3M9F | pdb_00003m9f

HIV protease complexed with compound 10b

• PDB DOI: https://doi.org/10.2210/pdb3M9F/pdb

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


• Deposited: 2010-03-22 Released: 2010-06-30 
• Deposition Author(s): Su, H.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.230 (Depositor), 0.217 (DCC) 
• R-Value Work: 
  0.187 (Depositor) 
• R-Value Observed: 
  0.190 (Depositor) 

Literature

Epsilon substituted lysinol derivatives as HIV-1 protease inhibitors.

Jones, K.L., Holloway, M.K., Su, H.P., Carroll, S.S., Burlein, C., Touch, S., DiStefano, D.J., Sanchez, R.I., Williams, T.M., Vacca, J.P., Coburn, C.A.

(2010) Bioorg Med Chem Lett 20: 4065-4068

• PubMed: 20547452 
• DOI: https://doi.org/10.1016/j.bmcl.2010.05.082
• Primary Citation Related Structures: 
  3M9F


• PubMed Abstract: 
  

  A series of HIV-1 protease inhibitors containing an epsilon substituted lysinol backbone was synthesized. Two novel synthetic routes using N-boc-L-glutamic acid alpha-benzyl ester and 2,6-diaminopimelic acid were developed. Incorporation of this epsilon substituent enabled access to the S2 pocket of the enzyme, affording high potency inhibitors. Modeling studies and synthetic efforts suggest the potency increase is due to both conformational bias and van der Waals interactions with the S2 pocket.

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Organizational Affiliation: 
• Department of Medicinal Chemistry, Merck Research Laboratories, PO Box 4, West Point, PA 19486, USA. [e-mail]

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: 23.07 kDa 
• Atom Count: 1,730 
• Modeled Residue Count: 198 
• Deposited Residue Count: 198 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HIV-1 protease	A, B	99	Human immunodeficiency virus 1	Mutation(s): 0
UniProt
Find proteins for Q9WFL7 (Human immunodeficiency virus type 1) Explore Q9WFL7  Go to UniProtKB:  Q9WFL7

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
595	C [auth A], E [auth B]	N-[(1S,5S)-5-{[(4-aminophenyl)sulfonyl](3-methylbutyl)amino}-1-methyl-6-oxohexyl]-Nalpha-(methoxycarbonyl)-beta-phenyl-L-phenylalaninamide C35 H46 N4 O6 S JSZGHYRPBNJGPM-ZMAXYJRFSA-N
CL	D [auth A], F [auth B], G [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.230 (Depositor), 0.217 (DCC) 
• R-Value Work:  0.187 (Depositor) 
• R-Value Observed: 0.190 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.173	α = 90
b = 85.934	β = 90
c = 46.134	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-06-30 
Deposition Author(s): Su, H.P.

Revision History  

• Version 1.0: 2010-06-30
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2024-02-21
  Changes: Data collection, Database references, Derived calculations