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: 1556 
• Residue Count: 198 
• Unique protein chains: 1

1QBS

HIV-1 PROTEASE INHIBITORS WIIH LOW NANOMOLAR POTENCY

• DOI: 10.2210/pdb1QBS/pdb

• Classification: ASPARTYL PROTEASE
• Organism(s): Human immunodeficiency virus 1
• Expression System: Escherichia coli
• Mutation(s): Yes 


• 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: 0.189 
• R-Value Observed: 0.189 

Literature

Cyclic HIV protease inhibitors: synthesis, conformational analysis, P2/P2' structure-activity relationship, and molecular recognition of cyclic ureas.

Lam, P.Y., Ru, Y., Jadhav, P.K., Aldrich, P.E., DeLucca, G.V., Eyermann, C.J., Chang, C.H., Emmett, G., Holler, E.R., Daneker, W.F., Li, L., Confalone, P.N., McHugh, R.J., Han, Q., Li, R., Markwalder, J.A., Seitz, S.P., Sharpe, T.R., Bacheler, L.T., Rayner, M.M., Klabe, R.M., Shum, L., Winslow, D.L., Kornhauser, D.M., Jackson, D.A., Erickson-Viitanen, S., Hodge, C.N.

(1996) J Med Chem 39: 3514-3525

• PubMed: 8784449 
• DOI: 10.1021/jm9602571
• Primary Citation of Related Structures:  
  1QBS


• PubMed Abstract: 
  

High-resolution X-ray structures of the complexes of HIV-1 protease (HIV-1PR) with peptidomimetic inhibitors reveal the presence of a structural water molecule which is hydrogen bonded to both the mobile flaps of the enzyme and the two carbonyls flanking the transition-state mimic of the inhibitors. Using the structure-activity relationships of C2-symmetric diol inhibitors, computed-aided drug design tools, and first principles, we designed and synthesized a novel class of cyclic ureas that incorporates this structural water and preorganizes the side chain residues into optimum binding conformations. Conformational analysis suggested a preference for pseudodiaxial benzylic and pseudodiequatorial hydroxyl substituents and an enantiomeric preference for the RSSR stereochemistry. The X-ray and solution NMR structure of the complex of HIV-1PR and one such cyclic urea, DMP323, confirmed the displacement of the structural water. Additionally, the bound and "unbound" (small-molecule X-ray) ligands have similar conformations. The high degree of preorganization, the complementarity, and the entropic gain of water displacement are proposed to explain the high affinity of these small molecules for the enzyme. The small size probably contributes to the observed good oral bioavailability in animals. Extensive structure-based optimization of the side chains that fill the S2 and S2' pockets of the enzyme resulted in DMP323, which was studied in phase I clinical trials but found to suffer from variable pharmacokinetics in man. This report details the synthesis, conformational analysis, structure-activity relationships, and molecular recognition of this series of C2-symmetry HIV-1PR inhibitors. An initial series of cyclic ureas containing nonsymmetric P2/P2' is also discussed.

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Organizational Affiliation: 

DuPont Merck Pharmaceutical Company, DuPont Merck Experimental Station, Wilmington, Delaware 19880-0500, 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): 1  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
DMP	A	[4-R-(-4-ALPHA,5-ALPHA,6-BETA,7-BETA)]-HEXAHYDRO-5,6-BIS(HYDROXY)-[1,3-BIS([4-HYDROXYMETHYL-PHENYL]METHYL)-4,7-BIS(PHEN YLMETHYL)]-2H-1,3-DIAZEPINONE C35 H38 N2 O5 XCVGQMUMMDXKCY-WZJLIZBTSA-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 %)
DMP	Ki:  0.27000001072883606   nM  BindingDB
DMP	Kd:  3.8299999237060547   nM  BindingDB
DMP	Ki:  0.3199999928474426   nM  BindingDB
DMP	IC50:  15   nM  BindingDB
DMP	Ki:  0.3400000035762787   nM  Binding MOAD
DMP	Ki :  0.3400000035762787   nM  PDBBind
DMP	IC50:  110   nM  BindingDB
DMP	Ki:  0.27000001072883606   nM  BindingDB
DMP	Ki:  0.3100000023841858   nM  BindingDB
DMP	Ki:  0.3100000023841858   nM  BindingDB
DMP	Ki:  1   nM  BindingDB
DMP	Ki:  0.3400000035762787   nM  BindingDB
DMP	Ki:  0.28999999165534973   nM  BindingDB
DMP	Ki:  0.33000001311302185   nM  BindingDB

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Work: 0.189 
• R-Value Observed: 0.189 
• 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: 2012-02-22
  Changes: Database references
• Version 1.4: 2017-11-29
  Changes: Derived calculations, Other