5IVS | pdb_00005ivs

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 (Depositor), 0.193 (DCC) 
  • R-Value Work: 
    0.183 (Depositor), 0.178 (DCC) 
  • R-Value Observed: 
    0.184 (Depositor) 

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.2 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: 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.

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

Macromolecule Content 

  • Total Structure Weight: 22.42 kDa 
  • Atom Count: 1,820 
  • Modeled Residue Count: 198 
  • Deposited Residue Count: 198 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Protease
A, B
99Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: pol
UniProt
Find proteins for Q77VV3 (Human immunodeficiency virus type 1)
Explore Q77VV3 
Go to UniProtKB:  Q77VV3
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ77VV3
Sequence Annotations
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Reference Sequence

Small Molecules

Binding Affinity Annotations 
IDSourceBinding Affinity
6EF 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 (Depositor), 0.193 (DCC) 
  • R-Value Work:  0.183 (Depositor), 0.178 (DCC) 
  • R-Value Observed: 0.184 (Depositor) 
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

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

  • 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
  • Version 1.2: 2024-03-06
    Changes: Data collection, Database references, Derived calculations