Structure of PDB 6syt Chain A Binding Site BS01

Receptor Information
>6syt Chain A (length=1896) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAFSTNFRDTVDILVGSLTQQVSGWLQSLEA
FSTTLLGQFLEDMEAYAEDLSSVSLPKLAALLRVFSTVVRSIAYVTDVLY
RVMRCVTAANQVFFSEAVLTAANECVGVLLGSLDPSMTIHCDMVITYGLD
QLENCQTCGTDYIISVLNLLTLIVEQINTKLPSSFVEKLFIPSSKLLFLR
YHKEKEVVAVAHAVYQAVLSLKNIPVLETAYKLILGEMTCALNNLLHSLQ
LPEACSEIKHEAFKNHVFNVDNAKFVVIFDLSALTTIGNAKNLSPTVFAL
LSKNLMIVHSDLAVHFPAIQYAVLYTLYSHCTRHDHFISSSKKHFSIILN
LLGILLKKDNLNQDTRKLLMTWALEAAVLMRKSETYAPLFSLPSFHKFCK
GLLANTLVEDVNICLQACSSLHALSSSLPDDLLQRCVDVCRVQLVHSGTR
IRQAFGKLLKSIPLDVVLSNNNHTEIQEISLALRSHMSKAPSNTFHPQDF
SDVISFILYGNSHRTNWLERLFYSCQRLDKTIPRNLLKTDAVLWQWAIWE
AAQFTVLSKLRTPLGRAQDTFQTIEGIIRSLAAHTLNPDQDVSQWTTADN
DEGHGNNQLRLVLLLQYLENLEKLMYNAYEGCANALTRTFFYTNRQTCQD
WLTRIRLSIMRVGLLAGQPAVTVRHGFDLLTEMKTNELEVTIMMVVEALC
ELHCPEAIQGIAVWSSSINLLWINSVAQQAEGRFEKASVEYQEHLCAMTG
VDCCISSFDKSVLTLANSSPEVINYLGNKACECYISIADWAAVQEWQNAI
HDLKKSTSSTSLNLKADFNYIKSLSSFESGKFVECTEQLELLPGENINLD
MKKLLPNMLSPDPRELQKSIEVQLLRSSVCLATALNWQSITENVVKYLKQ
TSRIAIGPLRLSTLTVSQSLPVLSTLQLYCSSALENTVSNRLSTEDCLIP
LFSEALRSCKQHDVRPWMQALRYTMYQNQLLEKIKEQTVPIRSHLMELGL
TAAKFARKRGNVSLATRLLAQCSETTAQDLVQHFKKWGPELDIEKTKLLY
TAGQSTHAMEMLSSCAISFCKSVKAEYAVAKSILTLAKWIQAEWKEISGQ
LKQVYRAQHQLSTLSKNILTLIELPSESESTVHIGVGEPDFILGQLYHLS
SVQAPEVAKSWAALASWAYRWGRKVVDNASAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAEGVIKVWRKVVDRIFSLYKLSCSAYFTF
LKLNASTDDMIVMATLRLLRLLVKHAGELRQYLEHGLETPWRGIIPQLFS
RLNHPEVYVRQSICNLLCRVAQDSPHLILYPAIVGTIQAMMQDCYSKIVD
KLSSANPTMVLQVQMLVAELRRVTWDELWLGVLLQQHMYVLAAAAAAAAA
AAAAAAAPHEKWFQDNYGDAIENALEKLKAAAAAAAAAAAAAAAAYILRL
EEITNTEIALPGVTIHSVGTITILPTKPKKLLFLGSDSYPYLFKGLEDLH
LDERIMQFLSIVNTMFATINRQETPRFHARHYSVTPLGTRSGLIQWVDGA
TPLFGLYKRWQQREAALQAQKAAAAAAAAAAAAAAAAAAWPLHVMKAVLE
ELMEATPPNLLAKELWSSCTTPDEWWRVTQSYARSTAVMSMVGYIIGLGA
RHLDNVLIDMTTGEVVHIDYNVCFEKGKSLRVPEKVPFRMTQNIETALGV
TGVEGVFRLSCEQVLHIMRRGRETLLTLLEAFVYDPLVDWTSYAVSVWKR
VKAKLEGRDVDPNRRMSVAEQVDYVIKEATNLDNLAQLYEGWTAWV
Ligand information
Ligand IDIHP
InChIInChI=1S/C6H18O24P6/c7-31(8,9)25-1-2(26-32(10,11)12)4(28-34(16,17)18)6(30-36(22,23)24)5(29-35(19,20)21)3(1)27-33(13,14)15/h1-6H,(H2,7,8,9)(H2,10,11,12)(H2,13,14,15)(H2,16,17,18)(H2,19,20,21)(H2,22,23,24)/t1-,2-,3-,4+,5-,6-
InChIKeyIMQLKJBTEOYOSI-GPIVLXJGSA-N
SMILES
SoftwareSMILES
CACTVS 3.385O[P](O)(=O)O[CH]1[CH](O[P](O)(O)=O)[CH](O[P](O)(O)=O)[CH](O[P](O)(O)=O)[CH](O[P](O)(O)=O)[CH]1O[P](O)(O)=O
ACDLabs 12.01
OpenEye OEToolkits 2.0.7		C1(C(C(C(C(C1OP(=O)(O)O)OP(=O)(O)O)OP(=O)(O)O)OP(=O)(O)O)OP(=O)(O)O)OP(=O)(O)O
CACTVS 3.385O[P](O)(=O)O[C@@H]1[C@H](O[P](O)(O)=O)[C@H](O[P](O)(O)=O)[C@@H](O[P](O)(O)=O)[C@H](O[P](O)(O)=O)[C@H]1O[P](O)(O)=O
FormulaC6 H18 O24 P6
NameINOSITOL HEXAKISPHOSPHATE;
MYO-INOSITOL HEXAKISPHOSPHATE;
INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE
ChEMBLCHEMBL1233511
DrugBankDB14981
ZINCZINC000169289809
PDB chain6syt Chain A Residue 3701 [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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PDB6syt InsP6binding to PIKK kinases revealed by the cryo-EM structure of an SMG1-SMG8-SMG9 complex.
Resolution3.45 Å
Binding residue
(original residue number in PDB)		K1386 K1434 K1523 K1530 K1617
Binding residue
(residue number reindexed from 1)		K1060 K1108 K1181 K1188 K1259
Annotation score1
Enzymatic activity
Enzyme Commision number 2.7.11.1: non-specific serine/threonine protein kinase.
Gene Ontology
Molecular Function
GO:0003723 RNA binding
GO:0004672 protein kinase activity
GO:0004674 protein serine/threonine kinase activity
GO:0004697 diacylglycerol-dependent serine/threonine kinase activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0042162 telomeric DNA binding
GO:0044024 histone H2AS1 kinase activity
GO:0046872 metal ion binding
GO:0106310 protein serine kinase activity
Biological Process
GO:0000184 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay
GO:0006281 DNA repair
GO:0006338 chromatin remodeling
GO:0006406 mRNA export from nucleus
GO:0006974 DNA damage response
GO:0016310 phosphorylation
GO:0018105 peptidyl-serine phosphorylation
GO:0019219 regulation of nucleobase-containing compound metabolic process
GO:0032204 regulation of telomere maintenance
GO:0046777 protein autophosphorylation
GO:0046854 phosphatidylinositol phosphate biosynthetic process
Cellular Component
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0033391 chromatoid body

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6syt, PDBe:6syt, PDBj:6syt
PDBsum6syt
PubMed31792449
UniProtQ96Q15|SMG1_HUMAN Serine/threonine-protein kinase SMG1 (Gene Name=SMG1)

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