Structure of PDB 6p7i Chain B Binding Site BS02

Receptor Information
>6p7i Chain B (length=340) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PRRTKRERDQLYYECYSDVSVHEEMIADRVRTDAYRLGILRNWAALRGKT
VLDVGAGTGILSIFCAQAGARRVYAVEASAIWQQAREVVRFNGLEDRVHV
LPGPVETVELPEQVDAIVSEWMGYGLLHESMLSSVLHARTKWLKEGGLLL
PASAELFIVPISDQMLEWRLGFWSQVKQHYGVDMSCLEGFATRCLMGHSE
IVVQGLSGEDVLARPQRFAQLELSRAGLEQELEAGVGGRFRCSCYGSAPM
HGFAIWFQVTFPGGESEKPLVLSTSPFHPATHWKQALLYLNEPVQVEQDT
DVSGEITLLPSRDNPRRLRVLLRYKVGDQEEKTKDFAMED
Ligand information
Ligand IDO3P
InChIInChI=1S/C17H22N4O/c1-3-17(22)20-15-6-4-5-13(9-15)16-11-19-10-14(16)12-21(2)8-7-18/h3-6,9-11,19H,1,7-8,12,18H2,2H3,(H,20,22)
InChIKeyHVDMIAFOVVMNJF-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CN(CCN)Cc1c[nH]cc1c2cccc(NC(=O)C=C)c2
ACDLabs 12.01C(N)CN(C)Cc2cncc2c1cccc(c1)NC([C@H]=C)=O
OpenEye OEToolkits 2.0.7CN(CCN)Cc1c[nH]cc1c2cccc(c2)NC(=O)C=C
FormulaC17 H22 N4 O
NameN-[3-(4-{[(2-aminoethyl)(methyl)amino]methyl}-1H-pyrrol-3-yl)phenyl]prop-2-enamide
ChEMBLCHEMBL4463793
DrugBank
ZINC
PDB chain6p7i 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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PDB6p7i Discovery of a First-in-Class Protein Arginine Methyltransferase 6 (PRMT6) Covalent Inhibitor
Resolution2.0 Å
Binding residue
(original residue number in PDB)		Y47 C50 Y51 V56 E59 M60 E155 M157 Y159 E164 H317
Binding residue
(residue number reindexed from 1)		Y12 C15 Y16 V21 E24 M25 E120 M122 Y124 E129 H282
Annotation score1
Binding affinityBindingDB: IC50=1300nM,Ki=16nM
Enzymatic activity
Catalytic site (original residue number in PDB) D63 E155 E164 H317
Catalytic site (residue number reindexed from 1) D28 E120 E129 H282
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:6p7i, PDBe:6p7i, PDBj:6p7i
PDBsum6p7i
PubMed
UniProtQ96LA8|ANM6_HUMAN Protein arginine N-methyltransferase 6 (Gene Name=PRMT6)

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