Structure of PDB 4uwg Chain A Binding Site BS01

Receptor Information
>4uwg Chain A (length=544) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LKPNAATRDQLNIIVSYPPTKQLTYEEQDLVWKFRYYLTNQEKALTKFLK
CVNWDLPQEAKQALELLGKWKPMDVEDSLELLSSHYTNPTVRRYAVARLR
QADDEDLLMYLLQLVQALKYENFDDIKNGLEAEIDSSQIITSPLPLEQDL
CTFLISRACKNSTLANYLYWYVIVECEDQDTQQRDPKTHEMYLNVMRRFS
QALLKGDKSVRVMRSLLAAQQTFVDRLVHLMKAVQRESGNRKKKNERLQA
LLGDNEKMNLSDVELIPLPLEPQVKIRGIIPETATLFKSALMPAQLFFKT
EDGGKYPVIFKHGDDLRQDQLILQIISLMDKLLRKENLDLKLTPYKVLAT
STKHGFMQFIQSVPVAEVLDTEGSIQNFFRKYAPSENGPNGISAEVMDTY
VKSCAGYCVITYILGVGDRHLDNLLLTKTGKLFHIDFGYILGRDPKPLPP
PMKLNKEMVEGMGGTQSEQYQEFRKQCYTAFLHLRRYSNLILNLFSLMVD
ANIPDIALEPDKTVKKVQDKFRLDLSDEEAVHYMQSLIDESVHA
Ligand information
Ligand IDRBQ
InChIInChI=1S/C17H25F3N4O3/c1-12(2)27-10-7-23-13(17(18,19)20)3-4-24-15(25)11-14(21-16(23)24)22-5-8-26-9-6-22/h11-13H,3-10H2,1-2H3/t13-/m0/s1
InChIKeyMYULDSNSZNSXKG-ZDUSSCGKSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CC(C)OCCN1[C@@H](CCN2C(=O)C=C(N=C12)N3CCOCC3)C(F)(F)F
ACDLabs 12.01FC(F)(F)C3N(C2=NC(N1CCOCC1)=CC(=O)N2CC3)CCOC(C)C
OpenEye OEToolkits 1.7.6CC(C)OCCN1C(CCN2C1=NC(=CC2=O)N3CCOCC3)C(F)(F)F
CACTVS 3.385CC(C)OCCN1[CH](CCN2C(=O)C=C(N=C12)N3CCOCC3)C(F)(F)F
OpenEye OEToolkits 1.7.6CC(C)OCCN1[C@@H](CCN2C1=NC(=CC2=O)N3CCOCC3)C(F)(F)F
FormulaC17 H25 F3 N4 O3
Name(8S)-2-(morpholin-4-yl)-9-[2-(propan-2-yloxy)ethyl]-8-(trifluoromethyl)-6,7,8,9-tetrahydro-4H-pyrimido[1,2-a]pyrimidin-4-one
ChEMBLCHEMBL4470174
DrugBank
ZINCZINC000200661443
PDB chain4uwg Chain A Residue 1873 [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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PDB4uwg 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.
Resolution2.7 Å
Binding residue
(original residue number in PDB)		F612 P618 I634 Y670 M682 Q683 F684 I685 L750 I760
Binding residue
(residue number reindexed from 1)		F287 P293 I309 Y345 M357 Q358 F359 I360 L425 I435
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:4uwg, PDBe:4uwg, PDBj:4uwg
PDBsum4uwg
PubMed25402320
UniProtQ8NEB9|PK3C3_HUMAN Phosphatidylinositol 3-kinase catalytic subunit type 3 (Gene Name=PIK3C3)

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