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: 22.11 kDa 
• Atom Count: 1598 
• Residue Count: 198 
• Unique protein chains: 1

1QBU

HIV-1 PROTEASE INHIBITORS WIIH LOW NANOMOLAR POTENCY

• DOI: 10.2210/pdb1QBU/pdb

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


• Deposited: 1997-04-25 Released: 1997-10-15 
• Deposition Author(s): Ala, P., Chang, C.-H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Work: 0.190 
• R-Value Observed: 0.190 

Literature

Cyclic urea amides: HIV-1 protease inhibitors with low nanomolar potency against both wild type and protease inhibitor resistant mutants of HIV.

Jadhav, P.K., Ala, P., Woerner, F.J., Chang, C.H., Garber, S.S., Anton, E.D., Bacheler, L.T.

(1997) J Med Chem 40: 181-191

• PubMed: 9003516 
• DOI: 10.1021/jm960586t
• Primary Citation of Related Structures:  
  1QBU, 1QBT, 1QBR


• PubMed Abstract: 
  

Cyclic urea amides, a novel series of HIV-1 protease (HIV PR) inhibitors, have increased activity against drug-resistant mutants of the HIV PR. The design strategy for these inhibitors is based on the hypotheses that (i) the hydrogen-bonding interactions between the inhibitor and the protease backbone will remain constant for wild-type and mutant enzymes and (ii) inhibitors which are capable of forming many nonbonded interactions, distributed throughout the active site, will experience a lower percent change in binding energy as a result of mutation in the target enzyme than those that form fewer interactions by partial occupation of the active site. The cyclic urea amide, SD146, forms 14 hydrogen bonds and 191 van der Waals contacts to HIV PR. SD146 is a very potent antiviral agent (IC90 = 5.1 nM) against wild-type HIV and maintains the same or improved level of high potency against a range of mutant strains of HIV with resistance to a wide variety of HIV protease inhibitors.

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Organizational Affiliation: 

DuPont Merck Research Laboratories, DuPont Merck Pharmaceutical Company, Wilmington, Delaware 19880, USA. [e-mail]

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 (PDB Primary Data), 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
846	B	[4R--(1ALPHA,5ALPHA,7BETA)]-3-[(CYCLOPROPHYLMETHYL)HEXAHYDRO-5,6-DIHYDROXY-2-OXO-4,7-BIS(PHENYLMETHYL)-1H-1,3-DIAZEPIN] METHYL-2-THIAZOLYLBENZAMIDE C34 H36 N4 O4 S HFLCERPZYCWLSZ-VKONIRKNSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
846	Ki :  0.057999998331069946   nM  PDBBind
846	Ki:  0.057999998331069946   nM  Binding MOAD
846	Ki:  0.05999999865889549   nM  BindingDB

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Work: 0.190 
• R-Value Observed: 0.190 
• 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: 1997-04-25 
• Released Date: 1997-10-15 
Deposition Author(s): Ala, P., Chang, C.-H.

Revision History 

• Version 1.0: 1997-10-15
  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: 2017-11-29
  Changes: Derived calculations, Other