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: 22.15 kDa 
• Atom Count: 1560 
• Residue Count: 198 
• Unique protein chains: 1

1HVR

RATIONAL DESIGN OF POTENT, BIOAVAILABLE, NONPEPTIDE CYCLIC UREAS AS HIV PROTEASE INHIBITORS

• DOI: 10.2210/pdb1HVR/pdb

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


• Deposited: 1994-02-14 Released: 1995-01-26 
• Deposition Author(s): Chang, C.-H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Work: 0.193 
• R-Value Observed: 0.193 

Literature

Rational design of potent, bioavailable, nonpeptide cyclic ureas as HIV protease inhibitors.

Lam, P.Y., Jadhav, P.K., Eyermann, C.J., Hodge, C.N., Ru, Y., Bacheler, L.T., Meek, J.L., Otto, M.J., Rayner, M.M., Wong, Y.N., Chang, C.-H., Weber, P., Jackson, D.A., Sharpe, T.R., Erickson-Viitanen, S.

(1994) Science 263: 380-384

• PubMed: 8278812 
• DOI: 10.1126/science.8278812
• Primary Citation of Related Structures:  
  1HVR


• PubMed Abstract: 
  

Mechanistic information and structure-based design methods have been used to design a series of nonpeptide cyclic ureas that are potent inhibitors of human immunodeficiency virus (HIV) protease and HIV replication. A fundamental feature of these inhibitors is the cyclic urea carbonyl oxygen that mimics the hydrogen-bonding features of a key structural water molecule. The success of the design in both displacing and mimicking the structural water molecule was confirmed by x-ray crystallographic studies. Highly selective, preorganized inhibitors with relatively low molecular weight and high oral bioavailability were synthesized.

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Organizational Affiliation: 

Department of Virology Research, DuPont Merck Pharmaceutical Company, Wilmington, DE 19880.

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 P04585 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB2)) Explore P04585  Go to UniProtKB:  P04585

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
XK2	A	[4R-(4ALPHA,5ALPHA,6BETA,7BETA)]-HEXAHYDRO-5,6-DIHYDROXY-1,3-BIS[2-NAPHTHYL-METHYL]-4,7-BIS(PHENYLMETHYL)-2H-1,3-DIAZEPIN-2-ONE C41 H38 N2 O3 VUYPJDFAKYXJEV-WESAGZJESA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO	A,B	L-PEPTIDE LINKING	C3 H7 N O3 S		CYS

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
XK2	Ki:  0.3100000023841858   nM  Binding MOAD
XK2	Ki :  0.3100000023841858   nM  PDBBind
XK2	Ki:  0.3100000023841858   nM  BindingDB
XK2	Ki:  0.3100000023841858   nM  BindingDB
XK2	Kd:  0.30000001192092896   nM  BindingDB
XK2	Ki:  0.05000000074505806   nM  BindingDB

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Work: 0.193 
• R-Value Observed: 0.193 
• Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.8	α = 90
b = 62.8	β = 90
c = 83.5	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1994-02-14 
• Released Date: 1995-01-26 
Deposition Author(s): Chang, C.-H.

Revision History 

• Version 1.0: 1995-01-26
  Type: Initial release
  
• Version 1.1: 2008-03-03
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2012-02-29
  Changes: Database references
• Version 1.4: 2017-11-29
  Changes: Derived calculations, Other