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- PDB-9foc: Crystal structure of the PWWP1 domain of NSD2 bound by compound 11. -

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Basic information

Entry
Database: PDB / ID: 9foc
TitleCrystal structure of the PWWP1 domain of NSD2 bound by compound 11.
ComponentsHistone-lysine N-methyltransferase NSD2
KeywordsTRANSFERASE / drug discovery / NSD2 / DEL / cancer
Function / homology
Function and homology information


atrial septum secundum morphogenesis / [histone H3]-lysine36 N-dimethyltransferase / histone H3K36 dimethyltransferase activity / histone H4K20 methyltransferase activity / regulation of double-strand break repair via nonhomologous end joining / histone H3K36 trimethyltransferase activity / positive regulation of isotype switching to IgA isotypes / atrial septum primum morphogenesis / membranous septum morphogenesis / regulation of establishment of protein localization ...atrial septum secundum morphogenesis / [histone H3]-lysine36 N-dimethyltransferase / histone H3K36 dimethyltransferase activity / histone H4K20 methyltransferase activity / regulation of double-strand break repair via nonhomologous end joining / histone H3K36 trimethyltransferase activity / positive regulation of isotype switching to IgA isotypes / atrial septum primum morphogenesis / membranous septum morphogenesis / regulation of establishment of protein localization / histone H3K36 methyltransferase activity / histone H3 methyltransferase activity / Nonhomologous End-Joining (NHEJ) / G2/M DNA damage checkpoint / bone development / PKMTs methylate histone lysines / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / double-strand break repair / Processing of DNA double-strand break ends / methylation / sequence-specific DNA binding / chromatin binding / regulation of DNA-templated transcription / chromatin / nucleolus / negative regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
: / : / : / : / : / : / : / : / NSD, Cys-His rich domain / : ...: / : / : / : / : / : / : / : / NSD, Cys-His rich domain / : / : / NSD Cys-His rich domain / Histone-lysine N-methyltransferase NSD-like, PHD zinc finger / Histone-lysine N-methyltransferase NSD-like, variant PHD zinc finger / Histone-lysine N-methyltransferase NSD-like, PHD zinc finger 1 / : / AWS domain / AWS domain / AWS domain profile. / associated with SET domains / Cysteine-rich motif following a subset of SET domains / Post-SET domain / Post-SET domain profile. / HMG (high mobility group) box / HMG boxes A and B DNA-binding domains profile. / high mobility group / High mobility group box domain / High mobility group box domain superfamily / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain / SET domain superfamily / SET domain profile. / SET domain / domain with conserved PWWP motif / PWWP domain / PWWP domain profile. / PWWP domain / Zinc finger, PHD-type, conserved site / PHD-finger / Zinc finger PHD-type signature. / Ring finger / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
: / : / Histone-lysine N-methyltransferase NSD2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.618 Å
AuthorsCollie, G.W.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acs Med.Chem.Lett. / Year: 2025
Title: Structural and Molecular Insight into the PWWP1 Domain of NSD2 from the Discovery of Novel Binders Via DNA-Encoded Library Screening
Authors: Collie, G.W. / Ackroyd, B. / Corbishley, C. / O'Donovan, D.H. / Edwards, A. / Gohlke, A. / Guo, X. / Howells, B. / Li, Y. / Madin, A. / Milbradt, A.G. / Rivers, E.L. / Talapatra, S.K. / Underwood, E. / Webb, A.
History
DepositionJun 11, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 3, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histone-lysine N-methyltransferase NSD2
B: Histone-lysine N-methyltransferase NSD2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7716
Polymers39,2452
Non-polymers1,5264
Water3,495194
1
A: Histone-lysine N-methyltransferase NSD2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3853
Polymers19,6221
Non-polymers7632
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Histone-lysine N-methyltransferase NSD2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3853
Polymers19,6221
Non-polymers7632
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)28.630, 67.960, 159.690
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Histone-lysine N-methyltransferase NSD2 / Multiple myeloma SET domain-containing protein / MMSET / Nuclear SET domain-containing protein 2 / ...Multiple myeloma SET domain-containing protein / MMSET / Nuclear SET domain-containing protein 2 / Protein trithorax-5 / Wolf-Hirschhorn syndrome candidate 1 protein


Mass: 19622.342 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NSD2, KIAA1090, MMSET, TRX5, WHSC1 / Production host: Escherichia coli (E. coli)
References: UniProt: O96028, [histone H3]-lysine36 N-dimethyltransferase
#2: Chemical ChemComp-A1IFS / (2S)-1-[4-[[(3R)-1,1-bis(oxidanylidene)thiolan-3-yl]methyl-methyl-amino]-6-methyl-pyrimidin-2-yl]-N-methyl-pyrrolidine-2-carboxamide


Mass: 381.493 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H27N5O3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-A1IEG / (2S)-1-[4-[[(3S)-1,1-bis(oxidanylidene)thiolan-3-yl]methyl-methyl-amino]-6-methyl-pyrimidin-2-yl]-N-methyl-pyrrolidine-2-carboxamide


Mass: 381.493 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H27N5O3S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.98 Å3/Da / Density % sol: 37.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Morpheus, G1. Molecular Dimensions catalogue no.: MD1-47.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98011 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 13, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 1.616→159.69 Å / Num. obs: 28928 / % possible obs: 70.2 % / Redundancy: 12.8 % / Rmerge(I) obs: 0.165 / Rpim(I) all: 0.048 / Rrim(I) all: 0.172 / Net I/σ(I): 10.5 / Num. measured all: 370342
Reflection shellResolution: 1.616→1.817 Å / % possible obs: 12.1 % / Redundancy: 10.9 % / Rmerge(I) obs: 1.46 / Num. measured all: 15748 / Num. unique obs: 1446 / Rpim(I) all: 0.454 / Rrim(I) all: 1.533 / Net I/σ(I) obs: 1.7

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Processing

Software
NameVersionClassification
BUSTER2.11.8 (8-JUN-2022)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.618→19.96 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.921 / SU R Cruickshank DPI: 0.14 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.148 / SU Rfree Blow DPI: 0.139 / SU Rfree Cruickshank DPI: 0.135
RfactorNum. reflection% reflectionSelection details
Rfree0.2554 1411 4.89 %RANDOM
Rwork0.2145 ---
obs0.2166 28853 70.5 %-
Displacement parametersBiso mean: 25.98 Å2
Baniso -1Baniso -2Baniso -3
1-0.152 Å20 Å20 Å2
2--0.5243 Å20 Å2
3----0.6763 Å2
Refine analyzeLuzzati coordinate error obs: 0.26 Å
Refinement stepCycle: 1 / Resolution: 1.618→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2163 0 52 194 2409
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0092335HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.983175HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d807SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes380HARMONIC5
X-RAY DIFFRACTIONt_it2335HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.74
X-RAY DIFFRACTIONt_other_torsion15.83
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion273SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2027SEMIHARMONIC4
LS refinement shellResolution: 1.62→1.76 Å / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.2915 -5.36 %
Rwork0.2837 547 -
all0.2841 578 -
obs--6.57 %

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