Structure of PDB 6ccy Chain A Binding Site BS01

Receptor Information
>6ccy Chain A (length=326) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GSLRVTMNEFEYLKLLGKGTFGKVILVKEKATGRYYAMKILKKEVIVAKD
EVAHTLTESRVLQNSRHPFLTALKYSFQTHDRLCFVMEYANGGELFFHLS
RERVFSEDRARFYGAEIVSALDYLHSEKNVVYRDLKLENLMLDKDGHIKI
TDFGLCKEGIKDGATMKTFCGTPEYLAPEVLEDNDYGRAVDWWGLGVVMY
EMMCGRLPFYNQDHEKLFELILMEEIRFPRTLGPEAKSLLSGLLKKDPKQ
RLGGGPSDAKEIMQHRFFAGIVWQHVYEKKLSPPFKPQVTSEVDTRYFDE
EFTAQMITITEQEMFRDFDYIADWEG
Ligand information
Ligand IDEX4
InChIInChI=1S/C29H33F4N7O/c1-18-14-24(41)37-26-25(18)28(35-17-34-26)39-10-6-19(7-11-39)27-36-23(16-40(27)13-12-38-8-2-3-9-38)20-4-5-22(30)21(15-20)29(31,32)33/h4-5,15-19H,2-3,6-14H2,1H3,(H,34,35,37,41)/t18-/m1/s1
InChIKeyXIYKGCYSJCRNDN-GOSISDBHSA-N
SMILES
SoftwareSMILES
CACTVS 3.385C[CH]1CC(=O)Nc2ncnc(N3CCC(CC3)c4nc(cn4CCN5CCCC5)c6ccc(F)c(c6)C(F)(F)F)c12
ACDLabs 12.01c2c(c1ccc(F)c(c1)C(F)(F)F)nc(n2CCN3CCCC3)C4CCN(CC4)c6ncnc5NC(=O)CC(C)c56
OpenEye OEToolkits 2.0.6CC1CC(=O)Nc2c1c(ncn2)N3CCC(CC3)c4nc(cn4CCN5CCCC5)c6ccc(c(c6)C(F)(F)F)F
CACTVS 3.385C[C@@H]1CC(=O)Nc2ncnc(N3CCC(CC3)c4nc(cn4CCN5CCCC5)c6ccc(F)c(c6)C(F)(F)F)c12
OpenEye OEToolkits 2.0.6C[C@@H]1CC(=O)Nc2c1c(ncn2)N3CCC(CC3)c4nc(cn4CCN5CCCC5)c6ccc(c(c6)C(F)(F)F)F
FormulaC29 H33 F4 N7 O
Name(5R)-4-(4-{4-[4-fluoro-3-(trifluoromethyl)phenyl]-1-[2-(pyrrolidin-1-yl)ethyl]-1H-imidazol-2-yl}piperidin-1-yl)-5-methyl-5,8-dihydropyrido[2,3-d]pyrimidin-7(6H)-one
ChEMBLCHEMBL4128457
DrugBank
ZINC
PDB chain6ccy Chain A Residue 501 [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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PDB6ccy Discovery of chiral dihydropyridopyrimidinones as potent, selective and orally bioavailable inhibitors of AKT.
Resolution2.18 Å
Binding residue
(original residue number in PDB)		L156 G157 G159 G162 K163 V164 A177 T211 M227 E228 A230 E234 M281 F438 F442
Binding residue
(residue number reindexed from 1)		L16 G17 G19 G22 K23 V24 A37 T71 M87 E88 A90 E94 M141 F298 F302
Annotation score1
Binding affinityMOAD: ic50=0.003uM
PDBbind-CN: -logKd/Ki=8.52,IC50=0.003uM
Enzymatic activity
Catalytic site (original residue number in PDB) D274 K276 N279 D292 T312
Catalytic site (residue number reindexed from 1) D134 K136 N139 D152 T172
Enzyme Commision number 2.7.11.1: non-specific serine/threonine protein kinase.
2.7.11.13: protein kinase C.
Gene Ontology
Molecular Function
GO:0004672 protein kinase activity
GO:0004674 protein serine/threonine kinase activity
GO:0005524 ATP binding
Biological Process
GO:0006468 protein phosphorylation

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:6ccy, PDBe:6ccy, PDBj:6ccy
PDBsum6ccy
PubMed29655979
UniProtP31749|AKT1_HUMAN RAC-alpha serine/threonine-protein kinase (Gene Name=AKT1);
Q16513|PKN2_HUMAN Serine/threonine-protein kinase N2 (Gene Name=PKN2)

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