Structure of PDB 3u88 Chain A Binding Site BS02

Receptor Information
>3u88 Chain A (length=477) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GLKAAQKTLFPLRSIDDVVRLFAAELGREEPDLVLLSLVLGFVEHFLAVN
RVIPTNVPELTFQPSPAPDGGLTYFPVADLSIIAALYARFTAQIRGAVDL
SLYPREGGVSSRELVKKVSDVIWNSLSRSYFKDRAHIQSLFSFITGTKLD
SSGVAFAVVGACQALGLRDVHLALSEDHAWVVFGPNGEQTAEVTWHGKGN
EDRRGQTVNAGVAERSWLYLKGSYMRCDRKMEVAFMVCAINPSIDLHTDS
LELLQLQQKLLWLLYDLGHLERYPMALGNLADLEELEPTPGRPDPLTLYH
KGIASAKTYYRDEHIYPYMYLAGYHCRNRNVREALQAWADTATVIQDYNY
CREDEEIYKEFFEVANDVIPNLLKEAASLLEASALQDPECFAHLLRFYDG
ICKWEEGSPTPVLHVGWATFLVQSLGRFEGQVRQKVRIVSEGPVLTFQSE
KMKGMKELLVATKINSSAIKLQLTAQS
Ligand information
Ligand ID0BR
InChIInChI=1S/C20H26N2O2/c1-3-13-12-22-9-7-14(13)10-19(22)20(23)16-6-8-21-18-5-4-15(24-2)11-17(16)18/h4-6,8,11,13-14,19-20,23H,3,7,9-10,12H2,1-2H3/t13-,14+,19-,20+/m0/s1
InChIKeyLJOQGZACKSYWCH-FOEVPDMQSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6CC[C@H]1C[N@]2CC[C@@H]1C[C@H]2[C@@H](c3ccnc4c3cc(cc4)OC)O
CACTVS 3.370CC[C@H]1C[N@@]2CC[C@@H]1C[C@H]2[C@H](O)c3ccnc4ccc(OC)cc34
ACDLabs 12.01O(c4cc1c(nccc1C(O)C2N3CCC(C2)C(CC)C3)cc4)C
OpenEye OEToolkits 1.7.6CCC1CN2CCC1CC2C(c3ccnc4c3cc(cc4)OC)O
CACTVS 3.370CC[CH]1C[N]2CC[CH]1C[CH]2[CH](O)c3ccnc4ccc(OC)cc34
FormulaC20 H26 N2 O2
Name(4beta,8alpha,9R)-6'-methoxy-10,11-dihydrocinchonan-9-ol
ChEMBLCHEMBL531471
DrugBank
ZINCZINC000000156021
PDB chain3u88 Chain A Residue 612 [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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PDB3u88 The same pocket in menin binds both MLL and JUND but has opposite effects on transcription.
Resolution3.0 Å
Binding residue
(original residue number in PDB)		W126 L129 S130 R131 W198
Binding residue
(residue number reindexed from 1)		W123 L126 S127 R128 W195
Annotation score1
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0000400 four-way junction DNA binding
GO:0000403 Y-form DNA binding
GO:0000976 transcription cis-regulatory region binding
GO:0003677 DNA binding
GO:0003682 chromatin binding
GO:0003690 double-stranded DNA binding
GO:0005515 protein binding
GO:0030674 protein-macromolecule adaptor activity
GO:0051219 phosphoprotein binding
GO:0070412 R-SMAD binding
Biological Process
GO:0000122 negative regulation of transcription by RNA polymerase II
GO:0000165 MAPK cascade
GO:0001933 negative regulation of protein phosphorylation
GO:0002076 osteoblast development
GO:0006281 DNA repair
GO:0006325 chromatin organization
GO:0006357 regulation of transcription by RNA polymerase II
GO:0006974 DNA damage response
GO:0008285 negative regulation of cell population proliferation
GO:0009411 response to UV
GO:0010332 response to gamma radiation
GO:0030511 positive regulation of transforming growth factor beta receptor signaling pathway
GO:0043433 negative regulation of DNA-binding transcription factor activity
GO:0045064 T-helper 2 cell differentiation
GO:0045668 negative regulation of osteoblast differentiation
GO:0045736 negative regulation of cyclin-dependent protein serine/threonine kinase activity
GO:0045786 negative regulation of cell cycle
GO:0045815 transcription initiation-coupled chromatin remodeling
GO:0045892 negative regulation of DNA-templated transcription
GO:0045944 positive regulation of transcription by RNA polymerase II
GO:0046329 negative regulation of JNK cascade
Cellular Component
GO:0000781 chromosome, telomeric region
GO:0000785 chromatin
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005788 endoplasmic reticulum lumen
GO:0005829 cytosol
GO:0016363 nuclear matrix
GO:0017053 transcription repressor complex
GO:0032154 cleavage furrow
GO:0032991 protein-containing complex
GO:0035097 histone methyltransferase complex
GO:0044665 MLL1/2 complex
GO:0071339 MLL1 complex

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Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:3u88, PDBe:3u88, PDBj:3u88
PDBsum3u88
PubMed22327296
UniProtO00255|MEN1_HUMAN Menin (Gene Name=MEN1)

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