Structure of PDB 8r9u Chain A Binding Site BS01

Receptor Information
>8r9u Chain A (length=282) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KRYEKLDFLGEGQFATVYKARDKNTNQIVAIKKINRTALREIKLLQELSH
PNIIGLLDAFGSNISLVFDFMETDLEVIIKDNSLVLTPSHIKAYMLMTLQ
GLEYLHQHRILHRDLKPNNLLLDENGVLKLADFGLAKSFGDPNVVTRWYR
APELLFGARMYGVGVDMWAVGCILAELLLRVPFLPGDSDLDQLTRIFETL
GTPTEEQWPDMCSLPDYVTFKSFPGIPLHHIFSAAGDDLLDLIQGLFLFN
PCARITATQALKMKYFSNRPGPTPGCQLPRPN
Ligand information
Ligand IDYNK
InChIInChI=1S/C23H26F3N6OP/c1-22(2)8-7-14(10-30-22)31-21-29-12-17(23(24,25)26)18(32-21)16-11-28-19-15(16)6-5-13(9-27)20(19)34(3,4)33/h5-6,11-12,14,28,30H,7-8,10H2,1-4H3,(H,29,31,32)/t14-/m0/s1
InChIKeyJDJOUBVVSQDIRC-AWEZNQCLSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7CC1(CC[C@@H](CN1)Nc2ncc(c(n2)c3c[nH]c4c3ccc(c4P(=O)(C)C)C#N)C(F)(F)F)C
CACTVS 3.385CC1(C)CC[C@@H](CN1)Nc2ncc(c(n2)c3c[nH]c4c3ccc(C#N)c4[P](C)(C)=O)C(F)(F)F
CACTVS 3.385CC1(C)CC[CH](CN1)Nc2ncc(c(n2)c3c[nH]c4c3ccc(C#N)c4[P](C)(C)=O)C(F)(F)F
OpenEye OEToolkits 2.0.7CC1(CCC(CN1)Nc2ncc(c(n2)c3c[nH]c4c3ccc(c4P(=O)(C)C)C#N)C(F)(F)F)C
FormulaC23 H26 F3 N6 O P
Name7-dimethylphosphoryl-3-[2-[[(3~{S})-6,6-dimethylpiperidin-3-yl]amino]-5-(trifluoromethyl)pyrimidin-4-yl]-1~{H}-indole-6-carbonitrile
ChEMBL
DrugBank
ZINC
PDB chain8r9u Chain A Residue 401 [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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PDB8r9u Protein engineering enables a soakable crystal form of human CDK7 primed for high-throughput crystallography and structure-based drug design
Resolution1.937 Å
Binding residue
(original residue number in PDB)		L18 G19 E20 F23 V26 K41 F91 M94 E95 T96 D97 D155
Binding residue
(residue number reindexed from 1)		L9 G10 E11 F14 V17 K32 F68 M71 E72 T73 D74 D132
Annotation score1
Enzymatic activity
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: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
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Cellular Component
External links
PDB RCSB:8r9u, PDBe:8r9u, PDBj:8r9u
PDBsum8r9u
PubMed38870939
UniProtP50613|CDK7_HUMAN Cyclin-dependent kinase 7 (Gene Name=CDK7)

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