5EMJ

Crystal structure of PRMT5:MEP50 with Compound 8 and sinefungin

PDB DOI: https://doi.org/10.2210/pdb5EMJ/pdb

Classification: TRANSFERASE/TRANSFERASE INHIBITOR
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2015-11-06 Released: 2016-02-24
Deposition Author(s): Boriack-Sjodin, P.A., Jin, L.

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

Ligand Structure Quality Assessment

This is version 1.3 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

PubMed: 26985292 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1021/acsmedchemlett.5b00380
Primary Citation of Related Structures:
5EMJ, 5EMK, 5EML, 5EMM

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. 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.

Macromolecule Content

Total Structure Weight: 112.79 kDa
Atom Count: 7,774
Modelled Residue Count: 928
Deposited Residue Count: 995
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein arginine N-methyltransferase 5	A	645	Homo sapiens	Mutation(s): 0 Gene Names: PRMT5, HRMT1L5, IBP72, JBP1, SKB1 EC: 2.1.1 (PDB Primary Data), 2.1.1.125 (PDB Primary Data), 2.1.1.320 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for O14744 (Homo sapiens) Explore O14744 Go to UniProtKB: O14744
PHAROS: O14744 GTEx: ENSG00000100462
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O14744
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Methylosome protein 50	B	350	Homo sapiens	Mutation(s): 0 Gene Names: WDR77, MEP50, WD45, HKMT1069, Nbla10071
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BQA1 (Homo sapiens) Explore Q9BQA1 Go to UniProtKB: Q9BQA1
PHAROS: Q9BQA1 GTEx: ENSG00000116455
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9BQA1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
5QJ Query on 5QJ Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth 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		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
SFG Query on SFG Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	SINEFUNGIN C₁₅ H₂₃ N₇ O₅ LMXOHSDXUQEUSF-YECHIGJVSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth B] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth B]	E [auth A], F [auth A], G [auth A], H [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
5QJ	BindingDB: 5EMJ	IC50: min: 33, max: 180 (nM) from 3 assay(s)
SFG	BindingDB: 5EMJ	IC50: 8600 (nM) from 1 assay(s)

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 = 104.24	α = 90
b = 138.83	β = 90
c = 179.34	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
iMOSFLM	data reduction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2016-02-24

Deposition Author(s):

Boriack-Sjodin, P.A.

Jin, L.

Revision History (Full details and data files)

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
Version 1.3: 2024-10-23
Changes: Data collection, Database references, Structure summary