Structure of PDB 6xbz Chain J Binding Site BS01

Receptor Information
>6xbz Chain J (length=298) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KRYEKLDFLGEGQFATVYKARDKNTNQIVAIKKIKLAKDGINRTALREIK
LLQELSHPNIIGLLDAFGHKSNISLVFDFMETDLEVIIKDNSLVLTPSHI
KAYMLMTLQGLEYLHQHWILHRDLKPNNLLLDENGVLKLADFGLAKSFGS
PNRAYTHQVVTRWYRAPELLFGARMYGVGVDMWAVGCILAELLLRVPFLP
GDSDLDQLTRIFETLGTPTEEQWPDMCSLPDYVTFKSFPGIPLHHIFSAA
GDDLLDLIQGLFLFNPCARITATQALKMKYFSNRPGPTPGCQLPRPNC
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 chain6xbz Chain J Residue 402 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6xbz The cryoelectron microscopy structure of the human CDK-activating kinase.
Resolution2.8 Å
Binding residue
(original residue number in PDB)		L18 E20 G21 V26 A39 M94 L144
Binding residue
(residue number reindexed from 1)		L9 E11 G12 V17 A30 M80 L130
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) D137 K139 N142 D155 A168 T175
Catalytic site (residue number reindexed from 1) D123 K125 N128 D141 A154 T161
Enzyme Commision number 2.7.11.22: cyclin-dependent kinase.
2.7.11.23: [RNA-polymerase]-subunit 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:0008094 ATP-dependent activity, acting on DNA
GO:0008353 RNA polymerase II CTD heptapeptide repeat kinase activity
GO:0016301 kinase activity
GO:0106310 protein serine kinase activity
Biological Process
GO:0006281 DNA repair
GO:0006366 transcription by RNA polymerase II
GO:0006367 transcription initiation at RNA polymerase II promoter
GO:0006468 protein phosphorylation
GO:0016310 phosphorylation
GO:0042795 snRNA transcription by RNA polymerase II
GO:0045944 positive regulation of transcription by RNA polymerase II
GO:0050821 protein stabilization
GO:0051301 cell division
GO:0051726 regulation of cell cycle
GO:2000045 regulation of G1/S transition of mitotic cell cycle
Cellular Component
GO:0000307 cyclin-dependent protein kinase holoenzyme complex
GO:0000439 transcription factor TFIIH core complex
GO:0001650 fibrillar center
GO:0001673 male germ cell nucleus
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005675 transcription factor TFIIH holo complex
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005886 plasma membrane
GO:0048471 perinuclear region of cytoplasm
GO:0070516 CAK-ERCC2 complex
GO:0070985 transcription factor TFIIK complex

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6xbz, PDBe:6xbz, PDBj:6xbz
PDBsum6xbz
PubMed32855301
UniProtP50613|CDK7_HUMAN Cyclin-dependent kinase 7 (Gene Name=CDK7)

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