Structure of PDB 3ml9 Chain A Binding Site BS01

Receptor Information
>3ml9 Chain A (length=847) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SEESQAFQRQLTALIGYDVTDVSNVHDDELEFTRRGLVTPRMAEVASRDP
KLYAMHPWVTSKPLPEYLWKKIANNCIFIVIHRSTTSQTIKVSPDDTPGA
ILQSFFTKDFVLRVCGRDEYLVGETPIKNFQWVRHCLKNGEEIHVVLDTP
PDPALDEVRKETVSLWDCDRKFRVKIRGIDIPVLLTVFVEANIQHGQQVL
CQRRTSPKPFTEEVLWNVWLEFSIKIKDLPKGALLNLQIYCVRLLYYVNL
LLIDHRFLLRRGEYVLHMWQISGSFNADKLTSATNPDKENSMSISILLDN
YCHPIALPKRAEMPNQLRKQLEAIIATDPLNPLTAEDKELLWHFRYESLK
HPKAYPKLFSSVKWGQQEIVAKTYQLLARREVWDQSALDVGLTMQLLDCN
FSDENVRAIAVQKLESLEDDDVLHYLLQLVQAVKFEPYHDSALARFLLKR
GLRNKRIGHFLFWFLRSEIAQSRHYQQRFAVILEAYLRGCGTAMLHDFTQ
QVQVIEMLQKVTLDIKSLSDVSSQVISQLKQKLENLQNSQLPESFRVPYD
PGLKAGALAIEKCKVMASKKKPLWLEFKCADPTALSNETIGIIFKHGDDL
RQDMLILQILRIMESIWETESLDLCLLPYGCISTGDKIGMIEIVKDATTI
AKIQQSTVGNTGAFKDEVLNHWLKEKSPTEEKFQAAVERFVYSCAGYCVA
TFVLGIGDRHNDNIMITETGNLFHIDFGHILGNYERVPFVLTPDFLFVMG
TSGKKTSPHFQKFQDICVKAYLALRHHTNLLIILFSMMLMTGMPQLTSKE
DIEYIRDALTVGKNEEDAKKYFLDQIEVCRDKGWTVQFNWFLHLVLG
Ligand information
Ligand IDML9
InChIInChI=1S/C22H27N5O4/c1-13-17-11-18(14-3-8-19(30-2)24-12-14)21(29)27(20(17)26-22(23)25-13)15-4-6-16(7-5-15)31-10-9-28/h3,8,11-12,15-16,28H,4-7,9-10H2,1-2H3,(H2,23,25,26)/t15-,16-
InChIKeyXDLYKKIQACFMJG-WKILWMFISA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=C2C(=Cc1c(nc(nc1C)N)N2C3CCC(OCCO)CC3)c4ccc(OC)nc4
CACTVS 3.370COc1ccc(cn1)C2=Cc3c(C)nc(N)nc3N([CH]4CC[CH](CC4)OCCO)C2=O
CACTVS 3.370COc1ccc(cn1)C2=Cc3c(C)nc(N)nc3N([C@H]4CC[C@@H](CC4)OCCO)C2=O
OpenEye OEToolkits 1.7.0Cc1c2c(nc(n1)N)N(C(=O)C(=C2)c3ccc(nc3)OC)C4CCC(CC4)OCCO
FormulaC22 H27 N5 O4
Name2-amino-8-[trans-4-(2-hydroxyethoxy)cyclohexyl]-6-(6-methoxypyridin-3-yl)-4-methylpyrido[2,3-d]pyrimidin-7(8H)-one
ChEMBLCHEMBL1234354
DrugBankDB11974
ZINCZINC000117704832
PDB chain3ml9 Chain A Residue 9999 [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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PDB3ml9 Discovery of the Highly Potent PI3K/mTOR Dual Inhibitor PF-04979064 through Structure-Based Drug Design.
Resolution2.55 Å
Binding residue
(original residue number in PDB)		M804 W812 I831 K833 D841 Y867 I879 E880 V882 K890 M953 D964
Binding residue
(residue number reindexed from 1)		M566 W574 I593 K595 D603 Y629 I641 E642 V644 K652 M715 D726
Annotation score1
Enzymatic activity
Enzyme Commision number 2.7.11.1: non-specific serine/threonine protein kinase.
2.7.1.137: phosphatidylinositol 3-kinase.
2.7.1.153: phosphatidylinositol-4,5-bisphosphate 3-kinase.
2.7.1.154: phosphatidylinositol-4-phosphate 3-kinase.
Gene Ontology
Molecular Function
GO:0016301 kinase activity
Biological Process
GO:0046854 phosphatidylinositol phosphate biosynthetic process

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Molecular Function
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Biological Process
External links
PDB RCSB:3ml9, PDBe:3ml9, PDBj:3ml9
PDBsum3ml9
PubMed24900568
UniProtP48736|PK3CG_HUMAN Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform (Gene Name=PIK3CG)

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