5IVQ | pdb_00005ivq

Crystal Structure of HIV Protease complexed with methyl N-[(1S)-1-benzhydryl-2-(3-morpholin-4-ium-2-ylpropylamino)-2-oxo-ethyl]carbamate

• PDB DOI: https://doi.org/10.2210/pdb5IVQ/pdb

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


• Deposited: 2016-03-21 Released: 2016-05-18 
• Deposition Author(s): Su, H.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.57 Å
• R-Value Free: 
  0.221 (Depositor), 0.223 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.197 (DCC) 
• R-Value Observed: 
  0.194 (Depositor) 

Literature

Discovery of MK-8718, an HIV Protease Inhibitor Containing a Novel Morpholine Aspartate Binding Group.

Bungard, C.J., Williams, P.D., Ballard, J.E., Bennett, D.J., Beaulieu, C., Bahnck-Teets, C., Carroll, S.S., Chang, R.K., Dubost, D.C., Fay, J.F., Diamond, T.L., Greshock, T.J., Hao, L., Holloway, M.K., Felock, P.J., Gesell, J.J., Su, H.P., Manikowski, J.J., McKay, D.J., Miller, M., Min, X., Molinaro, C., Moradei, O.M., Nantermet, P.G., Nadeau, C., Sanchez, R.I., Satyanarayana, T., Shipe, W.D., Singh, S.K., Truong, V.L., Vijayasaradhi, S., Wiscount, C.M., Vacca, J.P., Crane, S.N., McCauley, J.A.

(2016) ACS Med Chem Lett 7: 702-707

• PubMed: 27437081 
• DOI: https://doi.org/10.1021/acsmedchemlett.6b00135
• Primary Citation Related Structures: 
  5IVQ, 5IVR, 5IVS, 5IVT


• PubMed Abstract: 
  

  A novel HIV protease inhibitor was designed using a morpholine core as the aspartate binding group. Analysis of the crystal structure of the initial lead bound to HIV protease enabled optimization of enzyme potency and antiviral activity. This afforded a series of potent orally bioavailable inhibitors of which MK-8718 was identified as a compound with a favorable overall profile.

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Organizational Affiliation: 
• Merck Research Laboratories , 770 Sumneytown Pike, PO Box 4, West Point, Pennsylvania 19486, United States.
Merck Frosst Centre for Therapeutic Research , 16711 TransCanada Highway, Kirkland, Quebec H9H 3L1, Canada.
Albany Molecular Research Singapore Research Center , 61 Science Park Road #05-01, The Galen Singapore Science Park II, Singapore 117525.

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: 22.19 kDa 
• Atom Count: 1,770 
• Modeled 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 1	Mutation(s): 0  Gene Names: pol
UniProt
Find proteins for Q77VV3 (Human immunodeficiency virus type 1) Explore Q77VV3  Go to UniProtKB:  Q77VV3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
6EH	C [auth A]	Nalpha-(methoxycarbonyl)-N-{3-[(2R)-morpholin-2-yl]propyl}-beta-phenyl-L-phenylalaninamide C24 H31 N3 O4 JLOXTJQCNGOWCO-IRLDBZIGSA-N
CL	D [auth A], E [auth B], F [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.57 Å
• R-Value Free:  0.221 (Depositor), 0.223 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.197 (DCC) 
• R-Value Observed: 0.194 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.12	α = 90
b = 86.18	β = 90
c = 46.52	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
BUSTER	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
BUSTER-TNT	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-05-18 
Deposition Author(s): Su, H.P.

Revision History  

• Version 1.0: 2016-05-18
  Type: Initial release
  
• Version 1.1: 2016-08-10
  Changes: Database references
• Version 1.2: 2024-03-06
  Changes: Data collection, Database references, Derived calculations