Structure of PDB 4uwk Chain A Binding Site BS01

Receptor Information
>4uwk 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]
KPNAATRDQLNIIVSYPPTKQLTYEEQDLVWKFRYYLTNQEKALTKFLKC
VNWDLPQEAKQALELLGKWKPMDVEDSLELLSSHYTNPTVRRYAVARLRQ
ADDEDLLMYLLQLVQALKYENFDDIKNGLEAEIDSSQIITSPLPNLEQDL
CTFLISRACKNSTLANYLYWYVIVECEDQDTQQRDPKTHEMYLNVMRRFS
QALLKGDKSVRVMRSLLAAQQTFVDRLVHLMKAVQRESGNRKKKNERLQA
LLGDNEKMNLSDVELIPLPLEPQVKIRGIIPETATLFKSALMPAQLFFKT
EDGGKYPVIFKHGDDLRQDQLILQIISLMDKLLRKENLDLKLTPYKVLAT
STKHGFMQFIQSVPVAEVLDTEGSIQNFFRKYAPSENGPNGISAEVMDTY
VKSCAGYCVITYILGVGDRHLDNLLLTKTGKLFHIDFGYILGRDPKPLPP
PMKLNKEMVEGMGGTQSEQYQEFRKQCYTAFLHLRRYSNLILNLFSLMVD
ANIPDIALEPDKTVKKVQDKFRLDLSDEEAVHYMQSLIDESVHA
Ligand information
Ligand IDUJB
InChIInChI=1S/C19H22ClF3N4O2S/c1-11-9-29-10-12(2)27(11)16-7-17(28)25-6-5-14(19(21,22)23)26(18(25)24-16)8-13-3-4-15(20)30-13/h3-4,7,11-12,14H,5-6,8-10H2,1-2H3/t11-,12-,14+/m1/s1
InChIKeyMMAAITOCOBQYBQ-BZPMIXESSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6CC1COCC(N1C2=CC(=O)N3CCC(N(C3=N2)Cc4ccc(s4)Cl)C(F)(F)F)C
OpenEye OEToolkits 1.7.6C[C@@H]1COC[C@H](N1C2=CC(=O)N3CC[C@H](N(C3=N2)Cc4ccc(s4)Cl)C(F)(F)F)C
CACTVS 3.385C[C@@H]1COC[C@@H](C)N1C2=CC(=O)N3CC[C@H](N(Cc4sc(Cl)cc4)C3=N2)C(F)(F)F
ACDLabs 12.01Clc1sc(cc1)CN4C3=NC(N2C(C)COCC2C)=CC(=O)N3CCC4C(F)(F)F
CACTVS 3.385C[CH]1COC[CH](C)N1C2=CC(=O)N3CC[CH](N(Cc4sc(Cl)cc4)C3=N2)C(F)(F)F
FormulaC19 H22 Cl F3 N4 O2 S
Name(2S)-1-[(5-chloro-2-thienyl)methyl]-8-[(3R,5R)-3,5-dimethylmorpholin-4-yl]-2-(trifluoromethyl)-3,4-dihydro-2H-pyrimido[1,2-a]pyrimidin-6-one
ChEMBL
DrugBank
ZINCZINC000219083447
PDB chain4uwk Chain A Residue 1872 [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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PDB4uwk Discovery of (2S)-8-[(3R)-3-Methylmorpholin-4-Yl]-1-(3-Methyl-2-Oxo-Butyl)-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.
Resolution2.83 Å
Binding residue
(original residue number in PDB)		F612 P618 I634 K636 Y670 M682 Q683 I685 I760 D761
Binding residue
(residue number reindexed from 1)		F287 P293 I309 K311 Y345 M357 Q358 I360 I435 D436
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=9.00,IC50=1nM
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

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Molecular Function
View graph for
Biological Process
External links
PDB RCSB:4uwk, PDBe:4uwk, PDBj:4uwk
PDBsum4uwk
PubMed25402320
UniProtQ8NEB9|PK3C3_HUMAN Phosphatidylinositol 3-kinase catalytic subunit type 3 (Gene Name=PIK3C3)

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