Structure of PDB 4ph4 Chain B Binding Site BS01

Receptor Information
>4ph4 Chain B (length=529) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SGIRDQLNIIVSYPPTKQLTYEEQDLVWKFRYYLTNQEKALTKFLKCVNW
DLPQEAKQALELLGKWKPMDVEDSLELLSSHYTNPTVRRYAVARLRQADD
EDLLMYLLQLVQALKYENFDDIKNGLEPLEQDLCTFLISRACKNSTLANY
LYWYVIVECEDQDTQQRDPKTHEMYLNVMRRFSQALLKGDKSVRVMRSLL
AAQQTFVDRLVHLMKAVQRESGNRKKKNERLQALLGDNEKMNLSDVELIP
LPLEPQVKIRGIIPETATLFKSALMPAQLFFKTEDGGKYPVIFKHGDDLR
QDQLILQIISLMDKLLRKENLDLKLTPYKVLATSTKHGFMQFIQSVPVAE
VLDTEGSIQNFFRKYAPSENGPNGISAEVMDTYVKSCAGYCVITYILGVG
DRHLDNLLLTKTGKLFHIDFGYILGRDPKPLPPPMKLNKEMVEGMGGTQS
EQYQEFRKQCYTAFLHLRRYSNLILNLFSLMVDANIPDIALEPDKTVKKV
QDKFRLDLSDEEAVHYMQSLIDESVHALF
Ligand information
Ligand ID2UG
InChIInChI=1S/C17H17N7/c18-16-21-10-13(15(23-16)9-11-1-2-11)14-5-8-20-17(24-14)22-12-3-6-19-7-4-12/h3-8,10-11H,1-2,9H2,(H2,18,21,23)(H,19,20,22,24)
InChIKeyXXSDLQLNIVFIJI-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01n1c(ccnc1Nc2ccncc2)c3cnc(nc3CC4CC4)N
CACTVS 3.385Nc1ncc(c(CC2CC2)n1)c3ccnc(Nc4ccncc4)n3
OpenEye OEToolkits 1.9.2c1cnccc1Nc2nccc(n2)c3cnc(nc3CC4CC4)N
FormulaC17 H17 N7
Name4'-(cyclopropylmethyl)-N~2~-(pyridin-4-yl)-4,5'-bipyrimidine-2,2'-diamine
ChEMBLCHEMBL3781415
DrugBank
ZINCZINC000203692125
PDB chain4ph4 Chain B Residue 902 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4ph4 Selective VPS34 inhibitor blocks autophagy and uncovers a role for NCOA4 in ferritin degradation and iron homeostasis in vivo.
Resolution2.8 Å
Binding residue
(original residue number in PDB)		F612 I634 K636 Y670 M682 F684 I685 S687 L750 I760
Binding residue
(residue number reindexed from 1)		F270 I292 K294 Y328 M340 F342 I343 S345 L408 I418
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=7.74,IC50=18nM
BindingDB: IC50=18nM
Enzymatic activity
Enzyme Commision number 2.7.1.137: phosphatidylinositol 3-kinase.
Gene Ontology
Molecular Function
GO:0016301 kinase activity
GO:0016303 1-phosphatidylinositol-3-kinase activity
Biological Process
GO:0046854 phosphatidylinositol phosphate biosynthetic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:4ph4, PDBe:4ph4, PDBj:4ph4
PDBsum4ph4
PubMed25327288
UniProtQ8NEB9|PK3C3_HUMAN Phosphatidylinositol 3-kinase catalytic subunit type 3 (Gene Name=PIK3C3)

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