5EMJ

Crystal structure of PRMT5:MEP50 with Compound 8 and sinefungin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.27 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.211 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure and Property Guided Design in the Identification of PRMT5 Tool Compound EPZ015666.

Duncan, K.W.Rioux, N.Boriack-Sjodin, P.A.Munchhof, M.J.Reiter, L.A.Majer, C.R.Jin, L.Johnston, L.D.Chan-Penebre, E.Kuplast, K.G.Porter Scott, M.Pollock, R.M.Waters, N.J.Smith, J.J.Moyer, M.P.Copeland, R.A.Chesworth, R.

(2016) ACS Med Chem Lett 7: 162-166

  • DOI: 10.1021/acsmedchemlett.5b00380
  • Primary Citation of Related Structures:  
    5EMM, 5EMJ, 5EML, 5EMK

  • PubMed Abstract: 
  • The recent publication of a potent and selective inhibitor of protein methyltransferase 5 (PRMT5) provides the scientific community with in vivo-active tool compound EPZ015666 (GSK3235025) to probe the underlying pharmacology of this key enzyme. Here ...

    The recent publication of a potent and selective inhibitor of protein methyltransferase 5 (PRMT5) provides the scientific community with in vivo-active tool compound EPZ015666 (GSK3235025) to probe the underlying pharmacology of this key enzyme. Herein, we report the design and optimization strategies employed on an initial hit compound with poor in vitro clearance to yield in vivo tool compound EPZ015666 and an additional potent in vitro tool molecule EPZ015866 (GSK3203591).


    Organizational Affiliation

    Epizyme, Inc. , 400 Technology Square, Cambridge, Massachusetts 02139, United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Protein arginine N-methyltransferase 5A645Homo sapiensMutation(s): 0 
Gene Names: PRMT5HRMT1L5IBP72JBP1SKB1
EC: 2.1.1 (PDB Primary Data), 2.1.1.125 (PDB Primary Data), 2.1.1.320 (UniProt)
Find proteins for O14744 (Homo sapiens)
Explore O14744 
Go to UniProtKB:  O14744
NIH Common Fund Data Resources
PHAROS  O14744
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Methylosome protein 50B350Homo sapiensMutation(s): 0 
Gene Names: WDR77MEP50WD45HKMT1069Nbla10071
Find proteins for Q9BQA1 (Homo sapiens)
Explore Q9BQA1 
Go to UniProtKB:  Q9BQA1
NIH Common Fund Data Resources
PHAROS  Q9BQA1
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
5QJ
Query on 5QJ

Download CCD File 
A
(2~{S})-1-(3,4-dihydro-1~{H}-isoquinolin-2-yl)-3-[[4-(3-methylbenzimidazol-5-yl)pyridin-2-yl]amino]propan-2-ol
C25 H27 N5 O
PNOIRPBZBNYURC-QFIPXVFZSA-N
 Ligand Interaction
SFG
Query on SFG

Download CCD File 
A
SINEFUNGIN
C15 H23 N7 O5
LMXOHSDXUQEUSF-YECHIGJVSA-N
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
A, B
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
5QJIC50:  33   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.27 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.211 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.24α = 90
b = 138.83β = 90
c = 179.34γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
iMOSFLMdata reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-02-24
    Type: Initial release
  • Version 1.1: 2016-07-27
    Changes: Data collection
  • Version 1.2: 2018-04-18
    Changes: Data collection, Database references, Derived calculations