6P7I

Crystal structure of Human PRMT6 in complex with S-Adenosyl-L-Homocysteine and YS17-117 Compound

PDB DOI: https://doi.org/10.2210/pdb6P7I/pdb

Classification: Transferase/Transferase Inhibitor
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): Yes

Deposited: 2019-06-05 Released: 2019-06-26
Deposition Author(s): Halabelian, L., Dong, A., Zeng, H., Li, Y., Seitova, A., Hutchinson, A., Bountra, C., Edwards, A.M., Arrowsmith, C.H., Brown, P.J., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.222 (Depositor), 0.227 (DCC)
R-Value Work:
0.184 (Depositor), 0.194 (DCC)
R-Value Observed:
0.185 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Discovery of a First-in-Class Protein Arginine Methyltransferase 6 (PRMT6) Covalent Inhibitor

Shen, Y., Li, F., Szewczyk, M.M., Halabelian, L., Park, K.S., Chau, I., Dong, A., Zeng, H., Chen, H., Meng, F., Barsyte-Lovejoy, D., Arrowsmith, C.H., Brown, P.J., Liu, J., Vedadi, M., Jin, J.

(2020) J Med Chem 63: 5477-5487

DOI: https://doi.org/10.1021/acs.jmedchem.0c00406

Macromolecule Content

Total Structure Weight: 171.22 kDa
Atom Count: 11,633
Modelled Residue Count: 1,351
Deposited Residue Count: 1,504
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein arginine N-methyltransferase 6	A, B, C, D	376	Homo sapiens	Mutation(s): 1 Gene Names: PRMT6, HRMT1L6 EC: 2.1.1.319
UniProt & NIH Common Fund Data Resources
Find proteins for Q96LA8 (Homo sapiens) Explore Q96LA8 Go to UniProtKB: Q96LA8
PHAROS: Q96LA8 GTEx: ENSG00000198890
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q96LA8
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SAH Query on SAH Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] SDF format, chain K [auth C] SDF format, chain M [auth D] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain K [auth C] MOL2 format, chain M [auth D] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain K [auth C] mmCIF format, chain M [auth D]	E [auth A], H [auth B], K [auth C], M [auth D]	S-ADENOSYL-L-HOMOCYSTEINE C₁₄ H₂₀ N₆ O₅ S ZJUKTBDSGOFHSH-WFMPWKQPSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain M [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain M [auth D]
O3S (Subject of Investigation/LOI) Query on O3S Download Ideal Coordinates CCD File SDF format, chain N [auth D] MOL2 format, chain N [auth D] mmCIF format, chain N [auth D]	N [auth D]	N-[3-(4-{[(2-aminoethyl)(methyl)amino]methyl}-1H-pyrrol-3-yl)phenyl]propanamide C₁₇ H₂₄ N₄ O ZXTYIIDDTFQCGV-UHFFFAOYSA-N		Interactions Focus chain N [auth D] Interactions & Density Focus chain N [auth D]
O3P Query on O3P Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain I [auth B] SDF format, chain L [auth C] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain L [auth C] mmCIF format, chain F [auth A] mmCIF format, chain I [auth B] mmCIF format, chain L [auth C]	F [auth A], I [auth B], L [auth C]	N-[3-(4-{[(2-aminoethyl)(methyl)amino]methyl}-1H-pyrrol-3-yl)phenyl]prop-2-enamide C₁₇ H₂₂ N₄ O HVDMIAFOVVMNJF-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain I [auth B] Focus chain L [auth C] Interactions & Density Focus chain F [auth A] Focus chain I [auth B] Focus chain L [auth C]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain J [auth B] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] mmCIF format, chain G [auth A] mmCIF format, chain J [auth B]	G [auth A], J [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain J [auth B] Interactions & Density Focus chain G [auth A] Focus chain J [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
O3P	BindingDB: 6P7I	Ki: 16 (nM) from 1 assay(s)
O3P	BindingDB: 6P7I	IC50: min: 18, max: 1300 (nM) from 2 assay(s)
O3S	BindingDB: 6P7I	IC50: 28 (nM) from 1 assay(s)
SAH	BindingDB: 6P7I	IC50: 2177 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.222 (Depositor), 0.227 (DCC)
R-Value Work: 0.184 (Depositor), 0.194 (DCC)
R-Value Observed: 0.185 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.091	α = 90
b = 135.133	β = 98.01
c = 83.206	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
REFMAC	phasing
HKL-3000	data reduction
HKL-3000	data collection

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2019-06-26

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2019-06-26
Type: Initial release
Version 1.1: 2022-02-23
Changes: Database references, Refinement description
Version 1.2: 2023-10-11
Changes: Data collection, Refinement description
Version 1.3: 2024-10-09
Changes: Data collection, Structure summary