1XL2

HIV-1 Protease in complex with pyrrolidinmethanamine

• PDB DOI: https://doi.org/10.2210/pdb1XL2/pdb

• Classification: HYDROLASE
• Organism(s): Human immunodeficiency virus 1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2004-09-30 Released: 2005-06-07 
• Deposition Author(s): Boettcher, J., Specker, E., Heine, A., Klebe, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.236 
• R-Value Work: 0.182 
• R-Value Observed: 0.182 

Starting Model: experimental

Literature

An Old Target Revisited: Two New Privileged Skeletons and an Unexpected Binding Mode For HIV-Protease Inhibitors

Specker, E., Boettcher, J., Lilie, H., Heine, A., Schoop, A., Muller, G., Griebenow, N., Klebe, G.

(2005) Angew Chem Int Ed Engl 44: 3140-3144

• PubMed: 15822136 
• DOI: https://doi.org/10.1002/anie.200462643
• Primary Citation of Related Structures:  
  1XL2, 1XL5

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Organizational Affiliation: 

Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032 Marburg, Germany.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 22.35 kDa 
• Atom Count: 1,774 
• Modelled Residue Count: 198 
• Deposited Residue Count: 198 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEASE RETROPEPSIN	A, B	99	Human immunodeficiency virus 1	Mutation(s): 0  Gene Names: gag-pol EC: 3.4.23.16
UniProt
Find proteins for P03367 (Human immunodeficiency virus type 1 group M subtype B (isolate BRU/LAI)) Explore P03367  Go to UniProtKB:  P03367

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
189	D [auth A]	N-BENZYL-2-(2,6-DIMETHYLPHENOXY)-N-[((3R,4S)-4-{[ISOBUTYL(PHENYLSULFONYL)AMINO]METHYL}PYRROLIDIN-3-YL)METHYL]ACETAMIDE C33 H43 N3 O4 S MQRMHPRUUKDEKO-LOYHVIPDSA-N
GOL	F [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	C [auth A], E [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.236 
• R-Value Work: 0.182 
• R-Value Observed: 0.182 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.9	α = 90
b = 57.7	β = 90
c = 62.2	γ = 90

Software Package:

Software Name	Purpose
MAR345	data collection
HKL-2000	data reduction
AMoRE	phasing
SHELXL-97	refinement
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-06-07 
Deposition Author(s): Boettcher, J., Specker, E., Heine, A., Klebe, G.

Revision History  

• Version 1.0: 2005-06-07
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 1.4: 2023-08-23
  Changes: Data collection, Database references, Derived calculations, Refinement description