Structure of PDB 7bdl Chain B Binding Site BS01

Receptor Information

>7bdl Chain B (length=1725) Species: 9606 (Homo sapiens)

LAPRQVLDLEDLVFTQGSHFMANKRCQLPDGSFRRQRKGYEEVHVPALKP
KPFGSEEQLLPVEKLPKYAQAGFEGFKTLNRIQSKLYRAALETDENLLLC
APTGAGKTNVALMCMLREIGKHINMDGTINVDDFKIIYIAPMRSLVQEMV
GSFGKRLATYGITVAELTGDHQLCKEEISATQIIVCTPEKWDIITRKGGE
RTYTQLVRLIILDEIHLLHDDRGPVLEALVARAIRNIEMTQEDVRLIGLS
ATLPNYEDVATFLRVDPAKGLFYFDNSFRPVPLEQTYVGITEKKAIKRFQ
IMNEIVYEKIMEHAGKNQVLVFVHSRKETGKTARAIRDMCLEKDTLGLFL
REGSASTEVLRTEAEQCKNLELKDLLPYGFAIHHAGMTRVDRTLVEDLFA
DKHIQVLVSTATLAWGVNLPAHTVIIKGTQVYSPEKGRWTELGALDILQM
LGRAGRPQYDTKGEGILITSHGELQYYLSLLNQQLPIESQMVSKLPDMLN
AEIVLGNVQNAKDAVNWLGYAYLYIRMLRSPTLYGISHDDLKGDPLLDQR
RLDLVHTAALMLDKNNLVKYDKKTGNFQVTELGRIASHYYITNDTVQTYN
QLLKPTLSEIELFRVFSLSSEFKNITVREEEKLELQKLLERVPIPVKESI
EEPSAKINVLLQAFISQLKLEGFALMADMVYVTQSAGRLMRAIFEIVLNR
GWAQLTDKTLNLCKMIDKRMWQSMCPLRQFRKLPEEVVKKIEKKNFPFER
LYDLNHNEIGELIRMPKMGKTIHKYVHLFPKLELSVHLQPITRSTLKVEL
TITPDFQWDEKVHGSSEAFWILVEDVDSEVILHHEYFLLKAKYAQDEHLI
TFFVPVFEPLPPQYFIRVVSDRWLSCETQLPVSFRHLILPEKYPPPTELL
DLQPLPVSALRNSAFESLYQDKFPFFNPIQTQVFNTVYNSDDNVFVGAPT
GSGKTICAEFAILRMLLQSSEGRCVYITPMEALAEQVYMDWYEKFQDRLN
KKVVLLTGETSTDLKLLGKGNIIISTPEKWDILSRRWKQRKNVQNINLFV
VDEVHLIGGENGPVLEVICSRMRYISSQIERPIRIVALSSSLSNAKDVAH
WLGCSATSTFNFHPNVRPVPLELHIQGFNISHTQTRLLSMAKPVYHAITK
HSPKKPVIVFVPSRKQTRLTAIDILTTCAADIQRQRFLHCTEKDLIPYLE
KLSDSTLKETLLNGVGYLHEGLSPMERRLVEQLFSSGAIQVVVASRSLCW
GMNVAAHLVIIMDTQYYNGKIHAYVDYPIYDVLQMVGHANRPLQDDEGRC
VIMCQGSKKDFFKKFLYEPLPVESHLDHCMHDHFNAEIVTKTIENKQDAV
DYLTWTFLYRRMTQNPNYYNLQGISHRHLSDHLSELVEQTLSDLEQSKCI
SIEDEMDVAPLNLGMIAAYYYINYTTIELFSMSLNAKTKVRGLIEIISNA
AEYENIPIRHHEDNLLRQLAQKVPHKLNNPKFNDPHVKTNLLLQAHLSRM
QLSAELQSDTEEILSKAIRLIQACVDVLSSNGWLSPALAAMELAQMVTQA
MWSKDSYLKQLPHFTSEHIKRCTDKGVESVFDIMEMEDEERNALLQLTDS
QIADVARFCNRYPNIELSYEVVDKDSIRSGGPVVVLVQLEREEEVTGPVI
APLFPQKREEGWWVVIGDAKSNSLISIKRLTLQQKAKVKLDFVAPATGAH
NYTLYFMSDAYMGCDQEYKFSVDVK

Ligand information

• Ligand ID: TG8
• InChI: InChI=1S/C18H22N6O11P2/c1-20-10-5-3-2-4-9(10)18(26)34-14-11(6-32-37(30,31)35-36(27,28)29)33-17(13(14)25)24-8-23-12-15(19)21-7-22-16(12)24/h2-5,7-8,11,13-14,17,20,25H,6H2,1H3,(H,30,31)(H2,19,21,22)(H2,27,28,29)/t11-,13-,14-,17-/m1/s1
• InChIKey: ANMCUTJZONROBG-LSCFUAHRSA-N
• SMILES:
  CACTVS 3.385: CNc1ccccc1C(=O)O[CH]2[CH](O)[CH](O[CH]2CO[P](O)(=O)O[P](O)(O)=O)n3cnc4c(N)ncnc34
  OpenEye OEToolkits 2.0.7: CNc1ccccc1C(=O)OC2C(OC(C2O)n3cnc4c3ncnc4N)COP(=O)(O)OP(=O)(O)O
  OpenEye OEToolkits 2.0.7: CNc1ccccc1C(=O)O[C@@H]2[C@H](O[C@H]([C@@H]2O)n3cnc4c3ncnc4N)COP(=O)(O)OP(=O)(O)O
  CACTVS 3.385: CNc1ccccc1C(=O)O[C@H]2[C@@H](O)[C@@H](O[C@@H]2CO[P](O)(=O)O[P](O)(O)=O)n3cnc4c(N)ncnc34
• Formula: C18 H22 N6 O11 P2
• Name: [(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-2-[[oxidanyl(phosphonooxy)phosphoryl]oxymethyl]oxolan-3-yl] 2-(methylamino)benzoate
• ChEMBL: CHEMBL399755
• PDB chain: 7bdl Chain B Residue 2201

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7bdl Long-range allostery mediates cooperative adenine nucleotide binding by the Ski2-like RNA helicase Brr2.
• Resolution: 2.69 Å
• Binding residue (original residue number in PDB): F478 L481 N482 Q485 T505 G506 G508 K509 T510 N511
• Binding residue (residue number reindexed from 1): F76 L79 N80 Q83 T103 G104 G106 K107 T108 N109
• Annotation score: 3

Enzymatic activity

• Enzyme Commision number: 3.6.4.13: RNA helicase.

Gene Ontology

Molecular Function

• GO:0003676 nucleic acid binding
• GO:0005524 ATP binding

External links

• PDB: RCSB:7bdl, PDBe:7bdl, PDBj:7bdl
• PDBsum: 7bdl
• PubMed: 34048711
• UniProt: O75643|U520_HUMAN U5 small nuclear ribonucleoprotein 200 kDa helicase (Gene Name=SNRNP200)