Structure of PDB 6z3r Chain A Binding Site BS02

Receptor Information
>6z3r Chain A (length=1943) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAALETVGEKKAFSSVMQLVMTSLQSILENVDT
PELLCKCVKCILLVARCYPHIFSTNFRDTVDILVGSLTQQVSGWLQSLEA
FSTTLLGQFLEDMEAYAEDLSSVSLPKLAALLRVFSTVVRSIAYVTDVLY
RVMRCVTAANQVFFSEAVLTAANECVGVLLGSLDPSMTIHCDMVITYGLD
QLENCQTCGTDYIISVLNLLTLIVEQINTKLPSSFVEKLFIPSSKLLFLR
YHKEKEVVAVAHAVYQAVLSLKNIPVLETAYKLILGEMTCALNNLLHSLQ
LPEACSEIKHEAFKNHVFNVDNAKFVVIFDLSALTTIGNAKNWALSPTVF
ALLSKNLMIVHSDLAVHFPAIQYAVLYTLYSHCTRHDHFISSSTVTTATK
KHFSIILNLLGILLKKDNLNQDTRKLLMTWALEAAVLMRKSETYAPLFSL
PSFHKFCKGLLANTLVEDVNICLQACSSLHALSSSLPDDLLQRCVDVCRV
QLVHSGTRIRQAFGKLLKSIPLDVVLSNNKHTEIQEISLALRSHMSKAPS
NTFHPQDFSDVISFILYGNSHRTNWLERLFYSCQRLDKTIPRNLLKTDAV
LWQWAIWEAAQFTVLSKLRTPLGRAQDTFQTIEGIIRSLAAHTLNPDQDV
SQWTTADNDEGHGNNQLRLVLLLQYLENLEKLMYNAYEGCANALTSPPKV
IRTFFYTNRQTCQDWLTRIRLSIMRVGLLAGQPAVTVRHGFDLLTEMKTN
ELEVTIMMVVEALCELHCPEAIQGIAVWSSSINLLWINSVAQQAEGRFEK
ASVEYQEHLCAMTGVDCCISSFDKSVLTLANSSPEVINYLGNKACECYIS
IADWAAVQEWQNSIHDLKKSTSSTSLNLKADFNYIKSLSSFESGKFVECT
EQLELLPGENINLDMKKLLPNMLSPDPRELQKSIEVQLLRSSVCLATALN
WQSITENVVKYLKQTSRIAIGPLRLSTLTVSQSLPVLSTLQLYCSSALEN
TVSNRLSTEDCLIPLFSEALRSCKQHDVRPWMQALRYTMYQNQLLEKIKE
QTVPIRSHLMELGLTAAKFARKRGNVSLATRLLAQCSETTAQDLVQHFKK
WGPELDIEKTKLLYTAGQSTHAMEMLSSCAISFCKSVKAEYAVAKSILTL
AKWIQAEWKEISGQLKQVYRAQHQLSTLSKNILTLIELPSIESESTVHIG
VGEPDFILGQLYHLSSVQAPEVAKSWAALASWAYRWGRKVVDNASAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAEGVIKVWRKVVDR
IFSLYKLSCSAYFTFLKLNAQSTDDMIVMATLRLLRLLVKHAGELRQYLE
HGLETTPTAPWRGIIPQLFSRLNHPEVYVRQSICNLLCRVAQDSPHLILY
PAIVGTIQAMMQDCYSKIVDKLSSANPTMVLQVQMLVAELRRVTWDELWL
GVLLQQHMYVLRRIQQLEDEVKRVQNNPHEKWFQDNYGDAIENALEKLKA
AAAAAAAAAAAAAAAYILRLEEIAAMTNTEIALPGEVSARDTVTIHSVGG
TITILPTKTKPKKLLFLGSDGKSYPYLFKGLEDLHLDERIMQFLSIVNTM
FATINRQETPRFHARHYSVTPLGTRSGLIQWVDGATPLFGLYKRWQQREA
ALQAQKIVPRPSELYYSKIGPALKTVGLSLDVSRRDWPLHVMKAVLEELM
EATPPNLLAKELWSSCTTPDEWWRVTQSYARSTAVMSMVGYIIGLGDRHL
DNVLIDMTTGEVVHIDYNVCFEKGKSLRVPEKVPFRMTQNIETALGVTGV
EGVFRLSCEQVLHIMRRGRETLLTLLEAFVYDPLVDWTSYAVSVWKRVKA
KLEGRDVDPNRRMSVAEQVDYVIKEATNLDNLAQLYEGWTAWV
Ligand information
Ligand IDANP
InChIInChI=1S/C10H17N6O12P3/c11-8-5-9(13-2-12-8)16(3-14-5)10-7(18)6(17)4(27-10)1-26-31(24,25)28-30(22,23)15-29(19,20)21/h2-4,6-7,10,17-18H,1H2,(H,24,25)(H2,11,12,13)(H4,15,19,20,21,22,23)/t4-,6-,7-,10-/m1/s1
InChIKeyPVKSNHVPLWYQGJ-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(NP(=O)(O)O)O)O)O)N
CACTVS 3.370Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)N[P](O)(O)=O)[CH](O)[CH]3O
CACTVS 3.370Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)N[P](O)(O)=O)[C@@H](O)[C@H]3O
ACDLabs 12.01O=P(O)(O)NP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.7.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(NP(=O)(O)O)O)O)O)N
FormulaC10 H17 N6 O12 P3
NamePHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
ChEMBLCHEMBL1230989
DrugBank
ZINCZINC000008660410
PDB chain6z3r 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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PDB6z3r Structure of substrate-bound SMG1-8-9 kinase complex reveals molecular basis for phosphorylation specificity.
Resolution2.97 Å
Binding residue
(original residue number in PDB)		T2133 K2134 W2207 I2353
Binding residue
(residue number reindexed from 1)		T1607 K1608 W1681 I1815
Annotation score3
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:0016301 kinase activity
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:6z3r, PDBe:6z3r, PDBj:6z3r
PDBsum6z3r
PubMed32469312
UniProtQ96Q15|SMG1_HUMAN Serine/threonine-protein kinase SMG1 (Gene Name=SMG1)

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