Structure of PDB 5egs Chain A Binding Site BS03

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 403 [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)		L162 S168 L267 L343 L344 P345
Binding residue
(residue number reindexed from 1)		L124 S130 L229 L303 L304 P305
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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