Structure of PDB 6by8 Chain A Binding Site BS01

Receptor Information
>6by8 Chain A (length=468) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GLKAAQKTLFPLRSIDDVVRLFAAELGREEPDLVLLSLVLGFVEHFLAVN
RVGLTYFPVADLSIIAALYARFTAQIRGAVDLSLYPREGGVSSRELVKKV
SDVIWNSLSRSYFKDRAHIQSLFSFITGTKLDSSGVAFAVVGACQALGLR
DVHLALSEDHAWVVFGPNGEQTAEVTWHGKGNEDRRGQTVNAGVAERSWL
YLKGSYMRCDRKMEVAFMVCAINPSIDLHTDSLELLQLQQKLLWLLYDLG
HLERYPMALGNLADLEELEPTPGRPDPLTLYHKGIASAKTYYRDEHIYPY
MYLAGYHCRNRNVREALQAWADTATVIQDYNYCREDEEIYKEFFEVANDV
IPNLLKEAASLLEAGSQGSALQDPECFAHLLRFYDGICKWEEGSPTPVLH
VGWATFLVQSLGRFEGQVRQKVRIVSVPPVLTFQSEKMKGMKELLVATKI
NSSAIKLQLTAQSQVQMK
Ligand information
Ligand IDFNV
InChIInChI=1S/C29H30F3N7O2S/c1-17-18(2-3-25-23(17)8-20(11-33)39(25)14-21-12-34-26(40)15-41-21)13-38-6-4-19(5-7-38)37-27-24-9-22(10-29(30,31)32)42-28(24)36-16-35-27/h2-3,8-9,16,19,21H,4-7,10,12-15H2,1H3,(H,34,40)(H,35,36,37)/t21-/m1/s1
InChIKeyJTUOGOXWKQAKOR-OAQYLSRUSA-N
SMILES
SoftwareSMILES
CACTVS 3.385Cc1c(CN2CCC(CC2)Nc3ncnc4sc(CC(F)(F)F)cc34)ccc5n(C[C@H]6CNC(=O)CO6)c(cc15)C#N
ACDLabs 12.01c12sc(cc1c(ncn2)NC3CCN(CC3)Cc6ccc5c(cc(C#N)n5CC4CNC(CO4)=O)c6C)CC(F)(F)F
OpenEye OEToolkits 2.0.6Cc1c(ccc2c1cc(n2CC3CNC(=O)CO3)C#N)CN4CCC(CC4)Nc5c6cc(sc6ncn5)CC(F)(F)F
OpenEye OEToolkits 2.0.6Cc1c(ccc2c1cc(n2C[C@H]3CNC(=O)CO3)C#N)CN4CCC(CC4)Nc5c6cc(sc6ncn5)CC(F)(F)F
CACTVS 3.385Cc1c(CN2CCC(CC2)Nc3ncnc4sc(CC(F)(F)F)cc34)ccc5n(C[CH]6CNC(=O)CO6)c(cc15)C#N
FormulaC29 H30 F3 N7 O2 S
Name4-methyl-1-{[(2R)-5-oxomorpholin-2-yl]methyl}-5-[(4-{[6-(2,2,2-trifluoroethyl)thieno[2,3-d]pyrimidin-4-yl]amino}piperidin-1-yl)methyl]-1H-indole-2-carbonitrile
ChEMBLCHEMBL4210580
DrugBank
ZINC
PDB chain6by8 Chain A Residue 601 [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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PDB6by8 Complexity of Blocking Bivalent Protein-Protein Interactions: Development of a Highly Potent Inhibitor of the Menin-Mixed-Lineage Leukemia Interaction.
Resolution1.9 Å
Binding residue
(original residue number in PDB)		S155 S178 H181 F238 Y276 M278 M322 Y323 W341 E363 E366
Binding residue
(residue number reindexed from 1)		S134 S157 H160 F217 Y255 M257 M301 Y302 W320 E342 E345
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=6.91,IC50=123nM
BindingDB: IC50=123nM
Enzymatic activity
Enzyme Commision number ?
Gene Ontology

View graph for
Cellular Component
External links
PDB RCSB:6by8, PDBe:6by8, PDBj:6by8
PDBsum6by8
PubMed29738674
UniProtO00255|MEN1_HUMAN Menin (Gene Name=MEN1)

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