Structure of PDB 7r2b Chain A Binding Site BS01

Receptor Information
>7r2b Chain A (length=794) Species: 10090 (Mus musculus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RVKKLINSQISLLIGKGLHEFDSLRDPEVNDFRTKMRQFCEEAAAHRQQL
GWVEWLQYSFPLQLEPNRALLVNVKFEGSEESFTFQVSTKDMPLALMACA
LRKKATVFRQQPEEYALQVNGRHEYLYGNYPLCHFQYICSCLHSGLTPHL
TMVHSSSILAMRDEQSNSLEQPFSIELIRKVNADERMKLVVQAGLFHGNE
MLCKTVSSSECSEPDISVCDLPRMARLCFALYAVDCPIAWANLMLFDYKD
QLKTGERCLYMWPSLLNPAGTVRGNPNTESAAALVIYLPEVAPVYFPALE
KILELLYEHEKDLVWKMRHEVQEHFPEALARLLLVTKWNKHEDVAQMLYL
LCSWPELPVLSALELLDFSFPDCYVGSFAIKSLRKLTDDELFQYLLQLVQ
VLKYESYLDCELTKFLLGRALANRKIGHFLFWHLRSEMHVPSVALRFGLI
MEAYCRGSTHHMKVLMKQGEALSKLKALNDFVKVSSQKTTKPQTKEMMHM
CMRQETYMEALSHLQSPLDPSTLLEEVCVEQCTFMDSKMKPLWIMYSSEE
AGSAGNVGIIFKNGDDLRQDMLTLQMIQLMDVLWKQEGLDLRMTPYGCLP
TGDRTGLIEVVLHSDTIANIQLNKSTAAFNKDALLNWLKSKNPGEALDRA
IEEFTLSCAGYCVATYVLGIGDRHSDNIMIRESGQLFHIDFGHFLGNVPF
ILTYDFVHVIQQGKTNNSEKFERFRGYCERAYTILRRHGLLFLHLFALMR
AAGLPELSCSKDIQYLKDSLALGKTEEEALKHFRVKFNEALRES
Ligand information
Ligand IDH5I
InChIInChI=1S/C17H18F3N7O3/c1-9-8-30-16(28)27(9)12-6-11(23-15(24-12)26-2-4-29-5-3-26)10-7-22-14(21)25-13(10)17(18,19)20/h6-7,9H,2-5,8H2,1H3,(H2,21,22,25)/t9-/m0/s1
InChIKeyFBOZVYXXWXOUOV-VIFPVBQESA-N
SMILES
SoftwareSMILES
CACTVS 3.385C[C@H]1COC(=O)N1c2cc(nc(n2)N3CCOCC3)c4cnc(N)nc4C(F)(F)F
OpenEye OEToolkits 2.0.7C[C@H]1COC(=O)N1c2cc(nc(n2)N3CCOCC3)c4cnc(nc4C(F)(F)F)N
CACTVS 3.385C[CH]1COC(=O)N1c2cc(nc(n2)N3CCOCC3)c4cnc(N)nc4C(F)(F)F
OpenEye OEToolkits 2.0.7CC1COC(=O)N1c2cc(nc(n2)N3CCOCC3)c4cnc(nc4C(F)(F)F)N
FormulaC17 H18 F3 N7 O3
Name(4~{S})-3-[6-[2-azanyl-4-(trifluoromethyl)pyrimidin-5-yl]-2-morpholin-4-yl-pyrimidin-4-yl]-4-methyl-1,3-oxazolidin-2-one
ChEMBL
DrugBank
ZINC
PDB chain7r2b 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

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB7r2b Identification of NVP-CLR457 as an Orally Bioavailable Non-CNS-Penetrant pan-Class IA Phosphoinositol-3-Kinase Inhibitor.
Resolution2.7 Å
Binding residue
(original residue number in PDB)		M752 W760 I777 K779 D787 I825 E826 V828 M900 I910 D911
Binding residue
(residue number reindexed from 1)		M535 W543 I560 K562 D570 I608 E609 V611 M679 I689 D690
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: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:7r2b, PDBe:7r2b, PDBj:7r2b
PDBsum7r2b
PubMed35500094
UniProtO35904|PK3CD_MOUSE Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit delta isoform (Gene Name=Pik3cd)

[Back to BioLiP]