6UE6 | pdb_00006ue6

PWWP1 domain of NSD2 in complex with MR837

PDB DOI: https://doi.org/10.2210/pdb6UE6/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2019-09-20 Released: 2019-11-13
Deposition Author(s): Liu, Y., Tempel, W., De Freitas, R.F., Schapira, M., Brown, P.J., Bountra, C., Edwards, A.M., Arrowsmith, C.H., Min, J., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.252 (Depositor), 0.273 (DCC)
R-Value Work:
0.235 (Depositor), 0.248 (DCC)
R-Value Observed:
0.236 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Discovery of Small-Molecule Antagonists of the PWWP Domain of NSD2.

Ferreira de Freitas, R., Liu, Y., Szewczyk, M.M., Mehta, N., Li, F., McLeod, D., Zepeda-Velazquez, C., Dilworth, D., Hanley, R.P., Gibson, E., Brown, P.J., Al-Awar, R., James, L.I., Arrowsmith, C.H., Barsyte-Lovejoy, D., Min, J., Vedadi, M., Schapira, M., Allali-Hassani, A.

(2021) J Med Chem 64: 1584-1592

PubMed: 33522809 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1021/acs.jmedchem.0c01768
Primary Citation Related Structures:
6UE6

PubMed Abstract:
Increased activity of the lysine methyltransferase NSD2 driven by translocation and activating mutations is associated with multiple myeloma and acute lymphoblastic leukemia, but no NSD2-targeting chemical probe has been reported to date. Here, we present the first antagonists that block the protein-protein interaction between the N-terminal PWWP domain of NSD2 and H3K36me2. Using virtual screening and experimental validation, we identified the small-molecule antagonist 3f , which binds to the NSD2-PWWP1 domain with a K _d of 3.4 μM and abrogates histone H3K36me2 binding to the PWWP1 domain in cells. This study establishes an alternative approach to targeting NSD2 and provides a small-molecule antagonist that can be further optimized into a chemical probe to better understand the cellular function of this protein.

Organizational Affiliation

Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada.

Macromolecule Content

Total Structure Weight: 130.79 kDa
Atom Count: 7,347
Modeled Residue Count: 966
Deposited Residue Count: 1,128
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone-lysine N-methyltransferase NSD2	A, B, C, D, E A, B, C, D, E, F, G, H	141	Homo sapiens	Mutation(s): 0 Gene Names: NSD2, KIAA1090, MMSET, TRX5, WHSC1 EC: 2.1.1.43 (PDB Primary Data), 2.1.1.357 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for O96028 (Homo sapiens) Explore O96028 Go to UniProtKB: O96028
PHAROS: O96028 GTEx: ENSG00000109685
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O96028
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
Q5D (Subject of Investigation/LOI) Query on Q5D Download:Ideal Coordinates CCD File SDF format, chain ZA [auth G] SDF format, chain UA [auth F] SDF format, chain S [auth B] SDF format, chain OA [auth E] SDF format, chain LB [auth H] SDF format, chain KA [auth D] SDF format, chain I [auth A] SDF format, chain EA [auth C] MOL2 format, chain ZA [auth G] MOL2 format, chain UA [auth F] MOL2 format, chain S [auth B] MOL2 format, chain OA [auth E] MOL2 format, chain LB [auth H] MOL2 format, chain KA [auth D] MOL2 format, chain I [auth A] MOL2 format, chain EA [auth C] mmCIF format, chain ZA [auth G] mmCIF format, chain UA [auth F] mmCIF format, chain S [auth B] mmCIF format, chain OA [auth E] mmCIF format, chain LB [auth H] mmCIF format, chain KA [auth D] mmCIF format, chain I [auth A] mmCIF format, chain EA [auth C]	EA [auth C] I [auth A] KA [auth D] LB [auth H] OA [auth E] EA [auth C], I [auth A], KA [auth D], LB [auth H], OA [auth E], S [auth B], UA [auth F], ZA [auth G]	4-cyano-N-cyclopropyl-N-[(thiophen-2-yl)methyl]benzamide C₁₆ H₁₄ N₂ O S WYAGGMZTARRIDX-UHFFFAOYSA-N		Interactions Focus chain EA [auth C] Focus chain I [auth A] Focus chain KA [auth D] Focus chain LB [auth H] Focus chain OA [auth E] Focus chain S [auth B] Focus chain UA [auth F] Focus chain ZA [auth G] Interactions & Density Focus chain EA [auth C] Focus chain I [auth A] Focus chain KA [auth D] Focus chain LB [auth H] Focus chain OA [auth E] Focus chain S [auth B] Focus chain UA [auth F] Focus chain ZA [auth G]
UNX Query on UNX Download:Ideal Coordinates CCD File SDF format, chain Z [auth B] SDF format, chain YA [auth F] SDF format, chain Y [auth B] SDF format, chain XA [auth F] SDF format, chain X [auth B] SDF format, chain WA [auth F] SDF format, chain W [auth B] SDF format, chain VA [auth F] SDF format, chain V [auth B] SDF format, chain U [auth B] SDF format, chain TA [auth E] SDF format, chain T [auth B] SDF format, chain SA [auth E] SDF format, chain RA [auth E] SDF format, chain R [auth A] SDF format, chain QA [auth E] SDF format, chain Q [auth A] SDF format, chain PA [auth E] SDF format, chain P [auth A] SDF format, chain OB [auth H] SDF format, chain O [auth A] SDF format, chain NB [auth H] SDF format, chain NA [auth D] SDF format, chain N [auth A] SDF format, chain MB [auth H] SDF format, chain MA [auth D] SDF format, chain M [auth A] SDF format, chain LA [auth D] SDF format, chain L [auth A] SDF format, chain KB [auth G] SDF format, chain K [auth A] SDF format, chain JB [auth G] SDF format, chain JA [auth C] SDF format, chain J [auth A] SDF format, chain IB [auth G] SDF format, chain IA [auth C] SDF format, chain HB [auth G] SDF format, chain HA [auth C] SDF format, chain GB [auth G] SDF format, chain GA [auth C] SDF format, chain FB [auth G] SDF format, chain FA [auth C] SDF format, chain EB [auth G] SDF format, chain DB [auth G] SDF format, chain DA [auth B] SDF format, chain CB [auth G] SDF format, chain CA [auth B] SDF format, chain BB [auth G] SDF format, chain BA [auth B] SDF format, chain AB [auth G] SDF format, chain AA [auth B] MOL2 format, chain Z [auth B] MOL2 format, chain YA [auth F] MOL2 format, chain Y [auth B] MOL2 format, chain XA [auth F] MOL2 format, chain X [auth B] MOL2 format, chain WA [auth F] MOL2 format, chain W [auth B] MOL2 format, chain VA [auth F] MOL2 format, chain V [auth B] MOL2 format, chain U [auth B] MOL2 format, chain TA [auth E] MOL2 format, chain T [auth B] MOL2 format, chain SA [auth E] MOL2 format, chain RA [auth E] MOL2 format, chain R [auth A] MOL2 format, chain QA [auth E] MOL2 format, chain Q [auth A] MOL2 format, chain PA [auth E] MOL2 format, chain P [auth A] MOL2 format, chain OB [auth H] MOL2 format, chain O [auth A] MOL2 format, chain NB [auth H] MOL2 format, chain NA [auth D] MOL2 format, chain N [auth A] MOL2 format, chain MB [auth H] MOL2 format, chain MA [auth D] MOL2 format, chain M [auth A] MOL2 format, chain LA [auth D] MOL2 format, chain L [auth A] MOL2 format, chain KB [auth G] MOL2 format, chain K [auth A] MOL2 format, chain JB [auth G] MOL2 format, chain JA [auth C] MOL2 format, chain J [auth A] MOL2 format, chain IB [auth G] MOL2 format, chain IA [auth C] MOL2 format, chain HB [auth G] MOL2 format, chain HA [auth C] MOL2 format, chain GB [auth G] MOL2 format, chain GA [auth C] MOL2 format, chain FB [auth G] MOL2 format, chain FA [auth C] MOL2 format, chain EB [auth G] MOL2 format, chain DB [auth G] MOL2 format, chain DA [auth B] MOL2 format, chain CB [auth G] MOL2 format, chain CA [auth B] MOL2 format, chain BB [auth G] MOL2 format, chain BA [auth B] MOL2 format, chain AB [auth G] MOL2 format, chain AA [auth B] mmCIF format, chain Z [auth B] mmCIF format, chain YA [auth F] mmCIF format, chain Y [auth B] mmCIF format, chain XA [auth F] mmCIF format, chain X [auth B] mmCIF format, chain WA [auth F] mmCIF format, chain W [auth B] mmCIF format, chain VA [auth F] mmCIF format, chain V [auth B] mmCIF format, chain U [auth B] mmCIF format, chain TA [auth E] mmCIF format, chain T [auth B] mmCIF format, chain SA [auth E] mmCIF format, chain RA [auth E] mmCIF format, chain R [auth A] mmCIF format, chain QA [auth E] mmCIF format, chain Q [auth A] mmCIF format, chain PA [auth E] mmCIF format, chain P [auth A] mmCIF format, chain OB [auth H] mmCIF format, chain O [auth A] mmCIF format, chain NB [auth H] mmCIF format, chain NA [auth D] mmCIF format, chain N [auth A] mmCIF format, chain MB [auth H] mmCIF format, chain MA [auth D] mmCIF format, chain M [auth A] mmCIF format, chain LA [auth D] mmCIF format, chain L [auth A] mmCIF format, chain KB [auth G] mmCIF format, chain K [auth A] mmCIF format, chain JB [auth G] mmCIF format, chain JA [auth C] mmCIF format, chain J [auth A] mmCIF format, chain IB [auth G] mmCIF format, chain IA [auth C] mmCIF format, chain HB [auth G] mmCIF format, chain HA [auth C] mmCIF format, chain GB [auth G] mmCIF format, chain GA [auth C] mmCIF format, chain FB [auth G] mmCIF format, chain FA [auth C] mmCIF format, chain EB [auth G] mmCIF format, chain DB [auth G] mmCIF format, chain DA [auth B] mmCIF format, chain CB [auth G] mmCIF format, chain CA [auth B] mmCIF format, chain BB [auth G] mmCIF format, chain BA [auth B] mmCIF format, chain AB [auth G] mmCIF format, chain AA [auth B]	AA [auth B] AB [auth G] BA [auth B] BB [auth G] CA [auth B] AA [auth B], AB [auth G], BA [auth B], BB [auth G], CA [auth B], CB [auth G], DA [auth B], DB [auth G], EB [auth G], FA [auth C], FB [auth G], GA [auth C], GB [auth G], HA [auth C], HB [auth G], IA [auth C], IB [auth G], J [auth A], JA [auth C], JB [auth G], K [auth A], KB [auth G], L [auth A], LA [auth D], M [auth A], MA [auth D], MB [auth H], N [auth A], NA [auth D], NB [auth H], O [auth A], OB [auth H], P [auth A], PA [auth E], Q [auth A], QA [auth E], R [auth A], RA [auth E], SA [auth E], T [auth B], TA [auth E], U [auth B], V [auth B], VA [auth F], W [auth B], WA [auth F], X [auth B], XA [auth F], Y [auth B], YA [auth F], Z [auth B]	UNKNOWN ATOM OR ION X		Interactions Focus chain AA [auth B] Focus chain AB [auth G] Focus chain BA [auth B] Focus chain BB [auth G] Focus chain CA [auth B] Focus chain CB [auth G] Focus chain DA [auth B] Focus chain DB [auth G] Focus chain EB [auth G] Focus chain FA [auth C] Focus chain FB [auth G] Focus chain GA [auth C] Focus chain GB [auth G] Focus chain HA [auth C] Focus chain HB [auth G] Focus chain IA [auth C] Focus chain IB [auth G] Focus chain J [auth A] Focus chain JA [auth C] Focus chain JB [auth G] Focus chain K [auth A] Focus chain KB [auth G] Focus chain L [auth A] Focus chain LA [auth D] Focus chain M [auth A] Focus chain MA [auth D] Focus chain MB [auth H] Focus chain N [auth A] Focus chain NA [auth D] Focus chain NB [auth H] Focus chain O [auth A] Focus chain OB [auth H] Focus chain P [auth A] Focus chain PA [auth E] Focus chain Q [auth A] Focus chain QA [auth E] Focus chain R [auth A] Focus chain RA [auth E] Focus chain SA [auth E] Focus chain T [auth B] Focus chain TA [auth E] Focus chain U [auth B] Focus chain V [auth B] Focus chain VA [auth F] Focus chain W [auth B] Focus chain WA [auth F] Focus chain X [auth B] Focus chain XA [auth F] Focus chain Y [auth B] Focus chain YA [auth F] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain AB [auth G] Focus chain BA [auth B] Focus chain BB [auth G] Focus chain CA [auth B] Focus chain CB [auth G] Focus chain DA [auth B] Focus chain DB [auth G] Focus chain EB [auth G] Focus chain FA [auth C] Focus chain FB [auth G] Focus chain GA [auth C] Focus chain GB [auth G] Focus chain HA [auth C] Focus chain HB [auth G] Focus chain IA [auth C] Focus chain IB [auth G] Focus chain J [auth A] Focus chain JA [auth C] Focus chain JB [auth G] Focus chain K [auth A] Focus chain KB [auth G] Focus chain L [auth A] Focus chain LA [auth D] Focus chain M [auth A] Focus chain MA [auth D] Focus chain MB [auth H] Focus chain N [auth A] Focus chain NA [auth D] Focus chain NB [auth H] Focus chain O [auth A] Focus chain OB [auth H] Focus chain P [auth A] Focus chain PA [auth E] Focus chain Q [auth A] Focus chain QA [auth E] Focus chain R [auth A] Focus chain RA [auth E] Focus chain SA [auth E] Focus chain T [auth B] Focus chain TA [auth E] Focus chain U [auth B] Focus chain V [auth B] Focus chain VA [auth F] Focus chain W [auth B] Focus chain WA [auth F] Focus chain X [auth B] Focus chain XA [auth F] Focus chain Y [auth B] Focus chain YA [auth F] Focus chain Z [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
Q5D	BindingDB: 6UE6	Kd: min: 349, max: 7000 (nM) from 3 assay(s)
Q5D	BindingDB: 6UE6	IC50: min: 1.73e+4, max: 2.47e+4 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.252 (Depositor), 0.273 (DCC)
R-Value Work: 0.235 (Depositor), 0.248 (DCC)
R-Value Observed: 0.236 (Depositor)

Diffraction Data:

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.21	α = 90
b = 70.32	β = 90
c = 228.83	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
PHASER	phasing
XDS	data scaling

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2019-11-13

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2019-11-13
Type: Initial release
Version 1.1: 2021-04-21
Changes: Database references
Version 1.2: 2023-10-11
Changes: Data collection, Database references, Refinement description