Structure of PDB 8r9s Chain B Binding Site BS01

Receptor Information
>8r9s Chain B (length=290) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AKRYEKLDFLGEGQFATVYKARDKNTNQIVAIKKIKLGHRGINRTALREI
KLLQELSHPNIIGLLDAFGHKSNISLVFDFMETDLEVIIKDNSLVLTPSH
IKAYMLMTLQGLEYLHQHRILHRDLKPNNLLLDENGVLKLADFGLAKSFQ
VVTRWYRAPELLFGARMYGVGVDMWAVGCILAELLLRVPFLPGDSDLDQL
TRIFETLGTPTEEQWPDMCSLPDYVTFKSFPGIPLHHIFSAAGDDLLDLI
QGLFLFNPCARITATQALKMKYFSNRPGPTPGCQLPRPNC
Ligand information
Ligand IDYPK
InChIInChI=1S/C26H41N7O3/c1-18(2)22-16-27-33-23(15-19(3)28-25(22)33)29-20-8-12-31(13-9-20)26(35)36-21-10-14-32(17-21)24(34)7-6-11-30(4)5/h15-16,18,20-21,29H,6-14,17H2,1-5H3/t21-/m0/s1
InChIKeyGRQNIAZNGVLLKQ-NRFANRHFSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7Cc1cc(n2c(n1)c(cn2)C(C)C)NC3CCN(CC3)C(=O)OC4CCN(C4)C(=O)CCCN(C)C
OpenEye OEToolkits 2.0.7Cc1cc(n2c(n1)c(cn2)C(C)C)NC3CCN(CC3)C(=O)O[C@H]4CCN(C4)C(=O)CCCN(C)C
CACTVS 3.385CC(C)c1cnn2c(NC3CCN(CC3)C(=O)O[CH]4CCN(C4)C(=O)CCCN(C)C)cc(C)nc12
CACTVS 3.385CC(C)c1cnn2c(NC3CCN(CC3)C(=O)O[C@H]4CCN(C4)C(=O)CCCN(C)C)cc(C)nc12
FormulaC26 H41 N7 O3
Name[(3S)-1-[4-(dimethylamino)butanoyl]pyrrolidin-3-yl] 4-[(5-methyl-3-propan-2-yl-pyrazolo[1,5-a]pyrimidin-7-yl)amino]piperidine-1-carboxylate;
HYDROXYETHYLAMINE BACE INHIBITOR
ChEMBL
DrugBank
ZINC
PDB chain8r9s Chain B Residue 403 [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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PDB8r9s Protein engineering enables a soakable crystal form of human CDK7 primed for high-throughput crystallography and structure-based drug design
Resolution2.78 Å
Binding residue
(original residue number in PDB)		A39 I75 F91 M94 E95 T96 L144 N311 C312
Binding residue
(residue number reindexed from 1)		A31 I62 F78 M81 E82 T83 L131 N289 C290
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
View graph for
Cellular Component
External links
PDB RCSB:8r9s, PDBe:8r9s, PDBj:8r9s
PDBsum8r9s
PubMed38870939
UniProtP50613|CDK7_HUMAN Cyclin-dependent kinase 7 (Gene Name=CDK7)

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