Structure of PDB 5eds Chain A Binding Site BS01

Receptor Information
>5eds Chain A (length=823) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SQAFQRQLTALIGYDVTDVSNVHDDELEFTRRGLVTPRMAEVASRDPKLY
AMHPWVTSKPLPEYLWKKIANNCIFIVIHRSTTSQTIKVSPDDTPGAILQ
SDFVLRVCGRDEYLVGETPIKNFQWVRHCLKNGEEIHVVLDTPPDPALDE
VRKEVSLWDCDRKFRVKIRGIDIPVLDLTVFVEANIQHGQQVLCQRRTSP
KPFTEEVLWNVWLEFSIKIKDLPKGALLNLQIYCKVQLLYYVNLLLIDHR
FLLRRGEYVLHMWQISSFNADKLTSATNPDKENSMSISILLDPIALPKHE
MPNQLRKQLEAIIATDPLNPLTAEDKELLWHFRYESLKHPKAYPKLFSSV
KWGQQEIVAKTYQLLARREVWDQSALDVGLTMQLLDCNFSDENVRAIAVQ
KLESLEDDDVLHYLLQLVQAVKFEPYHDSALARFLLKRGLRNKRIGHFLF
WFLRSEIAQSRHYQQRFAVILEAYLRGCGTAMLHDFTQQVQVIEMLQKVT
LDIKSLSAVSSQVISQLKQKLENLQNSQLPESFRVPYDPGLKAGALAIEK
CKVMASKKKPLWLEFKCADPTALSNETIGIIFKHGDDLRQDMLILQILRI
MESIWETESLDLCLLPYGCISTGDKIGMIEIVKDATTIAKIQQSTVGAFK
DEVLNHWLKEKSPTEEKFQAAVERFVYSCAGYCVATFVLGIGDRHNDNIM
ITETGNLFHIDFGHKERVPFVLTPDFLFVMGTSGKKTSPHFQKFQDICVK
AYLALRHHTNLLIILFSMMLMTGMPQLTSKEDIEYIRDALTVGKNEEDAK
KYFLDQIEVCRDKGWTVQFNWFL
Ligand information
Ligand ID5MT
InChIInChI=1S/C21H18FN7O2S/c1-12(27-20-16(10-23)19(24)25-11-26-20)21-28-17-7-6-13(22)8-18(17)29(21)14-4-3-5-15(9-14)32(2,30)31/h3-9,11-12H,1-2H3,(H3,24,25,26,27)/t12-/m0/s1
InChIKeyARGMEIUNNDIMNN-LBPRGKRZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.4CC(c1nc2ccc(cc2n1c3cccc(c3)S(=O)(=O)C)F)Nc4c(c(ncn4)N)C#N
CACTVS 3.385C[CH](Nc1ncnc(N)c1C#N)c2nc3ccc(F)cc3n2c4cccc(c4)[S](C)(=O)=O
CACTVS 3.385C[C@H](Nc1ncnc(N)c1C#N)c2nc3ccc(F)cc3n2c4cccc(c4)[S](C)(=O)=O
OpenEye OEToolkits 2.0.4C[C@@H](c1nc2ccc(cc2n1c3cccc(c3)S(=O)(=O)C)F)Nc4c(c(ncn4)N)C#N
FormulaC21 H18 F N7 O2 S
Name4-azanyl-6-[[(1~{S})-1-[6-fluoranyl-1-(3-methylsulfonylphenyl)benzimidazol-2-yl]ethyl]amino]pyrimidine-5-carbonitrile
ChEMBLCHEMBL4788529
DrugBank
ZINCZINC000141603938
PDB chain5eds Chain A Residue 1204 [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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PDB5eds Discovery, Optimization, and in Vivo Evaluation of Benzimidazole Derivatives AM-8508 and AM-9635 as Potent and Selective PI3K delta Inhibitors.
Resolution2.8 Å
Binding residue
(original residue number in PDB)		M804 P810 W812 I831 Y867 E880 K890 M953 I963
Binding residue
(residue number reindexed from 1)		M554 P560 W562 I581 Y617 E630 K640 M700 I710
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=5.54,IC50=2.88uM
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:5eds, PDBe:5eds, PDBj:5eds
PDBsum5eds
PubMed26652588
UniProtP48736|PK3CG_HUMAN Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform (Gene Name=PIK3CG)

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