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- PDB-7vln: NSD2-PWWP1 domain bound with an imidazol-5-yl benzonitrile compound -

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Basic information

Entry
Database: PDB / ID: 7vln
TitleNSD2-PWWP1 domain bound with an imidazol-5-yl benzonitrile compound
ComponentsHistone-lysine N-methyltransferase NSD2
KeywordsTRANSFERASE / Histone-lysine N-methyltransferase NSD2
Function / homology
Function and homology information


atrial septum secundum morphogenesis / [histone H3]-lysine36 N-dimethyltransferase / histone H4K20 methyltransferase activity / regulation of double-strand break repair via nonhomologous end joining / histone H3K36 dimethyltransferase activity / histone H3K36 trimethyltransferase activity / positive regulation of isotype switching to IgA isotypes / regulation of establishment of protein localization / atrial septum primum morphogenesis / membranous septum morphogenesis ...atrial septum secundum morphogenesis / [histone H3]-lysine36 N-dimethyltransferase / histone H4K20 methyltransferase activity / regulation of double-strand break repair via nonhomologous end joining / histone H3K36 dimethyltransferase activity / histone H3K36 trimethyltransferase activity / positive regulation of isotype switching to IgA isotypes / regulation of establishment of protein localization / atrial septum primum morphogenesis / membranous septum morphogenesis / histone H3K36 methyltransferase activity / histone H3 methyltransferase activity / Nonhomologous End-Joining (NHEJ) / bone development / G2/M DNA damage checkpoint / PKMTs methylate histone lysines / double-strand break repair / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / 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 / nucleoplasm / nucleus / metal ion binding / cytoplasm
Similarity search - Function
: / : / : / : / : / : / : / : / NSD, Cys-His rich domain / NSD Cys-His rich domain ...: / : / : / : / : / : / : / : / NSD, Cys-His rich domain / NSD Cys-His rich domain / 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 superfamily / SET domain / 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 / Ring finger / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, RING-type / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Chem-7QC / Histone-lysine N-methyltransferase NSD2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.09 Å
AuthorsCao, D.Y. / Li, Y.L. / Li, J. / Xiong, B.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Med.Chem. / Year: 2022
Title: Structure-Based Discovery of a Series of NSD2-PWWP1 Inhibitors.
Authors: Li, N. / Yang, H. / Liu, K. / Zhou, L. / Huang, Y. / Cao, D. / Li, Y. / Sun, Y. / Yu, A. / Du, Z. / Yu, F. / Zhang, Y. / Wang, B. / Geng, M. / Li, J. / Xiong, B. / Xu, S. / Huang, X. / Liu, T.
History
DepositionOct 5, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 6, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2022Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jul 27, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
C: Histone-lysine N-methyltransferase NSD2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7734
Polymers45,4253
Non-polymers3481
Water00
1
A: Histone-lysine N-methyltransferase NSD2


Theoretical massNumber of molelcules
Total (without water)15,1421
Polymers15,1421
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Histone-lysine N-methyltransferase NSD2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4902
Polymers15,1421
Non-polymers3481
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Histone-lysine N-methyltransferase NSD2


Theoretical massNumber of molelcules
Total (without water)15,1421
Polymers15,1421
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.120, 70.120, 230.670
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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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: 15141.505 Da / Num. of mol.: 3 / Fragment: PWWP1 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NSD2, KIAA1090, MMSET, TRX5, WHSC1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: O96028, [histone H3]-lysine36 N-dimethyltransferase
#2: Chemical ChemComp-7QC / 4-[5-[4-(aminomethyl)-2,6-dimethoxy-phenyl]-3-methyl-imidazol-4-yl]benzenecarbonitrile


Mass: 348.398 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H20N4O2 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: 3.71 Å3/Da / Density % sol: 66.89 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 1.6 M ammonium sulfate, 0.01 M magnesium chloride, 0.1 M HEPES, pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 16, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 3.09→30.3643 Å / Num. obs: 12759 / % possible obs: 99.8 % / Redundancy: 19.3 % / Biso Wilson estimate: 93.035517398 Å2 / Rpim(I) all: 0.043 / Net I/σ(I): 18.9
Reflection shellResolution: 3.09→3.17 Å / Num. unique obs: 912 / Rpim(I) all: 0.442

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6xcg

6xcg


Resolution: 3.09→30.3643 Å / SU ML: 0.514671900821 / Cross valid method: NONE / σ(F): 1.34760655436 / Phase error: 45.3566353974
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.34524153404 598 4.7520661157 %
Rwork0.291524218032 11986 -
obs0.294329894931 12584 98.8764044944 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 109.17626597 Å2
Refinement stepCycle: LAST / Resolution: 3.09→30.3643 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3048 0 26 0 3074
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00941463951553158
X-RAY DIFFRACTIONf_angle_d1.336574461874254
X-RAY DIFFRACTIONf_chiral_restr0.0634159443318433
X-RAY DIFFRACTIONf_plane_restr0.0123857785341528
X-RAY DIFFRACTIONf_dihedral_angle_d7.290168896331862
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0902-3.40080.4538531455491360.3673105116032881X-RAY DIFFRACTION98.0181936322
3.4008-3.8920.3803416770331370.3189974610042976X-RAY DIFFRACTION98.606271777
3.892-4.90020.342999420981740.2819932506542943X-RAY DIFFRACTION99.141221374
4.9002-30.36430.3202901009111510.2755742020173186X-RAY DIFFRACTION99.7608370703

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