Structure of PDB 4og6 Chain A Binding Site BS01

Receptor Information
>4og6 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 ID2S9
InChIInChI=1S/C27H33FN2O2/c28-25-8-3-7-24(19-25)27(31,22-5-1-2-6-22)23-13-16-30(17-14-23)15-4-18-32-26-11-9-21(20-29)10-12-26/h3,7-12,19,22-23,31H,1-2,4-6,13-18H2/t27-/m1/s1
InChIKeyFTSMDZBUBLYVKI-HHHXNRCGSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6c1cc(cc(c1)F)C(C2CCCC2)(C3CCN(CC3)CCCOc4ccc(cc4)C#N)O
CACTVS 3.385O[C@](C1CCCC1)(C2CCN(CCCOc3ccc(cc3)C#N)CC2)c4cccc(F)c4
ACDLabs 12.01Fc1cccc(c1)C(O)(C3CCN(CCCOc2ccc(C#N)cc2)CC3)C4CCCC4
CACTVS 3.385O[C](C1CCCC1)(C2CCN(CCCOc3ccc(cc3)C#N)CC2)c4cccc(F)c4
OpenEye OEToolkits 1.7.6c1cc(cc(c1)F)[C@@](C2CCCC2)(C3CCN(CC3)CCCOc4ccc(cc4)C#N)O
FormulaC27 H33 F N2 O2
Name4-(3-{4-[(R)-cyclopentyl(3-fluorophenyl)hydroxymethyl]piperidin-1-yl}propoxy)benzonitrile
ChEMBL
DrugBank
ZINCZINC000098208257
PDB chain4og6 Chain A Residue 602 [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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PDB4og6 High-Affinity Small-Molecule Inhibitors of the Menin-Mixed Lineage Leukemia (MLL) Interaction Closely Mimic a Natural Protein-Protein Interaction.
Resolution1.49 Å
Binding residue
(original residue number in PDB)		S178 D180 H181 F238 A242 M278 Y319 M322 Y323 E363
Binding residue
(residue number reindexed from 1)		S157 D159 H160 F217 A221 M257 Y298 M301 Y302 E342
Annotation score1
Binding affinityMOAD: ic50=197nM
PDBbind-CN: -logKd/Ki=6.71,IC50=197nM
BindingDB: IC50=197nM
Enzymatic activity
Enzyme Commision number ?
Gene Ontology

View graph for
Cellular Component
External links
PDB RCSB:4og6, PDBe:4og6, PDBj:4og6
PDBsum4og6
PubMed24472025
UniProtO00255|MEN1_HUMAN Menin (Gene Name=MEN1)

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