Structure of PDB 5ncz Chain A Binding Site BS01

Receptor Information
>5ncz Chain A (length=827) 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
MLCKTVSSSEVNVEPVWKQRLEFDISVCDLPRMARLCFALYAVVDCPIAW
ANLMLFDYKDQLKTGERCLYMWPSVLLNPAGTVRGNPNTESAAALVIYLP
EVAPVYFPALEKILELGRITEEELREILERELYEHEKDLVWKMRHEVQEH
FPEALARLLLVTKWNKHEDVAQMLYLLCSWPELPVLSALELLDFSFPDCY
VGSFAIKSLRKLTDDELFQYLLQLVQVLKYESYLDCELTKFLLGRALANR
KIGHFLFWHLRSEMHVPSVALRFGLIMEAYCRGSTHHMKVLMKQGEALSK
LKALNDFVKVSSQKTTKPQTKEMMHMCMRQETYMEALSHLQSPLDPSTLL
EEVCVEQCTFMDSKMKPLWIMYSSEEAGSAGNVGIIFKNGDDLRQDMLTL
QMIQLMDVLWKQEGLDLRMTPYGCLPTGDRTGLIEVVLHSDTIANIQLNK
SNMAATAAFNKDALLNWLKSKNPGEALDRAIEEFTLSCAGYCVATYVLGI
GDRHSDNIMIRESGQLFHIDFGHFLGNFRVPFILTYDFVHVIQQGKTNNS
EKFERFRGYCERAYTILRRHGLLFLHLFALMRAAGLPELSCSKDIQYLKD
SLALGKTEEEALKHFRVKFNEALRESW
Ligand information
Ligand ID8TN
InChIInChI=1S/C24H25N7OS/c1-14-12-33-20-9-18(15(2)29-23-19(10-25)22(26)27-13-28-23)21(24(32)31(14)20)17-7-5-6-16(8-17)11-30(3)4/h5-9,12-13,15H,11H2,1-4H3,(H3,26,27,28,29)/t15-/m0/s1
InChIKeyOQIHNLNLZCEEGI-HNNXBMFYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385C[CH](Nc1ncnc(N)c1C#N)C2=C(C(=O)N3C(=CSC3=C2)C)c4cccc(CN(C)C)c4
CACTVS 3.385C[C@H](Nc1ncnc(N)c1C#N)C2=C(C(=O)N3C(=CSC3=C2)C)c4cccc(CN(C)C)c4
OpenEye OEToolkits 2.0.6CC1=CSC2=CC(=C(C(=O)N12)c3cccc(c3)CN(C)C)C(C)Nc4c(c(ncn4)N)C#N
OpenEye OEToolkits 2.0.6CC1=CSC2=CC(=C(C(=O)N12)c3cccc(c3)CN(C)C)[C@H](C)Nc4c(c(ncn4)N)C#N
FormulaC24 H25 N7 O S
Name4-azanyl-6-[[(1~{S})-1-[6-[3-[(dimethylamino)methyl]phenyl]-3-methyl-5-oxidanylidene-[1,3]thiazolo[3,2-a]pyridin-7-yl]ethyl]amino]pyrimidine-5-carbonitrile
ChEMBL
DrugBank
ZINC
PDB chain5ncz Chain A Residue 1105 [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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PDB5ncz Design and Synthesis of Soluble and Cell-Permeable PI3K delta Inhibitors for Long-Acting Inhaled Administration.
Resolution1.94 Å
Binding residue
(original residue number in PDB)		F751 M752 P758 W760 I777 Y813 I825 V827 V828 D832 M900 I910
Binding residue
(residue number reindexed from 1)		F560 M561 P567 W569 I586 Y622 I634 V636 V637 D641 M709 I719
Annotation score1
Binding affinityMOAD: ic50=0.79nM
PDBbind-CN: -logKd/Ki=9.10,IC50=0.8nM
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:0005524 ATP binding
GO:0016301 kinase activity
GO:0016303 1-phosphatidylinositol-3-kinase activity
GO:0046934 1-phosphatidylinositol-4,5-bisphosphate 3-kinase activity
Biological Process
GO:0001782 B cell homeostasis
GO:0002250 adaptive immune response
GO:0006629 lipid metabolic process
GO:0006935 chemotaxis
GO:0006954 inflammatory response
GO:0007166 cell surface receptor signaling pathway
GO:0010628 positive regulation of gene expression
GO:0016310 phosphorylation
GO:0030154 cell differentiation
GO:0036092 phosphatidylinositol-3-phosphate biosynthetic process
GO:0042113 B cell activation
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:0048872 homeostasis of number of cells
GO:0050832 defense response to fungus
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5ncz, PDBe:5ncz, PDBj:5ncz
PDBsum5ncz
PubMed28520415
UniProtO35904|PK3CD_MOUSE Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit delta isoform (Gene Name=Pik3cd)

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