5EMJ

Crystal structure of PRMT5:MEP50 with Compound 8 and sinefungin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.273 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.209 

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


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein arginine N-methyltransferase 5
A
645Homo sapiensMutation(s): 0 
Gene Names: PRMT5 (HRMT1L5, IBP72, JBP1, SKB1)
EC: 2.1.1.320
Find proteins for O14744 (Homo sapiens)
Go to Gene View: PRMT5
Go to UniProtKB:  O14744
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Methylosome protein 50
B
350Homo sapiensMutation(s): 0 
Gene Names: WDR77 (MEP50, WD45)
Find proteins for Q9BQA1 (Homo sapiens)
Go to Gene View: WDR77
Go to UniProtKB:  Q9BQA1
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
SFG
Query on SFG

Download SDF File 
Download CCD File 
A
SINEFUNGIN
ADENOSYL-ORNITHINE
C15 H23 N7 O5
LMXOHSDXUQEUSF-YECHIGJVSA-N
 Ligand Interaction
5QJ
Query on 5QJ

Download SDF File 
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
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
5QJIC50: 33 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.273 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.209 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 104.240α = 90.00
b = 138.830β = 90.00
c = 179.340γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
PDB_EXTRACTdata extraction
iMOSFLMdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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