Structure of PDB 4y30 Chain A Binding Site BS01

Receptor Information
>4y30 Chain A (length=337) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TKRERDQLYYECYSDVSVHEEMIADRVRTDAYRLGILRNWAALRGKTVLD
VGAGTGILSIFCAQAGARRVYAVEASAIWQQAREVVRFNGLEDRVHVLPG
PVETVELPEQVDAIVSEWMGYGLLHESMLSSVLHARTKWLKEGGLLLPAS
AELFIAPISDQMLEWRLGFWSQVKQHYGVDMSCLEGFATRCLMGHSEIVV
QGLSGEDVLARPQRFAQLELSRAGLEQELQAGVGGRFRCSCYGSAPMHGF
AIWFQVTFPGGESEKPLVLSTSPFHPATHWKQALLYLNEPVQVEQDTDVS
GEITLLPSRDNPRRLRVLLRYKVGDQEEKTKDFAMED
Ligand information
Ligand IDSAH
InChIInChI=1S/C14H20N6O5S/c15-6(14(23)24)1-2-26-3-7-9(21)10(22)13(25-7)20-5-19-8-11(16)17-4-18-12(8)20/h4-7,9-10,13,21-22H,1-3,15H2,(H,23,24)(H2,16,17,18)/t6-,7+,9+,10+,13+/m0/s1
InChIKeyZJUKTBDSGOFHSH-WFMPWKQPSA-N
SMILES
SoftwareSMILES
CACTVS 3.341N[CH](CCSC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23)C(O)=O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)CSCCC(C(=O)O)N)O)O)N
CACTVS 3.341N[C@@H](CCSC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23)C(O)=O
ACDLabs 10.04O=C(O)C(N)CCSCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CSCC[C@@H](C(=O)O)N)O)O)N
FormulaC14 H20 N6 O5 S
NameS-ADENOSYL-L-HOMOCYSTEINE
ChEMBLCHEMBL418052
DrugBankDB01752
ZINCZINC000004228232
PDB chain4y30 Chain A Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB4y30 Aryl Pyrazoles as Potent Inhibitors of Arginine Methyltransferases: Identification of the First PRMT6 Tool Compound.
Resolution2.1 Å
Binding residue
(original residue number in PDB)		Y48 Y51 M60 R66 G90 A91 L96 E112 A113 P139 V140 E141 E155 M166 S169
Binding residue
(residue number reindexed from 1)		Y10 Y13 M22 R28 G52 A53 L58 E74 A75 P101 V102 E103 E117 M128 S131
Annotation score5
Enzymatic activity
Catalytic site (original residue number in PDB) D63 E155 E164 H317
Catalytic site (residue number reindexed from 1) D25 E117 E126 H279
Enzyme Commision number 2.1.1.319: type I protein arginine methyltransferase.
Gene Ontology
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
GO:0140938 histone H3 methyltransferase activity
Biological Process
GO:0000122 negative regulation of transcription by RNA polymerase II
GO:0006281 DNA repair
GO:0006284 base-excision 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:0045652 regulation of megakaryocyte differentiation
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4y30, PDBe:4y30, PDBj:4y30
PDBsum4y30
PubMed26101569
UniProtQ96LA8|ANM6_HUMAN Protein arginine N-methyltransferase 6 (Gene Name=PRMT6)

[Back to BioLiP]