BioLiP

Receptor Information

>7nud Chain A (length=335) Species: 10090 (Mus musculus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

TKSERDQLYYECYSDVSVHEEMIADQVRTEAYRLGILKNWAALRGKTVLD
VGAGTGILSIFCAQAGARRVYAVEASAIWQQAREVVRLNGLEDRVHVLPG
PVETVELPERVDAIVSEWMGYGLLHESMLSSVLHARTKWLKEGGLLLPAS
AELFVAPISDQMLEWRLGFWSQVKQHYGVDMSCMESFATRCLMGHSEIVV
QDLSGEDVLARPQRFAQLELARAGLEQELEAGVGGRFRCSCYGSAPLHGF
AVWFQVTFPGGDSEKPLVLSTSPLHPATHWKQALLYLNEPVPVEQDTDIS
GEITLLPSPDNPRRLRILLRYKVGDHEEKTKDFAM

Ligand ID

LRZ

InChI

InChI=1S/C27H32N10O7/c1-43-25(41)14-7-13-3-4-15(9-16(13)17(38)8-14)36-27(42)31-6-2-5-30-26(29)32-10-18-20(39)21(40)24(44-18)37-12-35-19-22(28)33-11-34-23(19)37/h3-4,7-9,11-12,18,20-21,24,38-40H,2,5-6,10H2,1H3,(H2,28,33,34)(H3,29,30,32)(H2,31,36,42)/t18-,20-,21-,24-/m1/s1

InChIKey

GJPQENHVEQGHGP-UMCMBGNQSA-N

SMILES

Software	SMILES
CACTVS 3.385	COC(=O)c1cc(O)c2cc(NC(=O)NCCCNC(=N)NC[CH]3O[CH]([CH](O)[CH]3O)n4cnc5c(N)ncnc45)ccc2c1
CACTVS 3.385	COC(=O)c1cc(O)c2cc(NC(=O)NCCCNC(=N)NC[C@H]3O[C@H]([C@H](O)[C@@H]3O)n4cnc5c(N)ncnc45)ccc2c1
OpenEye OEToolkits 2.0.7	COC(=O)c1cc2ccc(cc2c(c1)O)NC(=O)NCCCNC(=N)NCC3C(C(C(O3)n4cnc5c4ncnc5N)O)O
OpenEye OEToolkits 2.0.7	[H]/N=C(\NCCCNC(=O)Nc1ccc2cc(cc(c2c1)O)C(=O)OC)/NC[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4ncnc5N)O)O

Formula

C27 H32 N10 O7

Name

methyl 6-[3-[[~{N}-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl]carbamimidoyl]amino]propylcarbamoylamino]-4-oxidanyl-naphthalene-2-carboxylate

PDB chain

7nud Chain A Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure

Global view

Local view

Structure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]

PDB	7nud Turning Nonselective Inhibitors of Type I Protein Arginine Methyltransferases into Potent and Selective Inhibitors of Protein Arginine Methyltransferase 4 through a Deconstruction-Reconstruction and Fragment-Growing Approach.
Resolution	1.65 Å
Binding residue (original residue number in PDB)	Y50 Y51 Y54 G93 E115 A116 S117 P142 V143 E144 E167 S168 M169 S172
Binding residue (residue number reindexed from 1)	Y9 Y10 Y13 G52 E74 A75 S76 P101 V102 E103 E126 S127 M128 S131
Annotation score	1

Enzyme Commision number

2.1.1.319: type I protein arginine methyltransferase.

	Molecular Function
GO:0003682	chromatin binding
GO:0005515	protein binding
GO:0008168	methyltransferase activity
GO:0008469	histone arginine N-methyltransferase activity
GO:0016274	protein-arginine N-methyltransferase activity
GO:0035241	protein-arginine omega-N monomethyltransferase activity
GO:0035242	protein-arginine omega-N asymmetric methyltransferase activity
GO:0042054	histone methyltransferase activity
GO:0042393	histone binding
GO:0044020	histone H4R3 methyltransferase activity
GO:0070611	histone H3R2 methyltransferase activity
GO:0070612	histone H2AR3 methyltransferase activity

	Biological Process
GO:0000122	negative regulation of transcription by RNA polymerase II
GO:0006281	DNA repair
GO:0006325	chromatin organization
GO:0006338	chromatin remodeling
GO:0010821	regulation of mitochondrion organization
GO:0018216	peptidyl-arginine methylation
GO:0032259	methylation
GO:0036211	protein modification process
GO:0045892	negative regulation of DNA-templated transcription
GO:0090398	cellular senescence
GO:1901796	regulation of signal transduction by p53 class mediator
GO:2000059	negative regulation of ubiquitin-dependent protein catabolic process

	Cellular Component
GO:0005634	nucleus
GO:0005654	nucleoplasm
GO:0005730	nucleolus

PDB	RCSB:7nud, PDBe:7nud, PDBj:7nud
PDBsum	7nud
PubMed	35482954
UniProt	Q6NZB1\|ANM6_MOUSE Protein arginine N-methyltransferase 6 (Gene Name=Prmt6)

[Back to BioLiP]

Structure of PDB 7nud Chain A Binding Site BS01