positions, were cocrystallized with HIV-1 protease, and the crystal structures were determined to 2.0 A resolution. The structure of the urea 2 showed a conformation similar to that reported for the related urea 3 by Lam et al., while the sulfamide 1 adopted an unanticipated conformation in which the P1' and P2' side chains were transposed.

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Organizational Affiliation: 

Department of Molecular Biology, Uppsala University, Sweden.

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: 22.18 kDa 
• Atom Count: 1,632 
• 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: PROTEASE EC: 3.4.23.16
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
NMB	C [auth A]	2,7-DIBENZYL-1,1-DIOXO-3,6-BIS-PHENOXYMETHYL-[1,2,7]THIADIAZEPANE-4,5-DIOL C32 H34 N2 O6 S CAGHBXQSDLNCES-ZRTHHSRSSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
NMB	PDBBind:  1AJV	Ki: 19.1 (nM) from 1 assay(s)
	BindingDB:  1AJV	Ki: min: 19, max: 23 (nM) from 3 assay(s)
		IC50: 200 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.247 
• R-Value Work: 0.187 
• R-Value Observed: 0.187 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58	α = 90
b = 85.8	β = 90
c = 46.5	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1997-08-20 
Deposition Author(s): Backbro, K., Unge, T.

Revision History  

• Version 1.0: 1997-08-20
  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: 2023-08-02
  Changes: Database references, Derived calculations, Other, Refinement description
• Version 1.4: 2024-05-22
  Changes: Data collection