Structure of PDB 3u88 Chain B Binding Site BS02

Receptor Information
>3u88 Chain B (length=485) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GLKAAQKTLFPLRSIDDVVRLFAAELGREEPDLVLLSLVLGFVEHFLAVN
RVIPTNVPELTFQPSPAPDPPGGLTYFPVADLSIIAALYARFTAQIRGAV
DLSLYPREGGVSSRELVKKVSDVIWNSLSRSYFKDRAHIQSLFSFITGTK
LDSSGVAFAVVGACQALGLRDVHLALSEDHAWVVFGPNGEQTAEVTWHGK
GNEDRRGQTVNAGVAERSWLYLKGSYMRCDRKMEVAFMVCAINPSIDLHT
DSLELLQLQQKLLWLLYDLGHLERYPMALGNLADLEELEPTPGRPDPLTL
YHKGIASAKTYYRDEHIYPYMYLAGYHCRNRNVREALQAWADTATVIQDY
NYCREDEEIYKEFFEVANDVIPNLLKEAASLLEAGQGSALQDPECFAHLL
RFYDGICKWEEGSPTPVLHVGWATFLVQSLGRFEGQVRQKVRIVSGPPPE
GPVLTFQSEKMKGMKELLVATKINSSAIKLQLTAQ
Ligand information
Ligand IDGGB
InChIInChI=1S/C5H12N4O3/c6-3(4(10)11)1-2-12-9-5(7)8/h3H,1-2,6H2,(H,10,11)(H4,7,8,9)/t3-/m0/s1
InChIKeyFSBIGDSBMBYOPN-VKHMYHEASA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=C(O)C(N)CCONC(=[N@H])N
OpenEye OEToolkits 1.5.0[H]N=C(N)NOCCC(C(=O)O)N
CACTVS 3.341N[CH](CCONC(N)=N)C(O)=O
CACTVS 3.341N[C@@H](CCONC(N)=N)C(O)=O
OpenEye OEToolkits 1.5.0[H]/N=C(\N)/NOCC[C@@H](C(=O)O)N
FormulaC5 H12 N4 O3
NameL-CANAVANINE;
L-2-AMINO-4-(GUANIDINOOXY)BUTYRIC ACID
ChEMBLCHEMBL443732
DrugBankDB01833
ZINCZINC000003869452
PDB chain3u88 Chain B Residue 615 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
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)		Y133 F134 R137 K151
Binding residue
(residue number reindexed from 1)		Y132 F133 R136 K150
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

View graph for
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)

[Back to BioLiP]