5IVS

Crystal Structure of HIV Protease complexed with methyl N-[(1S)-1-benzhydryl-2-[2-[2-[(2R,5S)-5-(benzylcarbamoyloxymethyl)morpholin-2-yl]ethyl]anilino]-2-oxo-ethyl]carbamate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.46 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.184 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


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

  • DOI: 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 ...

    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.


    Organizational Affiliation

    Merck Research Laboratories , 770 Sumneytown Pike, PO Box 4, West Point, Pennsylvania 19486, United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ProteaseA, B99Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: pol
UniProt
Find proteins for Q77VV3 (Human immunodeficiency virus 1)
Explore Q77VV3 
Go to UniProtKB:  Q77VV3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ77VV3
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
6EF
Query on 6EF

Download Ideal Coordinates CCD File 
D [auth B]N-(2-{2-[(2R,5S)-5-{[(benzylcarbamoyl)oxy]methyl}morpholin-2-yl]ethyl}phenyl)-Nalpha-(methoxycarbonyl)-beta-phenyl-L-phenylalaninamide
C38 H42 N4 O6
MYPZZBCHYVILMP-UKAHRKLESA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
C [auth A],
E [auth B],
F [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
6EF Binding MOAD:  5IVS IC50: 6.1 (nM) from 1 assay(s)
BindingDB:  5IVS IC50: 6.1 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.46 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.184 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.79α = 90
b = 86.14β = 90
c = 46.06γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
BUSTERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 



Entry History 

Deposition Data

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

Revision History  (Full details and data files)

  • Version 1.0: 2016-05-18
    Type: Initial release
  • Version 1.1: 2016-08-10
    Changes: Database references