Structure of PDB 4y2h Chain B Binding Site BS02

Receptor Information
>4y2h Chain B (length=352) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SIAAEREAALERPRRTKRERDQLYYECYSDVSVHEEMIADRVRTDAYRLG
ILRNWAALRGKTVLDVGAGTGILSIFCAQAGARRVYAVEASAIWQQAREV
VRFNGLEDRVHVLPGPVETVELPEQVDAIVSEWMGYGLLHESMLSSVLHA
RTKWLKEGGLLLPASAELFIAPISDQMLEWRLGFWSQVKQHYGVDMSCLE
GFATRCLMGHSEIVVQGLSGEDVLARPQRFAQLELSRAGLEQELEAGVGG
RFRCSCYGSAPMHGFAIWFQVTFPGGESEKPLVLSTSPFHPATHWKQALL
YLNEPVQVEQDTDVSGEITLLPSRDNPRRLRVLLRYKVGDQEEKTKDFAM
ED
Ligand information
Ligand ID49K
InChIInChI=1S/C13H17FN4/c1-18(7-6-15)9-11-8-16-17-13(11)10-2-4-12(14)5-3-10/h2-5,8H,6-7,9,15H2,1H3,(H,16,17)
InChIKeyWJJPSVIYQWOSFK-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CN(CCN)Cc1cn[nH]c1c2ccc(F)cc2
OpenEye OEToolkits 1.9.2CN(CCN)Cc1cn[nH]c1c2ccc(cc2)F
ACDLabs 12.01Fc2ccc(c1c(cnn1)CN(C)CCN)cc2
FormulaC13 H17 F N4
NameN-{[5-(4-fluorophenyl)-1H-pyrazol-4-yl]methyl}-N-methylethane-1,2-diamine
ChEMBLCHEMBL3589912
DrugBank
ZINC
PDB chain4y2h Chain B Residue 402 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB4y2h Aryl Pyrazoles as Potent Inhibitors of Arginine Methyltransferases: Identification of the First PRMT6 Tool Compound.
Resolution2.37 Å
Binding residue
(original residue number in PDB)		Y51 V56 E59 M60 E155 M157 Y159 E164 H317
Binding residue
(residue number reindexed from 1)		Y28 V33 E36 M37 E132 M134 Y136 E141 H294
Annotation score1
Binding affinityMOAD: ic50=0.011uM
BindingDB: IC50=11nM
Enzymatic activity
Catalytic site (original residue number in PDB) D63 E155 E164 H317
Catalytic site (residue number reindexed from 1) D40 E132 E141 H294
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

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:4y2h, PDBe:4y2h, PDBj:4y2h
PDBsum4y2h
PubMed26101569
UniProtQ96LA8|ANM6_HUMAN Protein arginine N-methyltransferase 6 (Gene Name=PRMT6)

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