Structure of PDB 4uwf Chain A Binding Site BS01

Receptor Information
>4uwf Chain A (length=550) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LKPNAATRDQLNIIVSYPPTKQLTYEEQDLVWKFRYYLTNQEKALTKFLK
CVNWDLPQEAKQALELLGKWKPMDVEDSLELLSSHYTNPTVRRYAVARLR
QADDEDLLMYLLQLVQALKYENFDDIKNGLEINSAEIDSSQIITSPLLEQ
DLCTFLISRACKNSTLANYLYWYVIVECEDQDTQQRDPKTHEMYLNVMRR
FSQALLKGDKSVRVMRSLLAAQQTFVDRLVHLMKAVQRESGNRKKKNERL
QALLGDNEKMNLSDVELIPLPLEPQVKIRGIIPETATLFKSALMPAQLFF
KTEDGGKYPVIFKHGDDLRQDQLILQIISLMDKLLRKENLDLKLTPYKVL
ATSTKHGFMQFIQSVPVAEVLDTEGSIQNFFRKYAPSENGPNGISAEVMD
TYVKSCAGYCVITYILGVGDRHLDNLLLTKTGKLFHIDFGYILGRDPKPL
PPPMKLNKEMVEGMGGTQSEQYQEFRKQCYTAFLHLRRYSNLILNLFSLM
VDANIPDIALEPDKTVKKVQDKFRLDLSDEEAVHYMQSLIDESVHALFAA
Ligand information
Ligand IDEUT
InChIInChI=1S/C18H17F5N4O2/c19-11-7-12(20)9-13(8-11)27-14(18(21,22)23)1-2-26-16(28)10-15(24-17(26)27)25-3-5-29-6-4-25/h7-10,14H,1-6H2/t14-/m0/s1
InChIKeyXTBZCKNQFVGNFT-AWEZNQCLSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6c1c(cc(cc1F)F)N2[C@@H](CCN3C2=NC(=CC3=O)N4CCOCC4)C(F)(F)F
ACDLabs 12.01Fc1cc(cc(F)c1)N4C3=NC(N2CCOCC2)=CC(=O)N3CCC4C(F)(F)F
CACTVS 3.385Fc1cc(F)cc(c1)N2[CH](CCN3C(=O)C=C(N=C23)N4CCOCC4)C(F)(F)F
OpenEye OEToolkits 1.7.6c1c(cc(cc1F)F)N2C(CCN3C2=NC(=CC3=O)N4CCOCC4)C(F)(F)F
CACTVS 3.385Fc1cc(F)cc(c1)N2[C@@H](CCN3C(=O)C=C(N=C23)N4CCOCC4)C(F)(F)F
FormulaC18 H17 F5 N4 O2
Name(8S)-9-[3,5-bis(fluoranyl)phenyl]-2-morpholin-4-yl-8-(trifluoromethyl)-7,8-dihydro-6H-pyrimido[1,2-a]pyrimidin-4-one
ChEMBLCHEMBL4536855
DrugBank
ZINCZINC000144989825
PDB chain4uwf Chain A Residue 4000 [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]
PDB4uwf Discovery of (2S)-8-[(3R)-3-Methylmorpholin-4-Yl]-1-(3-Methyl-2-Oxobutyl)-2-(Trifluoromethyl)-3,4-Dihydro-2H-Pyrimido[1,2-A]Pyrimidin-6-One: A Novel Potent and Selective Inhibitor of Vps34 for the Treatment of Solid Tumors.
Resolution2.99 Å
Binding residue
(original residue number in PDB)		F612 P618 I634 K636 Y670 M682 Q683 F684 I685 I760
Binding residue
(residue number reindexed from 1)		F289 P295 I311 K313 Y347 M359 Q360 F361 I362 I437
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=8.15,IC50=7nM
BindingDB: IC50=7.0nM
Enzymatic activity
Enzyme Commision number 2.7.1.137: phosphatidylinositol 3-kinase.
Gene Ontology
Molecular Function
GO:0016301 kinase activity
Biological Process
GO:0046854 phosphatidylinositol phosphate biosynthetic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:4uwf, PDBe:4uwf, PDBj:4uwf
PDBsum4uwf
PubMed25402320
UniProtQ8NEB9|PK3C3_HUMAN Phosphatidylinositol 3-kinase catalytic subunit type 3 (Gene Name=PIK3C3)

[Back to BioLiP]