Structure of PDB 4x5y Chain A Binding Site BS01

Receptor Information
>4x5y Chain A (length=467) 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
VGWATFLVQSLGRFEGQVRQKVRIVSPVLTFQSEKMKGMKELLVATKINS
SAIKLQLTAQSQVQMKK
Ligand information
Ligand ID3XW
InChIInChI=1S/C28H27F3N8S/c1-17-19(2-3-25-23(17)8-21(11-32)39(25)14-18-12-35-36-13-18)15-38-6-4-20(5-7-38)37-26-24-9-22(10-28(29,30)31)40-27(24)34-16-33-26/h2-3,8-9,12-13,16,20H,4-7,10,14-15H2,1H3,(H,35,36)(H,33,34,37)
InChIKeyDETOMBLLEOZTMZ-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.9.2Cc1c(ccc2c1cc(n2Cc3c[nH]nc3)C#N)CN4CCC(CC4)Nc5c6cc(sc6ncn5)CC(F)(F)F
CACTVS 3.385Cc1c(CN2CCC(CC2)Nc3ncnc4sc(CC(F)(F)F)cc34)ccc5n(Cc6c[nH]nc6)c(cc15)C#N
ACDLabs 12.01N#Cc2n(c1ccc(c(c1c2)C)CN5CCC(Nc3ncnc4sc(cc34)CC(F)(F)F)CC5)Cc6cnnc6
FormulaC28 H27 F3 N8 S
Name4-methyl-1-(1H-pyrazol-4-ylmethyl)-5-[(4-{[6-(2,2,2-trifluoroethyl)thieno[2,3-d]pyrimidin-4-yl]amino}piperidin-1-yl)methyl]-1H-indole-2-carbonitrile;
MI-503
ChEMBLCHEMBL3780822
DrugBank
ZINCZINC000231128670
PDB chain4x5y 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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PDB4x5y Pharmacologic Inhibition of the Menin-MLL Interaction Blocks Progression of MLL Leukemia In Vivo.
Resolution1.59 Å
Binding residue
(original residue number in PDB)		S155 L177 S178 H181 F238 Y276 M278 M322 Y323 E363 E366
Binding residue
(residue number reindexed from 1)		S134 L156 S157 H160 F217 Y255 M257 M301 Y302 E342 E345
Annotation score1
Binding affinityMOAD: Kd=9.3nM
PDBbind-CN: -logKd/Ki=8.03,Kd=9.3nM
BindingDB: IC50=15nM,Kd=10.0nM
Enzymatic activity
Enzyme Commision number ?
Gene Ontology

View graph for
Cellular Component
External links
PDB RCSB:4x5y, PDBe:4x5y, PDBj:4x5y
PDBsum4x5y
PubMed25817203
UniProtO00255|MEN1_HUMAN Menin (Gene Name=MEN1)

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