Structure of PDB 6mum Chain A Binding Site BS01

Receptor Information
>6mum Chain A (length=826) Species: 10090 (Mus musculus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VKKLINSQISLLIGKGLHEFDSLRDPEVNDFRTKMRQFCEEAAAHRQQLG
WVEWLQYSFPLQLEPNRALLVNVKFEGSEESFTFQVSTKDMPLALMACAL
RKKATVFRQQPEEYALQVNGRHEYLYGNYPLCHFQYICSCLHSGLTPHLT
MVHSSSILAMRDEQSNLWSLEQPFSIELIEGRKVNAMKLVVQAGLFHGNE
MLCKTVSSSEVNVCSEPVWKQRLEFDISVCDLPRMARLCFALYAVVDCPI
AWANLMLFDYKDQLKTGERCLYMWPSVLLNPAGTVRGNPNTESAAALVIY
LPEVAPVYFPALEKILELQLQLREILERELYEHEKDLVWKMRHEVQEHFP
EALARLLLVTKWNKHEDVAQMLYLLCSWPELPVLSALELLDFSFPDCYVG
SFAIKSLRKLTDDELFQYLLQLVQVLKYESYLDCELTKFLLGRALANRKI
GHFLFWHLRSEMHVPSVALRFGLIMEAYCRGSTHHMKVLMKQGEALSKLK
ALNDFVKVSSQKTTKPQTKEMMHMCMRQETYMEALSHLQSPLDPSTLLEE
VCVEQCTFMDSKMKPLWIMYSSEEAGSAGNVGIIFKNGDDLRQDMLTLQM
IQLMDVLWKQEGLDLRMTPYGCLPTGDRTGLIEVVLHSDTIANIQLNKSN
MAATAAFNKDALLNWLKSKNPGEALDRAIEEFTLSCAGYCVATYVLGIGD
RHSDNIMIRESGQLFHIDFGHFLGNFKRVPFILTYDFVHVIQQGKTNNSE
KFERFRGYCERAYTILRRHGLLFLHLFALMRAAGLPELSCSKDIQYLKDS
LALGKTEEEALKHFRVKFNEALRESW
Ligand information
Ligand IDK47
InChIInChI=1S/C22H29N7O3/c1-4-29-14(2)17(11-25-29)19-26-18-20(27(19)3)23-13-24-21(18)32-16-5-8-28(12-16)22(30)15-6-9-31-10-7-15/h11,13,15-16H,4-10,12H2,1-3H3/t16-/m0/s1
InChIKeyFHKPLLOSJHHKNU-INIZCTEOSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6CCn1c(c(cn1)c2nc3c(n2C)ncnc3OC4CCN(C4)C(=O)C5CCOCC5)C
CACTVS 3.385CCn1ncc(c1C)c2nc3c(O[C@H]4CCN(C4)C(=O)C5CCOCC5)ncnc3n2C
CACTVS 3.385CCn1ncc(c1C)c2nc3c(O[CH]4CCN(C4)C(=O)C5CCOCC5)ncnc3n2C
ACDLabs 12.01n1(c3c(nc1c2c(C)n(nc2)CC)c(ncn3)OC5CN(C(=O)C4CCOCC4)CC5)C
OpenEye OEToolkits 2.0.6CCn1c(c(cn1)c2nc3c(n2C)ncnc3O[C@H]4CCN(C4)C(=O)C5CCOCC5)C
FormulaC22 H29 N7 O3
Name[(3S)-3-{[8-(1-ethyl-5-methyl-1H-pyrazol-4-yl)-9-methyl-9H-purin-6-yl]oxy}pyrrolidin-1-yl](oxan-4-yl)methanone
ChEMBLCHEMBL4570812
DrugBank
ZINC
PDB chain6mum Chain A Residue 9001 [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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PDB6mum Structure Overhaul Affords a Potent Purine PI3K delta Inhibitor with Improved Tolerability.
Resolution3.06 Å
Binding residue
(original residue number in PDB)		T750 W760 I777 Y813 I825 V828 M900 I910
Binding residue
(residue number reindexed from 1)		T557 W567 I584 Y620 I632 V635 M707 I717
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=8.41,IC50=3.9nM
Enzymatic activity
Enzyme Commision number 2.7.1.137: phosphatidylinositol 3-kinase.
2.7.1.153: phosphatidylinositol-4,5-bisphosphate 3-kinase.
Gene Ontology
Molecular Function
GO:0016301 kinase activity
GO:0016303 1-phosphatidylinositol-3-kinase activity
Biological Process
GO:0043491 phosphatidylinositol 3-kinase/protein kinase B signal transduction
GO:0046854 phosphatidylinositol phosphate biosynthetic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:6mum, PDBe:6mum, PDBj:6mum
PDBsum6mum
PubMed30986068
UniProtO35904|PK3CD_MOUSE Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit delta isoform (Gene Name=Pik3cd)

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