5IVR | pdb_00005ivr

Crystal Structure of HIV Protease complexed with methyl N-[(1S)-1-[[2-[(3S)-3-[(4-aminophenyl)methylamino]-4-hydroxy-butyl]phenyl]carbamoyl]-2,2-diphenyl-ethyl]carbamate

• PDB DOI: https://doi.org/10.2210/pdb5IVR/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: 1.50 Å
• R-Value Free: 
  0.207 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.193 (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 of 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.

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: 22.37 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	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
6EG	E [auth B]	N-{2-[(3S)-3-{[(4-aminophenyl)methyl]amino}-4-hydroxybutyl]phenyl}-Nalpha-(methoxycarbonyl)-beta-phenyl-L-phenylalaninamide C34 H38 N4 O4 OMLKMYZREOOQQQ-NYDCQLBNSA-N
CL	C [auth A], 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: 1.50 Å
• R-Value Free:  0.207 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.193 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.19	α = 90
b = 85.96	β = 90
c = 46.35	γ = 90

Software Package:

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