Structure of PDB 7lm2 Chain A Binding Site BS01

Receptor Information
>7lm2 Chain A (length=935) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
WTKEENQSVVVDFLLPTGVYLNFPVSRNANLSTIKQLLWHRAQYEPLFHM
LSGPEAYVFTCINQTAEQQELEDEQRRLCDVQPFLPVLRLVAREGDRVKK
LINSQISLLIGKGLHEFDSLCDPEVNDFRAKMCQFCEEAAARRQQLGWEA
WLQYSFPLQLEPSLPNRALLVNVKFEGSEESFTFQVSTKDVPLALMACAL
RKKARQQPEDYTLQVNGRHEYLYGSYPLCQFQYICSCLHSGLTPHLTMVH
SSSILAMRDEQSSLWSLEQPFRIELIQGSKVNADERMKLVVQAGLFHGNE
MLCKTVSSSEVSVCSEPVWKQRLEFDINICDLPRMARLCFALYAVIEKDC
PIAWANLMLFDYKDQLKTGERCLYMWPSVPDEKGELLNPTGTVRSNPNTD
SAAALLICLPEVAPHPVYYPALEKILELGRHTEEEQLQLREILERYEHEK
DLVWKLRHEVQEHFPEALARLLLVTKWNKHEDVAQMLYLLCSWPELPVLS
ALELLDFSFPDCHVGSFAIKSLRKLTDDELFQYLLQLVQVLKYESYLDCE
LTKFLLDRALANRKIGHFLFWHLRSEMHVPSVALRFGLILEAYCRGSTHH
MKVLMKQGEALSKLKALNDFVKLSSQKTPKPQTKELMHLCMRQEAYLEAL
SHLQSPLDPSTLLAEVCVEQCTFMDSKMKPLWIMYSNEEAGSGGSVGIIF
KNGDDLRQDMLTLQMIQLMDVLWKQEGLDLRMTPYGCLPTGDRTGLIEVV
LRSDTIANIQLNKDALLNWLKSKNPGEALDRAIEEFTLSCAGYCVATYVL
GIGDRHSDNIMIRESGQLFHIDFGHFLGNFRERVPFILTYDFVHVIQQGK
TNNSEKFERFRGYCERAYTILRRHGLLFLHLFALMRAAGLPELSCSKDIQ
YLKDSLALGKTEEEALKHFRVKFNEALRESWKTKV
Ligand information
Ligand IDY5Y
InChIInChI=1S/C20H24N8O/c1-3-28-18(14-8-21-12(2)22-9-14)26-16-17(23-11-24-19(16)28)25-15-6-7-27(10-15)20(29)13-4-5-13/h8-9,11,13,15H,3-7,10H2,1-2H3,(H,23,24,25)/t15-/m0/s1
InChIKeyDADGJAZOHPBTCZ-HNNXBMFYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7CCn1c2c(c(ncn2)N[C@H]3CCN(C3)C(=O)C4CC4)nc1c5cnc(nc5)C
OpenEye OEToolkits 2.0.7CCn1c2c(c(ncn2)NC3CCN(C3)C(=O)C4CC4)nc1c5cnc(nc5)C
CACTVS 3.385CCn1c2ncnc(N[CH]3CCN(C3)C(=O)C4CC4)c2nc1c5cnc(C)nc5
CACTVS 3.385CCn1c2ncnc(N[C@H]3CCN(C3)C(=O)C4CC4)c2nc1c5cnc(C)nc5
ACDLabs 12.01CCn4c(nc1c4ncnc1NC3CCN(C(C2CC2)=O)C3)c5cnc(nc5)C
FormulaC20 H24 N8 O
Namecyclopropyl[(3S)-3-{[9-ethyl-8-(2-methylpyrimidin-5-yl)-9H-purin-6-yl]amino}pyrrolidin-1-yl]methanone
ChEMBLCHEMBL4853960
DrugBank
ZINC
PDB chain7lm2 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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PDB7lm2 Projected Dose Optimization of Amino- and Hydroxypyrrolidine Purine PI3K delta Immunomodulators.
Resolution2.79 Å
Binding residue
(original residue number in PDB)		M752 W760 Y813 I825 E826 V828 M900
Binding residue
(residue number reindexed from 1)		M674 W682 Y735 I747 E748 V750 M811
Annotation score1
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
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Biological Process
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Cellular Component
External links
PDB RCSB:7lm2, PDBe:7lm2, PDBj:7lm2
PDBsum7lm2
PubMed33797901
UniProtO00329|PK3CD_HUMAN Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit delta isoform (Gene Name=PIK3CD)

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