Structure of PDB 7z52 Chain B Binding Site BS02

Receptor Information
>7z52 Chain B (length=706) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MPRVKVQSVETVEGCTHEVALPAEEDYLPLKPRVGKAAKEYPFILDAFQR
EAIQCVDNNQSVLVSAHTSAGKTVCAEYAIALALREKQRVIFTSPIKALS
NQKYREMYEEFQDVGLMTGDVTINPTASCLVMTTEILRSMLYRGSEVMRE
VAWVIFDEIHYMRDSERGVVWEETIILLPDNVHYVFLSATIPNARQFAEW
ICHLHKQPCHVIYTDYRPTPLQHYIFPAGGDGLHLVVDENGDFREDNFNT
AMQVLRDAGSNVFKIVKMIMERNFQPVIIFSFSKKDCEAYALQMTKLDFN
TDEEKKMVEEVFSNAIDCLSDEDKKLPQVEHVLPLLKRGIGIHHGGLLPI
LKETIEILFSEGLIKALFATETFAMGINMPARTVLFTNARKFDGKDFRWI
SSGEYIQMSGRAGRRGMDDRGIVILMVDEKMSPTIGKQLLKGSADPLNSA
FHLTYNMVLNLLRVEEINPEYMLEKSFYQFQHYRAIPGVVEKVKDIKSAK
RELKKARTVLQMDELKCRKRVLRRLGFATSSDVIEMKGRVACEISSADEL
LLTEMMFNGLFNDLSAEQATALLSCFVFQENSSEMPKLTEQLAGPLRQMQ
ECAKRIAKVSAEAKLEIDEETYLSSFKPHLMDVVYTWATGATFAHICKMT
DVFEGSIIRCMRRLEELLRQMCQAAKAIGNTELENKFAEGITKIKRDIVF
AASLYL
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 chain7z52 Chain B Residue 2001 [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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PDB7z52 Structure and regulation of the nuclear exosome targeting complex guides RNA substrates to the exosome.
Resolution3.4 Å
Binding residue
(original residue number in PDB)		F138 T168 N490
Binding residue
(residue number reindexed from 1)		F43 T73 N378
Annotation score3
Enzymatic activity
Enzyme Commision number 3.6.4.13: RNA helicase.
Gene Ontology
Molecular Function
GO:0003676 nucleic acid binding
GO:0003723 RNA binding
GO:0003724 RNA helicase activity
GO:0004386 helicase activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0016787 hydrolase activity
GO:0016887 ATP hydrolysis activity
Biological Process
GO:0000398 mRNA splicing, via spliceosome
GO:0000460 maturation of 5.8S rRNA
GO:0006364 rRNA processing
GO:0006397 mRNA processing
GO:0006401 RNA catabolic process
GO:0006974 DNA damage response
GO:0008380 RNA splicing
GO:0016076 snRNA catabolic process
Cellular Component
GO:0000176 nuclear exosome (RNase complex)
GO:0000178 exosome (RNase complex)
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005681 spliceosomal complex
GO:0005730 nucleolus
GO:0016607 nuclear speck
GO:0031499 TRAMP complex
GO:0071013 catalytic step 2 spliceosome

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:7z52, PDBe:7z52, PDBj:7z52
PDBsum7z52
PubMed35688157
UniProtP42285|MTREX_HUMAN Exosome RNA helicase MTR4 (Gene Name=MTREX)

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