Structure of PDB 3sd5 Chain A Binding Site BS01

Receptor Information
>3sd5 Chain A (length=817) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SEESQAFQRQLTALIGYDVTDVSNVHDDELEFTRRGLVTPRMAEVASRDP
KLYAMHPWVTSKPLPEYLWKNCIFIVIHRSTTSQTIKVSPDDTPGAILQS
FFTKMQDFVLRVCGRDEYLVGETPIKNFQWVRHCLKNGEEIHVVLDTPPD
PALDEVRKCDRKFRVKIRGIDIPVLTVFVEANIQHGQQVLCQRRTSPKPF
TEEVLWNVWLEFSIKIKDLPKGALLNLQIYCVRLLYYVNLLLIDHRFLLR
RGEYVLHMWQISGNADKLTSATNPDKENSMSISILLDNMPNQLRKQLEAI
IATDPLNPLTAEDKELLWHFRYESLKHPKAYPKLFSSVKWGQQEIVAKTY
QLLARREVWDQSALDVGLTMQLLDCNFSDENVRAIAVQKLESLEDDDVLH
YLLQLVQAVKFEPYHDSALARFLLKRGLRNKRIGHFLFWFLRSEIAQSRH
YQQRFAVILEAYLRGCGTAMLHDFTQQVQVIEMLQKVTLDIKSLSAEKYD
VSSQVISQLKQKLENLQNSQLPESFRVPYDPGLKAGALAIEKCKVMASKK
KPLWLEFKCADPTANETIGIIFKHGDDLRQDMLILQILRIMESIWETESL
DLCLLPYGCISTGDKIGMIEIVKDATTIAKIQQSTVTGAFKDEVLNHWLK
EKSPTEEKFQAAVERFVYSCAGYCVATFVLGIGDRHNDNIMITETGNLFH
IDFGHILGNRVPFVLTPDFLFVMGTSKTSPHFQKFQDICVKAYLALRHHT
NLLIILFSMMLMTGMQLTSKEDIEYIRDALTVGKNEEDAKKYFLDQIEVC
RDKGWTVQFNWFLHLVL
Ligand information
Ligand IDSD5
InChIInChI=1S/C18H21F3N6O2/c19-18(20,21)13-9-15(22)23-11-12(13)14-10-16(26-1-5-28-6-2-26)25-17(24-14)27-3-7-29-8-4-27/h9-11H,1-8H2,(H2,22,23)
InChIKeyCWHUFRVAEUJCEF-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.2c1c(c(cnc1N)c2cc(nc(n2)N3CCOCC3)N4CCOCC4)C(F)(F)F
CACTVS 3.370Nc1cc(c(cn1)c2cc(nc(n2)N3CCOCC3)N4CCOCC4)C(F)(F)F
ACDLabs 12.01FC(F)(F)c1cc(ncc1c3nc(nc(N2CCOCC2)c3)N4CCOCC4)N
FormulaC18 H21 F3 N6 O2
Name5-[2,6-di(morpholin-4-yl)pyrimidin-4-yl]-4-(trifluoromethyl)pyridin-2-amine
ChEMBLCHEMBL2017974
DrugBankDB11666
ZINCZINC000043154039
PDB chain3sd5 Chain A Residue 1 [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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PDB3sd5 Identification and Characterization of NVP-BKM120, an Orally Available Pan-Class I PI3-Kinase Inhibitor.
Resolution3.2 Å
Binding residue
(original residue number in PDB)		M804 P810 I831 I879 E880 V882 T887 D964
Binding residue
(residue number reindexed from 1)		M546 P552 I571 I619 E620 V622 T627 D702
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=6.58,IC50=262nM
BindingDB: Kd=130nM,IC50=262nM
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

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:3sd5, PDBe:3sd5, PDBj:3sd5
PDBsum3sd5
PubMed22188813
UniProtP48736|PK3CG_HUMAN Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform (Gene Name=PIK3CG)

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