Structure of PDB 6pyr Chain A Binding Site BS01

Receptor Information
>6pyr Chain A (length=933) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NQSVVVDFLLPTGVYLNFPVSRNANLSTIKQLLWHRAQYEPLFHMLSGPE
AYVFTCINQTAEQQELEDEQRRLCDVQPFLPVLRLVAREGDRVKKLINSQ
ISLLIGKGLHEFDSLCDPEVNDFRAKMCQFCEEAAARRQQLGWEAWLQYS
FPLQLEPSNRALLVNVKFEGSEESFTFQVSTKDVPLALMACALRKKATVR
QVEQPEDYTLQVNGRHEYLYGSYPLCQFQYICSCLHSGLTPHLTMVHSSS
ILAMRDESSVSLWSLEQPFRIELIQGSKVNADERMKLVVQAGLFHGNEML
CKTVSSSEVSVCSEPVWKQRLEFDINICDLPRMARLCFALYAVIEKAADC
PIAWANLMLFDYKDQLKTGERCLYMWPSVPDEKGELLNPTGTVRSNPNTD
SAAALLICLPEVAPHPVYYPALEKILELGRHTEEEQLQLREILEGELYEH
EKDLVWKLRHEVQEHFPEALARLLLVTKWNKHEDVAQMLYLLCSWPELPV
LSALELLDFSFPDCHVGSFAIKSLRKLTDDELFQYLLQLVQVLKYESYLD
CELTKFLLDRALANRKIGHFLFWHLRSEMHVPSVALRFGLILEAYCRGST
HHMKVLMKQGEALSKLKALNDFVKLSSQKTPKPQTKELMHLCMRQEAYLE
ALSHLQSPLDPSTLLAEVCVEQCTFMDSKMKPLWIMYSNEESVGIIFKNG
DDLRQDMLTLQMIQLMDVLWKQEGLDLRMTPYGCLPTGDRTGLIEVVLRS
DTIANIQLNNKDALLNWLKSKNPGEALDRAIEEFTLSCAGYCVATYVLGI
GDRHSDNIMIRESGQLFHIDFGHFLGNFERVPFILTYDFVHVIQQGKTNN
SEKFERFRGYCERAYTILRRHGLLFLHLFALMRAAGLPELSCSKDIQYLK
DSLALGKTEEEALKHFRVKFNEALRESWKTKVN
Ligand information
Ligand IDP5J
InChIInChI=1S/C27H22N6O/c1-17-28-14-20(15-29-17)23-10-11-33-25(31-23)21(16-30-33)19-8-9-24-22(12-19)27(2,26(34)32-24)13-18-6-4-3-5-7-18/h3-12,14-16H,13H2,1-2H3,(H,32,34)/t27-/m0/s1
InChIKeyKQGDDLRQLMABOG-MHZLTWQESA-N
SMILES
SoftwareSMILES
CACTVS 3.385Cc1ncc(cn1)c2ccn3ncc(c4ccc5NC(=O)[C@@](C)(Cc6ccccc6)c5c4)c3n2
OpenEye OEToolkits 2.0.7Cc1ncc(cn1)c2ccn3c(n2)c(cn3)c4ccc5c(c4)C(C(=O)N5)(C)Cc6ccccc6
CACTVS 3.385Cc1ncc(cn1)c2ccn3ncc(c4ccc5NC(=O)[C](C)(Cc6ccccc6)c5c4)c3n2
ACDLabs 12.01c1(nc2c(cnn2cc1)c3ccc4NC(C(C)(c4c3)Cc5ccccc5)=O)c6cnc(nc6)C
OpenEye OEToolkits 2.0.7Cc1ncc(cn1)c2ccn3c(n2)c(cn3)c4ccc5c(c4)[C@](C(=O)N5)(C)Cc6ccccc6
FormulaC27 H22 N6 O
Name(3S)-3-benzyl-3-methyl-5-[5-(2-methylpyrimidin-5-yl)pyrazolo[1,5-a]pyrimidin-3-yl]-1,3-dihydro-2H-indol-2-one
ChEMBLCHEMBL4452905
DrugBank
ZINC
PDB chain6pyr Chain A Residue 1101 [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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PDB6pyr Design of selective PI3K delta inhibitors using an iterative scaffold-hopping workflow.
Resolution2.21 Å
Binding residue
(original residue number in PDB)		W760 I825 V828 N836 M900 D911
Binding residue
(residue number reindexed from 1)		W684 I744 V747 N755 M809 D820
Annotation score1
Binding affinityMOAD: ic50=1nM
PDBbind-CN: -logKd/Ki=9.00,IC50=1nM
BindingDB: IC50=1.000000nM
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:0005515 protein binding
GO:0005524 ATP binding
GO:0016301 kinase activity
GO:0016303 1-phosphatidylinositol-3-kinase activity
GO:0035005 1-phosphatidylinositol-4-phosphate 3-kinase activity
GO:0046934 1-phosphatidylinositol-4,5-bisphosphate 3-kinase activity
Biological Process
GO:0001779 natural killer cell differentiation
GO:0001819 positive regulation of cytokine production
GO:0001938 positive regulation of endothelial cell proliferation
GO:0002250 adaptive immune response
GO:0002551 mast cell chemotaxis
GO:0002679 respiratory burst involved in defense response
GO:0006468 protein phosphorylation
GO:0006629 lipid metabolic process
GO:0006935 chemotaxis
GO:0006954 inflammatory response
GO:0006955 immune response
GO:0007165 signal transduction
GO:0010595 positive regulation of endothelial cell migration
GO:0010628 positive regulation of gene expression
GO:0010818 T cell chemotaxis
GO:0016310 phosphorylation
GO:0030101 natural killer cell activation
GO:0030154 cell differentiation
GO:0030183 B cell differentiation
GO:0030217 T cell differentiation
GO:0030335 positive regulation of cell migration
GO:0030593 neutrophil chemotaxis
GO:0033031 positive regulation of neutrophil apoptotic process
GO:0035747 natural killer cell chemotaxis
GO:0035754 B cell chemotaxis
GO:0036092 phosphatidylinositol-3-phosphate biosynthetic process
GO:0038084 vascular endothelial growth factor signaling pathway
GO:0042110 T cell activation
GO:0042113 B cell activation
GO:0043303 mast cell degranulation
GO:0043491 phosphatidylinositol 3-kinase/protein kinase B signal transduction
GO:0045087 innate immune response
GO:0045766 positive regulation of angiogenesis
GO:0046854 phosphatidylinositol phosphate biosynthetic process
GO:0048015 phosphatidylinositol-mediated signaling
GO:0050852 T cell receptor signaling pathway
GO:0050853 B cell receptor signaling pathway
GO:0060374 mast cell differentiation
GO:0072672 neutrophil extravasation
GO:1905278 positive regulation of epithelial tube formation
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005886 plasma membrane
GO:0005942 phosphatidylinositol 3-kinase complex
GO:0005943 phosphatidylinositol 3-kinase complex, class IA

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Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6pyr, PDBe:6pyr, PDBj:6pyr
PDBsum6pyr
PubMed31416665
UniProtO00329|PK3CD_HUMAN Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit delta isoform (Gene Name=PIK3CD)

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