Structure of PDB 6e1a Chain A Binding Site BS01

Receptor Information
>6e1a Chain A (length=481) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GLKAAQKTLFPLRSIDDVVRLFAAELGREEPDLVLLSLVLGFVEHFLAVN
RVIPTNVPELTFQPSPAPDGLTYFPVADLSIIAALYARFTAQIRGAVDLS
LYPREGGVSSRELVKKVSDVIWNSLSRSYFKDRAHIQSLFSFITGTKLDS
SGVAFAVVGACQALGLRDVHLALSEDHAWVVFGPNGEQTAEVTWHGKGNE
DRRGQTVNAGVAERSWLYLKGSYMRCDRKMEVAFMVCAINPSIDLHTDSL
ELLQLQQKLLWLLYDLGHLERYPMALGNLADLEELEPTPGRPDPLTLYHK
GIASAKTYYRDEHIYPYMYLAGYHCRNRNVREALQAWADTATVIQDYNYC
REDEEIYKEFFEVANDVIPNLLKEAASLLEASALQDPECFAHLLRFYDGI
CKWEEGSPTPVLHVGWATFLVQSLGRFEGQVRQKVRIVSGTVAGTARGPV
LTFQSEKMKGMKELLVATKINSSAIKLQLTA
Ligand information
Ligand IDHL7
InChIInChI=1S/C37H47N5O4S/c1-38-36(43)46-35-9-5-8-34(35)37(26-40(2)25-28-6-3-4-7-33(28)37)29-16-20-41(21-17-29)22-27-23-42(24-27)30-10-12-31(13-11-30)47(44,45)32-14-18-39-19-15-32/h3-4,6-7,10-15,18-19,27,29,34-35H,5,8-9,16-17,20-26H2,1-2H3,(H,38,43)/t34-,35-,37-/m0/s1
InChIKeyRQQWEQZHCLJHSS-IWQNTTPNSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=C(NC)OC1CCCC1C6(C2CCN(CC2)CC3CN(C3)c5ccc(S(=O)(c4ccncc4)=O)cc5)CN(Cc7c6cccc7)C
CACTVS 3.385CNC(=O)O[CH]1CCC[CH]1[C]2(CN(C)Cc3ccccc23)C4CCN(CC4)CC5CN(C5)c6ccc(cc6)[S](=O)(=O)c7ccncc7
CACTVS 3.385CNC(=O)O[C@H]1CCC[C@@H]1[C@@]2(CN(C)Cc3ccccc23)C4CCN(CC4)CC5CN(C5)c6ccc(cc6)[S](=O)(=O)c7ccncc7
OpenEye OEToolkits 2.0.6CNC(=O)OC1CCCC1C2(CN(Cc3c2cccc3)C)C4CCN(CC4)CC5CN(C5)c6ccc(cc6)S(=O)(=O)c7ccncc7
OpenEye OEToolkits 2.0.6CNC(=O)O[C@H]1CCC[C@@H]1[C@@]2(CN(Cc3c2cccc3)C)C4CCN(CC4)CC5CN(C5)c6ccc(cc6)S(=O)(=O)c7ccncc7
FormulaC37 H47 N5 O4 S
Name(1S,2R)-2-[(4S)-2-methyl-4-{1-[(1-{4-[(pyridin-4-yl)sulfonyl]phenyl}azetidin-3-yl)methyl]piperidin-4-yl}-1,2,3,4-tetrahydroisoquinolin-4-yl]cyclopentyl methylcarbamate
ChEMBLCHEMBL4449381
DrugBank
ZINC
PDB chain6e1a Chain A Residue 701 [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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PDB6e1a Structure-Based Discovery of M-89 as a Highly Potent Inhibitor of the Menin-Mixed Lineage Leukemia (Menin-MLL) Protein-Protein Interaction.
Resolution3.1 Å
Binding residue
(original residue number in PDB)		S178 H181 F238 C241 A242 Y276 M278 Y319 M322 Y323 G326 W341 E363
Binding residue
(residue number reindexed from 1)		S174 H177 F234 C237 A238 Y272 M274 Y315 M318 Y319 G322 W337 E359
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=8.85,Kd=1.4nM
BindingDB: Ki=<1.000000nM,IC50=5.0nM,Kd=1400nM
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
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Biological Process
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Cellular Component
External links
PDB RCSB:6e1a, PDBe:6e1a, PDBj:6e1a
PDBsum6e1a
PubMed31244110
UniProtO00255|MEN1_HUMAN Menin (Gene Name=MEN1)

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