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- PDB-6izq: PRMT4 bound with a bicyclic compound -

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Basic information

Entry
Database: PDB / ID: 6izq
TitlePRMT4 bound with a bicyclic compound
ComponentsHistone-arginine methyltransferase CARM1
KeywordsTRANSFERASE / Histone-arginine methyltransferase CARM1
Function / homology
Function and homology information


negative regulation of dendrite development / type I protein arginine methyltransferase / protein-arginine omega-N asymmetric methyltransferase activity / histone arginine N-methyltransferase activity / protein methyltransferase activity / regulation of intracellular estrogen receptor signaling pathway / replication fork reversal / histone H3R17 methyltransferase activity / histone H3R2 methyltransferase activity / histone H3R8 methyltransferase activity ...negative regulation of dendrite development / type I protein arginine methyltransferase / protein-arginine omega-N asymmetric methyltransferase activity / histone arginine N-methyltransferase activity / protein methyltransferase activity / regulation of intracellular estrogen receptor signaling pathway / replication fork reversal / histone H3R17 methyltransferase activity / histone H3R2 methyltransferase activity / histone H3R8 methyltransferase activity / histone H3R26 methyltransferase activity / histone H3K37 methyltransferase activity / histone H4R3 methyltransferase activity / histone H4K12 methyltransferase activity / histone H3K56 methyltransferase activity / protein-arginine N-methyltransferase activity / positive regulation of epithelial cell apoptotic process / histone H2AQ104 methyltransferase activity / histone methyltransferase activity / positive regulation of transcription by RNA polymerase I / nuclear replication fork / positive regulation of fat cell differentiation / response to cAMP / : / Regulation of lipid metabolism by PPARalpha / BMAL1:CLOCK,NPAS2 activates circadian expression / Activation of gene expression by SREBF (SREBP) / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / : / Heme signaling / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / Cytoprotection by HMOX1 / beta-catenin binding / Transcriptional regulation of white adipocyte differentiation / RMTs methylate histone arginines / : / DNA-binding transcription factor binding / methylation / Estrogen-dependent gene expression / transcription coactivator activity / transcription cis-regulatory region binding / chromatin remodeling / positive regulation of cell population proliferation / regulation of DNA-templated transcription / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Histone-arginine methyltransferase CARM1, N-terminal / Coactivator-associated arginine methyltransferase 1 N terminal / Ribosomal protein L11 methyltransferase (PrmA) / Hnrnp arginine n-methyltransferase1 / Hnrnp arginine n-methyltransferase1 / : / Arginine methyltransferase oligomerization subdomain / Protein arginine N-methyltransferase / SAM-dependent methyltransferase PRMT-type domain profile. / Distorted Sandwich ...Histone-arginine methyltransferase CARM1, N-terminal / Coactivator-associated arginine methyltransferase 1 N terminal / Ribosomal protein L11 methyltransferase (PrmA) / Hnrnp arginine n-methyltransferase1 / Hnrnp arginine n-methyltransferase1 / : / Arginine methyltransferase oligomerization subdomain / Protein arginine N-methyltransferase / SAM-dependent methyltransferase PRMT-type domain profile. / Distorted Sandwich / PH-like domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Mainly Beta
Similarity search - Domain/homology
Chem-XJ2 / Histone-arginine methyltransferase CARM1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.449 Å
AuthorsXiong, B. / Cao, D.Y. / Guo, Z.H. / Li, Y.L. / Li, J. / Huang, X. / Shen, J.K.
CitationJournal: J.Med.Chem. / Year: 2019
Title: Design and Synthesis of Potent, Selective Inhibitors of Protein Arginine Methyltransferase 4 against Acute Myeloid Leukemia.
Authors: Guo, Z. / Zhang, Z. / Yang, H. / Cao, D. / Xu, X. / Zheng, X. / Chen, D. / Wang, Q. / Li, Y. / Li, J. / Du, Z. / Wang, X. / Chen, L. / Ding, J. / Shen, J. / Geng, M. / Huang, X. / Xiong, B.
History
DepositionDec 20, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 25, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone-arginine methyltransferase CARM1
B: Histone-arginine methyltransferase CARM1
C: Histone-arginine methyltransferase CARM1
D: Histone-arginine methyltransferase CARM1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,7685
Polymers151,5334
Non-polymers2341
Water99155
1
A: Histone-arginine methyltransferase CARM1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1182
Polymers37,8831
Non-polymers2341
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Histone-arginine methyltransferase CARM1


Theoretical massNumber of molelcules
Total (without water)37,8831
Polymers37,8831
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Histone-arginine methyltransferase CARM1


Theoretical massNumber of molelcules
Total (without water)37,8831
Polymers37,8831
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Histone-arginine methyltransferase CARM1


Theoretical massNumber of molelcules
Total (without water)37,8831
Polymers37,8831
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Histone-arginine methyltransferase CARM1
B: Histone-arginine methyltransferase CARM1
C: Histone-arginine methyltransferase CARM1
D: Histone-arginine methyltransferase CARM1
hetero molecules

A: Histone-arginine methyltransferase CARM1
B: Histone-arginine methyltransferase CARM1
C: Histone-arginine methyltransferase CARM1
D: Histone-arginine methyltransferase CARM1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)303,53510
Polymers303,0668
Non-polymers4692
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area23150 Å2
ΔGint-134 kcal/mol
Surface area95800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.788, 98.926, 206.792
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
Histone-arginine methyltransferase CARM1 / Coactivator-associated arginine methyltransferase 1 / Protein arginine N-methyltransferase 4


Mass: 37883.293 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CARM1, PRMT4 / Production host: Escherichia coli (E. coli)
References: UniProt: Q86X55, type I protein arginine methyltransferase
#2: Chemical ChemComp-XJ2 / (2R)-1-(methylamino)-3-(1,3,4,5-tetrahydro-2-benzazepin-2-yl)propan-2-ol


Mass: 234.337 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H22N2O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / Source method: isolated from a natural source / Formula: H2O

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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: 2.53 Å3/Da / Density % sol: 51.37 %
Crystal growTemperature: 298 K / Method: evaporation / Details: 22-27% PEG 3350, 0.15M sodium malate, pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97923 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97923 Å / Relative weight: 1
ReflectionResolution: 2.449→89.24 Å / Num. obs: 56632 / % possible obs: 98.68 % / Redundancy: 7 % / Net I/σ(I): 13.3
Reflection shellResolution: 2.449→2.5 Å

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
HKL-3000phasing
RefinementResolution: 2.449→89.24 Å / SU ML: 0.3 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 24.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2481 1997 3.53 %
Rwork0.1905 --
obs0.1925 56632 98.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.449→89.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10553 0 17 55 10625
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00810844
X-RAY DIFFRACTIONf_angle_d0.914712
X-RAY DIFFRACTIONf_dihedral_angle_d3.3096366
X-RAY DIFFRACTIONf_chiral_restr0.0531617
X-RAY DIFFRACTIONf_plane_restr0.0061882
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4492-2.51050.29551420.19853886X-RAY DIFFRACTION99
2.5105-2.57840.30841430.19983905X-RAY DIFFRACTION99
2.5784-2.65430.26121410.20173849X-RAY DIFFRACTION99
2.6543-2.73990.27531420.20853883X-RAY DIFFRACTION100
2.7399-2.83790.29281420.20673890X-RAY DIFFRACTION100
2.8379-2.95150.30381420.21983881X-RAY DIFFRACTION100
2.9515-3.08580.31041430.2193911X-RAY DIFFRACTION100
3.0858-3.24850.29311440.22053941X-RAY DIFFRACTION100
3.2485-3.45210.26731430.20633909X-RAY DIFFRACTION100
3.4521-3.71860.25491280.19013491X-RAY DIFFRACTION89
3.7186-4.09280.21891440.17983947X-RAY DIFFRACTION99
4.0928-4.6850.19911450.15693985X-RAY DIFFRACTION100
4.685-5.90250.22791470.17134021X-RAY DIFFRACTION100
5.9025-89.29950.21971510.19474136X-RAY DIFFRACTION98

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