Structure of PDB 4oys Chain A Binding Site BS01

Receptor Information
>4oys Chain A (length=553) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LKPNAATRDQLNIIVSYPPTKQLTYEEQDLVWKFRYYLTNQEKALTKFLK
CVNWDLPQEAKQALELLGKWKPMDVEDSLELLSSHYTNPTVRRYAVARLR
QADDEDLLMYLLQLVQALKYENFDDIKNGLEPINSAEIDSSQIITSPLPN
LEQDLCTFLISRACKNSTLANYLYWYVIVECEDQDTQQRDPKTHEMYLNV
MRRFSQALLKGDKSVRVMRSLLAAQQTFVDRLVHLMKAVQRESGNRKKKN
ERLQALLGDNEKMNLSDVELIPLPLEPQVKIRGIIPETATLFKSALMPAQ
LFFKTEDGGKYPVIFKHGDDLRQDQLILQIISLMDKLLRKENLDLKLTPY
KVLATSTKHGFMQFIQSVPVAEVLDTEGSIQNFFRKYAPSENGPNGISAE
VMDTYVKSCAGYCVITYILGVGDRHLDNLLLTKTGKLFHIDFGYILGRDP
KPLPPPMKLNKEMVEGMGGTQSEQYQEFRKQCYTAFLHLRRYSNLILNLF
SLMVDANIPDIALEPDKTVKKVQDKFRLDLSDEEAVHYMQSLIDESVHAL
FAA
Ligand information
Ligand ID1TT
InChIInChI=1S/C19H23ClF3N5O2/c1-12-11-30-5-4-26(12)16-7-17(29)27-3-2-15(19(21,22)23)28(18(27)25-16)10-13-6-14(20)9-24-8-13/h6,8-9,12,15,18H,2-5,7,10-11H2,1H3/t12-,15+,18+/m1/s1
InChIKeyHTJGYDUKBSAZGM-MRAWALMUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.9.2CC1COCCN1C2=NC3N(CCC(N3Cc4cc(cnc4)Cl)C(F)(F)F)C(=O)C2
CACTVS 3.385C[C@@H]1COCCN1C2=N[C@@H]3N(Cc4cncc(Cl)c4)[C@@H](CCN3C(=O)C2)C(F)(F)F
ACDLabs 12.01FC(F)(F)C3N(C2N=C(N1C(COCC1)C)CC(=O)N2CC3)Cc4cc(Cl)cnc4
OpenEye OEToolkits 1.9.2C[C@@H]1COCCN1C2=NC3N(CC[C@H](N3Cc4cc(cnc4)Cl)C(F)(F)F)C(=O)C2
CACTVS 3.385C[CH]1COCCN1C2=N[CH]3N(Cc4cncc(Cl)c4)[CH](CCN3C(=O)C2)C(F)(F)F
FormulaC19 H23 Cl F3 N5 O2
Name(8S)-9-[(5-chloranylpyridin-3-yl)methyl]-2-[(3R)-3-methylmorpholin-4-yl]-8-(trifluoromethyl)-6,7,8,9a-tetrahydro-3H-pyrimido[1,2-a]pyrimidin-4-one
ChEMBL
DrugBank
ZINCZINC000263620533
PDB chain4oys Chain A Residue 905 [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]
PDB4oys A highly potent and selective Vps34 inhibitor alters vesicle trafficking and autophagy.
Resolution2.9 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)		F292 P298 I314 Y350 M362 Q363 F364 I365 L430 I440
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=8.82,Kd=1.52nM
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:4oys, PDBe:4oys, PDBj:4oys
PDBsum4oys
PubMed25326666
UniProtQ8NEB9|PK3C3_HUMAN Phosphatidylinositol 3-kinase catalytic subunit type 3 (Gene Name=PIK3C3)

[Back to BioLiP]