Structure of PDB 6d6r Chain M Binding Site BS02

Receptor Information
>6d6r Chain M (length=709) 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
FHLTYNMVLNLLRVEEINPEYMLEKSFYQFQHYRAIPGVVEKVKNSEDIK
SAKRELKKARTVLQMDELKCRKRVLRRLGFATSSDVIEMKGRVACEISSA
DELLLTEMMFNGLFNDLSAEQATALLSCFVFQENSSEMPKLTEQLAGPLR
QMQECAKRIAKVSAEAKLEIDEETYLSSFKPHLMDVVYTWATGATFAHIC
KMTDVFEGSIIRCMRRLEELLRQMCQAAKAIGNTELENKFAEGITKIKRD
IVFAASLYL
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 chain6d6r Chain M 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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PDB6d6r Helicase-Dependent RNA Decay Illuminated by a Cryo-EM Structure of a Human Nuclear RNA Exosome-MTR4 Complex.
Resolution3.45 Å
Binding residue
(original residue number in PDB)		F138 G166 K167 T168 N490 R527
Binding residue
(residue number reindexed from 1)		F43 G71 K72 T73 N378 R415
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:6d6r, PDBe:6d6r, PDBj:6d6r
PDBsum6d6r
PubMed29906447
UniProtP42285|MTREX_HUMAN Exosome RNA helicase MTR4 (Gene Name=MTREX)

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