Biological Assembly 1  

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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: 22088.93 
• Atom Count: 1576 
• Residue Count: 198 
• Unique protein chains: 1

1AID

STRUCTURE OF A NON-PEPTIDE INHIBITOR COMPLEXED WITH HIV-1 PROTEASE: DEVELOPING A CYCLE OF STRUCTURE-BASED DRUG DESIGN

• DOI: 10.2210/pdb1AID/pdb

• Classification: HYDROLASE
• Organism(s): Human immunodeficiency virus type 1 group M subtype B
• Expression System: Escherichia coli


• Deposited: 1997-04-16 Released: 1997-10-15 
• Deposition Author(s): Rutenber, E.E., Fauman, E.B., Keenan, R.J., Stroud, R.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.2 Å
• R-Value Work: 0.174 

Literature

Structure of a non-peptide inhibitor complexed with HIV-1 protease. Developing a cycle of structure-based drug design.

Rutenber, E., Fauman, E.B., Keenan, R.J., Fong, S., Furth, P.S., Ortiz de Montellano, P.R., Meng, E., Kuntz, I.D., DeCamp, D.L., Salto, R., Rosb, J.R., Craik, C.S., Stroud, R.M.

(1993) J.Biol.Chem. 268: 15343-15346

• PubMed: 8340363 
• Primary Citation of Related Structures:  
  2AID


• PubMed Abstract: 
  

A stable, non-peptide inhibitor of the protease from type 1 human immunodeficiency virus has been developed, and the stereochemistry of binding defined through crystallographic three-dimensional structure determination. The initial compound, haloperidol, was discovered through computational screening of the Cambridge Structural Database using a shape complementarity algorithm. The subsequent modification is a non-peptidic lateral lead, which belongs to a family of compounds with well characterized pharmacological properties. This thioketal derivative of haloperidol and a halide counterion are bound within the enzyme active site in a mode distinct from the observed for peptide-based inhibitors. A variant of the protease cocrystallized with this inhibitor shows binding in the manner predicted during the initial computer-based search. The structures provide the context for subsequent synthetic modifications of the inhibitor.

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Organizational Affiliation: 

Department of Biochemistry and Biophysics, University of California, San Francisco 94143-0448.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
HUMAN IMMUNODEFICIENCY VIRUS PROTEASE	A, B	99	Human immunodeficiency virus type 1 group M subtype B	Mutation(s): 0  Gene Names: gag-pol
Find proteins for P03369 (Human immunodeficiency virus type 1 group M subtype B) Go to UniProtKB:  P03369

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
CL	B	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
THK	B	4-(4-CHLORO-PHENYL)-1-{3-[2-(4-FLUORO-PHENYL)-[1,3]DITHIOLAN-2-YL]-PROPYL}-PIPERIDIN-4-OL C23 H27 Cl F N O S2 KVDKNVPAAQKHKD-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
THK	Ki: 15000 nM BINDINGMOAD
THK	Ki: 15000 nM PDBBIND

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.2 Å
• R-Value Work: 0.174 
• Space Group: P 4₁

Unit Cell:

Length (Å)	Angle (°)
a = 50.200	α = 90.00
b = 50.200	β = 90.00
c = 100.400	γ = 90.00

Software Package:

Software Name	Purpose
X-PLOR	phasing
X-PLOR	refinement
XENGEN	data scaling
X-PLOR	model building
BUDDHA	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1997-04-16 
• Released Date: 1997-10-15 
• Deposition Author(s): Rutenber, E.E., Fauman, E.B., Keenan, R.J., Stroud, R.M.

Revision History 

• Version 1.0: 1997-10-15
  Type: Initial release
• Version 1.1: 2008-03-24
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance