Structure of PDB 5egs Chain A Binding Site BS02

Receptor Information
>5egs Chain A (length=335) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TKRERDQLYYECYSDVSVHEEMIADRVRTDAYRLGILRNWAALRGKTVLD
VGAGTGILSIFCAQAGARRVYAVEASAIWQQAREVVRFNGLEDRVHVLPG
PVETVELPEQVDAIVSEWMGYGLLHESMLSSVLHARTKWLKEGGLLLPAS
AELFIVPISDQMLEWRLGFWSQVKQHYGVDMSCLEGFATRCLMGHSEIVV
QGLSGEDVLARPQRFAQLELSRAGLEQELEAGVGGRFRCSCYGSAPMHGF
AIWFQVTFPGGEKPLVLSTSPFHPATHWKQALLYLNEPVQVEQDTDVSGE
ITLLPSRDNPRRLRVLLRYKVGDQEEKTKDFAMED
Ligand information
Ligand ID5NR
InChIInChI=1S/C14H22N2/c15-8-11-16-9-6-14(7-10-16)12-13-4-2-1-3-5-13/h1-5,14H,6-12,15H2
InChIKeyPCNDXYHWLSHXMV-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.4c1ccc(cc1)CC2CCN(CC2)CCN
CACTVS 3.385NCCN1CCC(CC1)Cc2ccccc2
FormulaC14 H22 N2
Name2-[4-(phenylmethyl)piperidin-1-yl]ethanamine
ChEMBLCHEMBL3780926
DrugBank
ZINCZINC000019367229
PDB chain5egs Chain A Residue 402 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5egs Discovery of a Potent Class I Protein Arginine Methyltransferase Fragment Inhibitor.
Resolution2.15 Å
Binding residue
(original residue number in PDB)		C50 Y51 V56 M60 E155 M157 Y159 E164 H317
Binding residue
(residue number reindexed from 1)		C12 Y13 V18 M22 E117 M119 Y121 E126 H277
Annotation score1
Binding affinityMOAD: Kd=0.97uM
PDBbind-CN: -logKd/Ki=6.01,Kd=0.97uM
BindingDB: Kd=970nM,IC50=21000nM
Enzymatic activity
Catalytic site (original residue number in PDB) D63 E155 E164 H317
Catalytic site (residue number reindexed from 1) D25 E117 E126 H277
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:5egs, PDBe:5egs, PDBj:5egs
PDBsum5egs
PubMed26824386
UniProtQ96LA8|ANM6_HUMAN Protein arginine N-methyltransferase 6 (Gene Name=PRMT6)

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