Structure of PDB 4kit Chain B Binding Site BS02

Receptor Information

>4kit Chain B (length=1722) Species: 9606 (Homo sapiens)

APRQVLDLEDLVFTQGSHFMANKRCQLPDGSFRRQRKGYEEVHVPALKPK
PFGSEEQLLPVEKLPKYAQAGFEGFKTLNRIQSKLYRAALETDENLLLCA
PTGAGKTNVALMCMLREIGKHINMDGTINVDDFKIIYIAPMRSLVQEMVG
SFGKRLATYGITVAELTGDHQLCKEEISATQIIVCTPEKWDIITRKGGER
TYTQLVRLIILDEIHLLHDDRGPVLEALVARAIRNIEMTQEDVRLIGLSA
TLPNYEDVATFLRVDPAKGLFYFDNSFRPVPLEQTYVGITEKKAIKRFQI
MNEIVYEKIMEHAGKNQVLVFVHSRKETGKTARAIRDMCLEKDTLGLFLR
EGSASTEVLRTEAEQCKNLELKDLLPYGFAIHHAGMTRVDRTLVEDLFAD
KHIQVLVSTATLAWGVNLPAHTVIIKGTQVYSPEKGRWTELGALDILQML
GRAGRPQYDTKGEGILITSHGELQYYLSLLNQQLPIESQMVSKLPDMLNA
EIVLGNVQNAKDAVNWLGYAYLYIRMLRSPTLYGISHDDLKGDPLLDQRR
LDLVHTAALMLDKNNLVKYDKKTGNFQVTELGRIASHYYITNDTVQTYNQ
LLKPTLSEIELFRVFSLSSEFKNITVREEEKLELQKLLERVPIPVKESIE
EPSAKINVLLQAFISQLKLEGFALMADMVYVTQSAGRLMRAIFEIVLNRG
WAQLTDKTLNLCKMIDKRMWQSMCPLRQFRKLPEEVVKKIEKKNFPFERL
YDLNHNEIGELIRMPKMGKTIHKYVHLFPKLELSVHLQPITRSTLKVELT
ITPDFQWDEKVHGSSEAFWILVEDVDSEVILHHEYFLLKAKYAQDEHLIT
FFVPVFEPLPPQYFIRVVSDRWLSCETQLPVSFRHLILPEKYPPPTELLD
LQPLPVSALRNSAFESLYQDKFPFFNPIQTQVFNTVYNSDDNVFVGAPTG
SGKTICAEFAILRMLLQSSEGRCVYITPMEALAEQVYMDWYEKFQDRLNK
KVVLLTGETSTDLKLLGKGNIIISTPEKWDILSRRWKQRKNVQNINLFVV
DEVHLIGGENGPVLEVICSRMRYISSQIERPIRIVALSSSLSNAKDVAHW
LGCSATSTFNFHPNVRPVPLELHIQGFNISHTQTRLLSMAKPVYHAITKH
SPKKPVIVFVPSRKQTRLTAIDILTTCAADIQRQRFLHCTEKDLIPYLEK
LSDSTLKETLLNGVGYLHEGLSPMERRLVEQLFSSGAIQVVVASRSLCWG
MNVAAHLVIIMDTQYYNGKIHAYVDYPIYDVLQMVGHANRPLQDDEGRCV
IMCQGSKKDFFKKFLYEPLPVESHLDHCMHDHFNAEIVTKTIENKQDAVD
YLTWTFLYRRMTQNPNYYNLQGISHRHLSDHLSELVEQTLSDLEQSKCIS
IEDEMDVAPLNLGMIAAYYYINYTTIELFSMSLNAKTKVRGLIEIISNAA
EYENIPIRHHEDNLLRQLAQKVPHKLNNPKFNDPHVKTNLLLQAHLSRMQ
LSAELQSDTEEILSKAIRLIQACVDVLSSNGWLSPALAAMELAQMVTQAM
WSKDSYLKQLPHFTSEHIKRCTDKGVESVFDIMEMEDEERNALLQLTDSQ
IADVARFCNRYPNIELSYEVVDKDSIRSGGPVVVLVQLEREEEVTGPVIA
PLFPQKREEGWWVVIGDAKSNSLISIKRLTLQQKAKVKLDFVAPATGAHN
YTLYFMSDAYMGCDQEYKFSVD

Ligand information

• Ligand ID: ADP
• InChI: InChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
• InChIKey: XTWYTFMLZFPYCI-KQYNXXCUSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N
  CACTVS 3.341: Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
  ACDLabs 10.04: O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
  CACTVS 3.341: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
• Formula: C10 H15 N5 O10 P2
• Name: ADENOSINE-5'-DIPHOSPHATE
• ChEMBL: CHEMBL14830
• DrugBank: DB16833
• ZINC: ZINC000012360703
• PDB chain: 4kit Chain B Residue 2202

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4kit Inhibition of RNA helicase Brr2 by the C-terminal tail of the spliceosomal protein Prp8.
• Resolution: 3.598 Å
• Binding residue (original residue number in PDB): F1325 Q1332 G1353 S1354 G1355 K1356 T1357 P1694
• Binding residue (residue number reindexed from 1): F922 Q929 G950 S951 G952 K953 T954 P1291
• Annotation score: 5

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:4kit, PDBe:4kit, PDBj:4kit
• PDBsum: 4kit
• PubMed: 23704370
• UniProt: O75643|U520_HUMAN U5 small nuclear ribonucleoprotein 200 kDa helicase (Gene Name=SNRNP200)