2XYF

HIV-1 Inhibitors with a Tertiary-Alcohol-containing Transition-State Mimic and various P2 and P1 prime Substituents

• PDB DOI: https://doi.org/10.2210/pdb2XYF/pdb

• Classification: HYDROLASE
• Organism(s): Human immunodeficiency virus type 1 (Z2/CDC-Z34 ISOLATE)
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2010-11-17 Released: 2011-12-07 
• Deposition Author(s): Ohrngren, P., Wu, X., Persson, M., Ekegren, J.K., Wallberg, H., Rosenquist, A., Samuelsson, B., Unge, T., Larhed, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.250 
• R-Value Work: 0.223 
• R-Value Observed: 0.223 

Literature

HIV-1 Protease Inhibitors with a Tertiary Alcohol Containing Transition-State Mimic and Various P2 and P1' Substituents

Ohrngren, P., Wu, X., Persson, M., Ekegren, J.K., Wallberg, H., Vrang, L., Rosenquist, A., Samuelsson, B., Unge, T., Larhed, M.

(2011) Medchemcomm 2: 701

• DOI: https://doi.org/10.1039/C1MD00077B

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 22.26 kDa 
• Atom Count: 1,704 
• Modelled Residue Count: 198 
• Deposited Residue Count: 198 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEASE	A, B	99	Human immunodeficiency virus type 1 (Z2/CDC-Z34 ISOLATE)	Mutation(s): 3  EC: 3.4.23.16
UniProt
Find proteins for P12499 (Human immunodeficiency virus type 1 group M subtype D (isolate Z2/CDC-Z34)) Explore P12499  Go to UniProtKB:  P12499

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
G40	C [auth B]	METHYL N-[(2S)-1-[2-[(4R)-5-[[(2S)-3,3-DIMETHYL-1-METHYLAMINO-1-OXO-BUTAN-2-YL]AMINO]-4-HYDROXY-5-OXO-4-(PHENYLMETHYL)PENTYL]-2-[(4-THIOPHEN-3-YLPHENYL)METHYL]HYDRAZINYL]-3,3-DIMETHYL-1-OXO-BUTAN-2-YL]CARBAMATE C38 H53 N5 O6 S XNAIGGHDLWCRFU-SQQFMCCZSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
G40	PDBBind:  2XYF	Ki: 3.6 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.250 
• R-Value Work: 0.223 
• R-Value Observed: 0.223 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.12	α = 90
b = 85.88	β = 90
c = 46.17	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
MOSFLM	data reduction
CCP4	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-12-07 
Deposition Author(s): Ohrngren, P., Wu, X., Persson, M., Ekegren, J.K., Wallberg, H., Rosenquist, A., Samuelsson, B., Unge, T., Larhed, M.

Revision History  

• Version 1.0: 2011-12-07
  Type: Initial release
  
• Version 1.1: 2012-04-04
  Changes: Other
• Version 1.2: 2018-01-17
  Changes: Data collection
• Version 1.3: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description