Structure of PDB 5e8r Chain B Binding Site BS02

Receptor Information
>5e8r Chain B (length=333) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KRERDQLYYECYSDVSVHEEMIADRVRTDAYRLGILRNWAALRGKTVLDV
GAGTGILSIFCAQAGARRVYAVEASAIWQQAREVVRFNGLEDRVHVLPGP
VETVELPEQVDAIVSEWMGYGLLHESMLSSVLHARTKWLKEGGLLLPASA
ELFIVPISDQMLEWRLGFWSQVKQHYGVDMSCLEGFATRCLMGHSEIVVQ
GLSGEDVLARPQRFAQLELSRAGLEQELEAGVGGRFRCSCYGSAPMHGFA
IWFQVTFPGGEKPLVLSTSPFHPATHWKQALLYLNEPVQVEQDTDVSGEI
TLLPSRDNPRRLRVLLRYKVGDQEEKTKDFAME
Ligand information
Ligand ID5L6
InChIInChI=1S/C17H25N3O/c1-13(2)21-16-6-4-14(5-7-16)17-11-19-10-15(17)12-20(3)9-8-18/h4-7,10-11,13,19H,8-9,12,18H2,1-3H3
InChIKeyFMTVWAGUJRUAKE-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385
OpenEye OEToolkits 1.9.2		CC(C)Oc1ccc(cc1)c2c[nH]cc2CN(C)CCN
ACDLabs 12.01c1cc(ccc1OC(C)C)c2c(cnc2)CN(CCN)C
FormulaC17 H25 N3 O
NameN-methyl-N-({4-[4-(propan-2-yloxy)phenyl]-1H-pyrrol-3-yl}methyl)ethane-1,2-diamine
ChEMBLCHEMBL3901808
DrugBank
ZINCZINC000263620427
PDB chain5e8r Chain B Residue 1002 [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]
PDB5e8r A Potent, Selective, and Cell-Active Inhibitor of Human Type I Protein Arginine Methyltransferases.
Resolution2.55 Å
Binding residue
(original residue number in PDB)		Y51 V56 E59 M60 E155 M157 Y159 E164 H317
Binding residue
(residue number reindexed from 1)		Y12 V17 E20 M21 E116 M118 Y120 E125 H276
Annotation score1
Binding affinityBindingDB: IC50=4.0nM,Ki=0.8nM,Kd=6nM
Enzymatic activity
Catalytic site (original residue number in PDB) D63 E155 E164 H317
Catalytic site (residue number reindexed from 1) D24 E116 E125 H276
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:5e8r, PDBe:5e8r, PDBj:5e8r
PDBsum5e8r
PubMed26598975
UniProtQ96LA8|ANM6_HUMAN Protein arginine N-methyltransferase 6 (Gene Name=PRMT6)

[Back to BioLiP]