Structure of PDB 5urj Chain A Binding Site BS01

Receptor Information
>5urj Chain A (length=1707) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LAPRQVLDLEDLVFTQGSHFMANKRCQLPDGSFRRQRKGYEEVHVPALKP
KPFGSEEQLLPVEKLPKYAQAGFEGFKTLNRIQSKLYRAALETDENLLLC
APTGAGKTNVALMCMLREIGKHINMDGTINVDDFKIIYIAPMRSLVQEMV
GSFGKRLATYGITVAELTGEISATQIIVCTPEKWDIITRKGGERTYTQLV
RLIILDEIHLLHDDRGPVLEALVARAIRNIEMTQEDVRLIGLSATLPNYE
DVATFLRVDPAKGLFYFDNSFRPVPLEQTYVGITEKKAIKRFQIMNEIVY
EKIMEHAGKNQVLVFVHSRKETGKTARAIRDMCLEKDTLGLFLREGSAST
EVLRTEAEQCKNLELKDLLPYGFAIHHAGMTRVDRTLVEDLFADKHIQVL
VSTATLAWGVNLPAHTVIIKGTQVYSPEKGRWTELGALDILQMLGRAGRP
QYDTKGEGILITSHGELQYYLSLLNQQLPIESQMVSKLPDMLNAEIVLGN
VQNAKDAVNWLGYAYLYIRMLRSPTLYGISHDDLKGDPLLDQRRLDLVHT
AALMLDKNNLVKYDKKTGNFQVTELGRIASHYYITNDTVQTYNQLLKPTL
SEIELFRVFSLSSEFKNITVREEEKLELQKLLERVPIPVKESIEEPSAKI
NVLLQAFISQLKLEGFALMADMVYVTQSAGRLMRAIFEIVLNRGWAQLTD
KTLNLCKMIDKRMWQSMCPLRQFRKLPEEVVKKIEKKNFPFERLYDLNHN
EIGELIRMPKMGKTIHKYVHLFPKLELSVHLQPITRSTLKVELTITPDFQ
WDEKVHGSSEAFWILVEDVDSEVILHHEYFLLKAKYAQDEHLITFFVPVF
EPLPPQYFIRVVSDRWLSCETQLPVSFRHLILPEKYPPPTELLDLQPLPV
SALRNSAFESLYQDKFPFFNPIQTQVFNTVYNSDDNVFVGAPTGSGKTIC
AEFAILRMLLQSSEGRCVYITPMEALAEQVYMDWYEKFQDRLNKKVVLLT
GETSTDLKLLGKGNIIISTPEKWDILSRRWKQRKNVQNINLFVVDEVHLI
GGENGPVLEVICSRMRYISSQIERPIRIVALSSSLSNAKDVAHWLGCSAT
STFNFHPNVRPVPLELHIQGFNISHTQTRLLSMAKPVYHAITKHSPKKPV
IVFVPSRKQTRLTAIDILTTCAADIQRQRFLHCTEKDLIPYLEKLSDSTL
KETLLNGVGYLHEGLSPMERRLVEQLFSSGAIQVVVASRSLCWGMNVAAH
LVIIMDTQYYNGKIHAYVDYPIYDVLQMVGHANRPLQDDEGRCVIMCQGS
KKDFFKKFLYEPLPVESHLDHCMHDHFNAEIVTKTIENKQDAVDYLTWTF
LYRRMTQNPNYYNLQGISHRHLSDHLSELVEQTLSDLEQSKCISIEDEMD
VAPLNLGMIAAYYYINYTTIELFSMSLNAKTKVRGLIEIISNAAEYENIP
IRHHEDNLLRQLAQKVPHKLNNPKFNDPHVKTNLLLQAHLSRMQLSAELQ
SDTEEILSKAIRLIQACVDVLSSNGWLSPALAAMELAQMVTQAMWSKDSY
LKQLPHFTSEHIKRCTDESVFDIDEERNALLQLTDSQIADVARFCNRYPN
IELSYEVVDKDSIRSGGPVVVLVQLEREEEVTGPVIAPLFPQKREEGWWV
VIGDAKSNSLISIKRLTLQQKAKVKLDFVAPATGAHNYTLYFMSDAYMGC
DQEYKFS
Ligand information
Ligand ID8LS
InChIInChI=1S/C29H25FN4O3/c1-18-12-20-9-10-25(28-22(30)8-5-11-31-28)37-26(20)14-24(18)34-17-21-16-33(15-19-6-3-2-4-7-19)27(35)13-23(21)32-29(34)36/h2-8,11-12,14,16,25H,9-10,13,15,17H2,1H3/t25-/m1/s1
InChIKeyIHLUBSALJUDYDX-RUZDIDTESA-N
SMILES
SoftwareSMILES
CACTVS 3.385Cc1cc2CC[CH](Oc2cc1N3CC4=CN(Cc5ccccc5)C(=O)CC4=NC3=O)c6ncccc6F
CACTVS 3.385Cc1cc2CC[C@@H](Oc2cc1N3CC4=CN(Cc5ccccc5)C(=O)CC4=NC3=O)c6ncccc6F
OpenEye OEToolkits 2.0.6Cc1cc2c(cc1N3CC4=CN(C(=O)CC4=NC3=O)Cc5ccccc5)OC(CC2)c6c(cccn6)F
OpenEye OEToolkits 2.0.6Cc1cc2c(cc1N3CC4=CN(C(=O)CC4=NC3=O)Cc5ccccc5)O[C@H](CC2)c6c(cccn6)F
ACDLabs 12.01c51CCC(Oc1cc(N4CC3=CN(Cc2ccccc2)C(CC3=NC4=O)=O)c(C)c5)c6c(cccn6)F
FormulaC29 H25 F N4 O3
Name6-benzyl-3-[(2R)-2-(3-fluoropyridin-2-yl)-6-methyl-3,4-dihydro-2H-1-benzopyran-7-yl]-4,6-dihydropyrido[4,3-d]pyrimidine-2,7(3H,8H)-dione
ChEMBL
DrugBank
ZINC
PDB chain5urj 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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PDB5urj Discovery of Allosteric Inhibitors Targeting the Spliceosomal RNA Helicase Brr2.
Resolution2.75 Å
Binding residue
(original residue number in PDB)
H1235 F1255 V1256 P1257 D1678 P1680 I1681 S1709 K1710 D1712 F1713 K1716 P1723
Binding residue
(residue number reindexed from 1)
H826 F846 V847 P848 D1269 P1271 I1272 S1300 K1301 D1303 F1304 K1307 P1314
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=5.28,IC50=5.3uM
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:5urj, PDBe:5urj, PDBj:5urj
PDBsum5urj
PubMed28586220
UniProtO75643|U520_HUMAN U5 small nuclear ribonucleoprotein 200 kDa helicase (Gene Name=SNRNP200)

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