Structure of PDB 4krc Chain A Binding Site BS01

Receptor Information
>4krc Chain A (length=297) Species: 559292 (Saccharomyces cerevisiae S288C) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SSSSQFKQLEKLGNGTYATVYKGLNKTTGVYVALKEVKLDSEEGTPSTAI
REISLMKELKHENIVRLYDVIHTENKLTLVFEFMDNDLKKYMDSRTPRGL
ELNLVKYFQWQLLQGLAFCHENKILHRDLKPQNLLINKRGQLKLGDFGLA
RAFGIPVNTFSSEVVTLWYRAPDVLMGSRTYSTSIDIWSCGCILAEMITG
KPLFPGTNDEEQLKLIFDIMGTPNESLWPSVTKLPKYNPNIQQRPPRDLR
QVLQPHTKEPLDGNLMDFLHGLLQLNPDMRLSAKQALHHPWFAEYYH
Ligand information
Ligand IDAGS
InChIInChI=1S/C10H16N5O12P3S/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(25-10)1-24-28(18,19)26-29(20,21)27-30(22,23)31/h2-4,6-7,10,16-17H,1H2,(H,18,19)(H,20,21)(H2,11,12,13)(H2,22,23,31)/t4-,6-,7-,10-/m1/s1
InChIKeyNLTUCYMLOPLUHL-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=S)(O)O)O)O)N
CACTVS 3.370Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=S)[C@@H](O)[C@H]3O
CACTVS 3.370Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=S)[CH](O)[CH]3O
OpenEye OEToolkits 1.7.6c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)OP(=O)(O)OP(=S)(O)O)O)O)N
ACDLabs 12.01O=P(O)(OP(=S)(O)O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
FormulaC10 H16 N5 O12 P3 S
NamePHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER;
ATP-GAMMA-S;
ADENOSINE 5'-(3-THIOTRIPHOSPHATE);
ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE);
ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE
ChEMBLCHEMBL131890
DrugBankDB02930
ZINCZINC000008295128
PDB chain4krc Chain A Residue 402 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB4krc New Structural Insights into Phosphorylation-free Mechanism for Full Cyclin-dependent Kinase (CDK)-Cyclin Activity and Substrate Recognition.
Resolution2.597 Å
Binding residue
(original residue number in PDB)		G16 T17 V21 A34 K36 M85 D88 K135 Q137 N138 L140 D151
Binding residue
(residue number reindexed from 1)		G15 T16 V20 A33 K35 M84 D87 K130 Q132 N133 L135 D146
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) D133 K135 Q137 N138 D151 T164 T171
Catalytic site (residue number reindexed from 1) D128 K130 Q132 N133 D146 T159 T166
Enzyme Commision number 2.7.11.22: cyclin-dependent kinase.
Gene Ontology
Molecular Function
GO:0004672 protein kinase activity
GO:0004674 protein serine/threonine kinase activity
GO:0004693 cyclin-dependent protein serine/threonine kinase activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0106310 protein serine kinase activity
Biological Process
GO:0000082 G1/S transition of mitotic cell cycle
GO:0000122 negative regulation of transcription by RNA polymerase II
GO:0001676 long-chain fatty acid metabolic process
GO:0005979 regulation of glycogen biosynthetic process
GO:0006355 regulation of DNA-templated transcription
GO:0006357 regulation of transcription by RNA polymerase II
GO:0006468 protein phosphorylation
GO:0006974 DNA damage response
GO:0009891 positive regulation of biosynthetic process
GO:0016239 positive regulation of macroautophagy
GO:0016242 negative regulation of macroautophagy
GO:0016310 phosphorylation
GO:0019216 regulation of lipid metabolic process
GO:0030952 establishment or maintenance of cytoskeleton polarity
GO:0031505 fungal-type cell wall organization
GO:0031647 regulation of protein stability
GO:0031648 protein destabilization
GO:0032878 regulation of establishment or maintenance of cell polarity
GO:0032880 regulation of protein localization
GO:0044843 cell cycle G1/S phase transition
GO:0045719 negative regulation of glycogen biosynthetic process
GO:0045936 negative regulation of phosphate metabolic process
GO:0046822 regulation of nucleocytoplasmic transport
GO:0050849 negative regulation of calcium-mediated signaling
GO:0051302 regulation of cell division
GO:0051726 regulation of cell cycle
GO:0055088 lipid homeostasis
GO:0071073 positive regulation of phospholipid biosynthetic process
GO:1901987 regulation of cell cycle phase transition
Cellular Component
GO:0000307 cyclin-dependent protein kinase holoenzyme complex
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005935 cellular bud neck
GO:1902554 serine/threonine protein kinase complex
GO:1990860 Pho85-Pho80 CDK-cyclin complex

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4krc, PDBe:4krc, PDBj:4krc
PDBsum4krc
PubMed24022486
UniProtP17157|PHO85_YEAST Cyclin-dependent protein kinase PHO85 (Gene Name=PHO85)

[Back to BioLiP]