Biological Assembly 1  

 3D View: Structure | Electron Density | 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: 22.51 kDa 
• Atom Count: 1793 
• Residue Count: 198 
• Unique protein chains: 1

4DJR

Crystal Structure of wild-type HIV-1 Protease in Complex with MKP97

• DOI: 10.2210/pdb4DJR/pdb

• Classification: HYDROLASE/HYDROLASE inhibitor
• Organism(s): Human immunodeficiency virus 1
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2012-02-02 Released: 2012-08-01 
• Deposition Author(s): Schiffer, C.A., Nalam, M.N.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.196 
• R-Value Work: 0.170 
• R-Value Observed: 0.172 

Literature

Design, synthesis, and biological and structural evaluations of novel HIV-1 protease inhibitors to combat drug resistance.

Parai, M.K., Huggins, D.J., Cao, H., Nalam, M.N., Ali, A., Schiffer, C.A., Tidor, B., Rana, T.M.

(2012) J Med Chem 55: 6328-6341

• PubMed: 22708897 
• DOI: 10.1021/jm300238h
• Primary Citation of Related Structures:  
  4DJR, 4DJO, 4DJP, 4DJQ


• PubMed Abstract: 
  

A series of new HIV-1 protease inhibitors (PIs) were designed using a general strategy that combines computational structure-based design with substrate-envelope constraints. The PIs incorporate various alcohol-derived P2 carbamates with acyclic and cyclic heteroatomic functionalities into the (R)-hydroxyethylamine isostere. Most of the new PIs show potent binding affinities against wild-type HIV-1 protease and three multidrug resistant (MDR) variants. In particular, inhibitors containing the 2,2-dichloroacetamide, pyrrolidinone, imidazolidinone, and oxazolidinone moieties at P2 are the most potent with K(i) values in the picomolar range. Several new PIs exhibit nanomolar antiviral potencies against patient-derived wild-type viruses from HIV-1 clades A, B, and C and two MDR variants. Crystal structure analyses of four potent inhibitors revealed that carbonyl groups of the new P2 moieties promote extensive hydrogen bond interactions with the invariant Asp29 residue of the protease. These structure-activity relationship findings can be utilized to design new PIs with enhanced enzyme inhibitory and antiviral potencies.

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Organizational Affiliation: 

Program for RNA Biology, Sanford-Burnham Medical Research Institute, La Jolla, CA 92037, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pol polyprotein	A, B	99	Human immunodeficiency virus 1	Mutation(s): 1  Gene Names: gag-pol, pol EC: 2.7.7.49 (UniProt), 3.1.26.13 (UniProt)
Find proteins for Q90K99 (Human immunodeficiency virus 1) Explore Q90K99  Go to UniProtKB:  Q90K99

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
0KJ	A	[(2S)-5-oxopyrrolidin-2-yl]methyl [(2S,3R)-4-{(1,3-benzothiazol-6-ylsulfonyl)[(2S)-2-methylbutyl]amino}-3-hydroxy-1-phenylbutan-2-yl]carbamate C28 H36 N4 O6 S2 CNYNOTFCYHOHBF-DFFQVNEFSA-N
PO4	A, B	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
0KJ	Ki :  0.003000000026077032   nM  PDBBind
0KJ	Ki:  0.003000000026077032   nM  Binding MOAD

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.196 
• R-Value Work: 0.170 
• R-Value Observed: 0.172 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.728	α = 90
b = 57.85	β = 90
c = 61.692	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-02-02 
• Released Date: 2012-08-01 
Deposition Author(s): Schiffer, C.A., Nalam, M.N.L.

Revision History 

• Version 1.0: 2012-08-01
  Type: Initial release
  
• Version 1.1: 2013-01-02
  Changes: Database references
• Version 1.2: 2017-11-15
  Changes: Refinement description