Structure of PDB 5urk Chain A Binding Site BS01

Receptor Information
>5urk Chain A (length=1706) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LAPRQVLDLEDLVFTQGSHFMANKRCQLPDGSFRRQRKGYEEVHVPALKP
KPFGSEEQLLPVEKLPKYAQAGFEGFKTLNRIQSKLYRAALETDENLLLC
APTGAGKTNVALMCMLREIGKHINMDGTINVDDFKIIYIAPMRSLVQEMV
GSFGKRLATYGITVAELTGKEEISATQIIVCTPEKWDIITRKGGERTYTQ
LVRLIILDEIHLLHDDRGPVLEALVARAIRNIEMTQEDVRLIGLSATLPN
YEDVATFLRVDPAKGLFYFDNSFRPVPLEQTYVGITEKKAIKRFQIMNEI
VYEKIMEHAGKNQVLVFVHSRKETGKTARAIRDMCLEKDTLGLFLREGSA
STEVLRTEAEQCKNLELKDLLPYGFAIHHAGMTRVDRTLVEDLFADKHIQ
VLVSTATLAWGVNLPAHTVIIKGTQVYSPEKGRWTELGALDILQMLGRAG
RPQYDTKGEGILITSHGELQYYLSLLNQQLPIESQMVSKLPDMLNAEIVL
GNVQNAKDAVNWLGYAYLYIRMLRSPTLYGISHDDLKGDPLLDQRRLDLV
HTAALMLDKNNLVKYDKKTGNFQVTELGRIASHYYITNDTVQTYNQLLKP
TLSEIELFRVFSLSSEFKNITVREEEKLELQKLLERVPIPVKESIEEPSA
KINVLLQAFISQLKLEGFALMADMVYVTQSAGRLMRAIFEIVLNRGWAQL
TDKTLNLCKMIDKRMWQSMCPLRQFRKLPEEVVKKIEKKNFPFERLYDLN
HNEIGELIRMPKMGKTIHKYVHLFPKLELSVHLQPITRSTLKVELTITPD
FQWDEKVHGSSEAFWILVEDVDSEVILHHEYFLLKAKYAQDEHLITFFVP
VFEPLPPQYFIRVVSDRWLSCETQLPVSFRHLILPEKYPPPTELLDLQPL
PVSALRNSAFESLYQDKFPFFNPIQTQVFNTVYNSDDNVFVGAPTGSGKT
ICAEFAILRMLLQSSEGRCVYITPMEALAEQVYMDWYEKFQDRLNKKVVL
LTGETSTDLKLLGKGNIIISTPEKWDILSRRWKQRKNVQNINLFVVDEVH
LIGGENGPVLEVICSRMRYISSQIERPIRIVALSSSLSNAKDVAHWLGCS
ATSTFNFHPNVRPVPLELHIQGFNISHTQTRLLSMAKPVYHAITKHSPKK
PVIVFVPSRKQTRLTAIDILTTCAADIQRQRFLHCTEKDLIPYLEKLSDS
TLKETLLNGVGYLHEGLSPMERRLVEQLFSSGAIQVVVASRSLCWGMNVA
AHLVIIMDTQYYNGKIHAYVDYPIYDVLQMVGHANRPLQDDEGRCVIMCQ
GSKKDFFKKFLYEPLPVESHLDHCMHDHFNAEIVTKTIENKQDAVDYLTW
TFLYRRMTQNPNYYNLQGISHRHLSDHLSELVEQTLSDLEQSKCISIEDE
MDVAPLNLGMIAAYYYINYTTIELFSMSLNAKTKVRGLIEIISNAAEYEN
IPIRHHEDNLLRQLAQKVPHKLNNPKFNDPHVKTNLLLQAHLSRMQLSAE
LQSDTEEILSKAIRLIQACVDVLSSNGWLSPALAAMELAQMVTQAMWSKD
SYLKQLPHFTSEHIKRCTESVFDIERNALLQLTDSQIADVARFCNRYPNI
ELSYEVVDKDSIRSGGPVVVLVQLEREEEVTGPVIAPLFPQKREEGWWVV
IGDAKSNSLISIKRLTLQQKAKVKLDFVAPATGAHNYTLYFMSDAYMGCD
QEYKFS
Ligand information
Ligand ID8LP
InChIInChI=1S/C27H23N3O3/c31-26-15-25-22(17-29(26)16-20-8-3-1-4-9-20)18-30(27(32)28-25)23-12-7-13-24(14-23)33-19-21-10-5-2-6-11-21/h1-15,17H,16,18-19H2,(H,28,32)
InChIKeyBHMKGMWMMMZMJN-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6c1ccc(cc1)CN2C=C3CN(C(=O)NC3=CC2=O)c4cccc(c4)OCc5ccccc5
CACTVS 3.385O=C1NC2=CC(=O)N(Cc3ccccc3)C=C2CN1c4cccc(OCc5ccccc5)c4
ACDLabs 12.01N5C=2C(=CN(Cc1ccccc1)C(C=2)=O)CN(c3cccc(c3)OCc4ccccc4)C5=O
FormulaC27 H23 N3 O3
Name6-benzyl-3-[3-(benzyloxy)phenyl]-4,6-dihydropyrido[4,3-d]pyrimidine-2,7(1H,3H)-dione
ChEMBLCHEMBL4065018
DrugBank
ZINC
PDB chain5urk Chain A Residue 2202 [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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PDB5urk Discovery of Allosteric Inhibitors Targeting the Spliceosomal RNA Helicase Brr2.
Resolution2.95 Å
Binding residue
(original residue number in PDB)		F1254 F1255 P1257 D1678 P1680 I1681 K1710 F1713 P1723
Binding residue
(residue number reindexed from 1)		F847 F848 P850 D1271 P1273 I1274 K1303 F1306 P1316
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=6.10,IC50=0.79uM
BindingDB: IC50=790nM
Enzymatic activity
Enzyme Commision number 3.6.4.13: RNA helicase.
Gene Ontology
Molecular Function
GO:0003676 nucleic acid binding
GO:0005524 ATP binding

View graph for
Molecular Function
External links
PDB RCSB:5urk, PDBe:5urk, PDBj:5urk
PDBsum5urk
PubMed28586220
UniProtO75643|U520_HUMAN U5 small nuclear ribonucleoprotein 200 kDa helicase (Gene Name=SNRNP200)

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