Structure of PDB 6xd3 Chain J Binding Site BS01

Receptor Information
>6xd3 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 IDV0G
InChIInChI=1S/C31H30ClN7O2/c1-39(2)16-6-11-28(40)35-21-14-12-20(13-15-21)30(41)36-22-7-5-8-23(17-22)37-31-34-19-26(32)29(38-31)25-18-33-27-10-4-3-9-24(25)27/h3-5,7-10,12-15,17-19,33H,6,11,16H2,1-2H3,(H,35,40)(H,36,41)(H,34,37,38)
InChIKeyTUERFPPIPKZNKE-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01c1c(ccc(c1)NC(=O)CCCN(C)C)C(=O)Nc2cccc(c2)Nc3nc(c(Cl)cn3)c4c5c(nc4)cccc5
OpenEye OEToolkits 2.0.7CN(C)CCCC(=O)Nc1ccc(cc1)C(=O)Nc2cccc(c2)Nc3ncc(c(n3)c4c[nH]c5c4cccc5)Cl
CACTVS 3.385CN(C)CCCC(=O)Nc1ccc(cc1)C(=O)Nc2cccc(Nc3ncc(Cl)c(n3)c4c[nH]c5ccccc45)c2
FormulaC31 H30 Cl N7 O2
NameN-(3-{[5-chloro-4-(1H-indol-3-yl)pyrimidin-2-yl]amino}phenyl)-4-{[4-(dimethylamino)butanoyl]amino}benzamide
ChEMBLCHEMBL4303279
DrugBank
ZINCZINC000521836464
PDB chain6xd3 Chain J Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6xd3 The cryoelectron microscopy structure of the human CDK-activating kinase.
Resolution3.3 Å
Binding residue
(original residue number in PDB)		L18 V26 A39 F91 M94 E95 L144 D155 N311 C312
Binding residue
(residue number reindexed from 1)		L9 V17 A30 F77 M80 E81 L130 D141 N297 C298
Annotation score1
Binding affinityBindingDB: IC50=194nM
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:6xd3, PDBe:6xd3, PDBj:6xd3
PDBsum6xd3
PubMed32855301
UniProtP50613|CDK7_HUMAN Cyclin-dependent kinase 7 (Gene Name=CDK7)

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