5EML

Crystal structure of PRMT5:MEP50 with Compound 10 and SAM


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.39 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.208 

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
5QK
Query on 5QK

Download SDF File 
Download CCD File 
A
~{N}-[(2~{R})-3-(3,4-dihydro-1~{H}-isoquinolin-2-yl)-2-oxidanyl-propyl]-2-quinolin-8-yloxy-ethanamide
C23 H25 N3 O3
ZVCIZCPAJITPQB-HXUWFJFHSA-N
 Ligand Interaction
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
SAM
Query on SAM

Download SDF File 
Download CCD File 
A
S-ADENOSYLMETHIONINE
C15 H22 N6 O5 S
MEFKEPWMEQBLKI-FCKMPRQPSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
5QKIC50: 23 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.39 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.208 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 103.400α = 90.00
b = 138.130β = 90.00
c = 178.920γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
Aimlessdata scaling
PDB_EXTRACTdata extraction

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