Structure of PDB 8p76 Chain J Binding Site BS01

Receptor Information
>8p76 Chain J (length=286) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KRYEKLDFLGEGQFATVYKARIVAIKKKDGINRTALREIKLLQELSHPNI
IGLLDAFGHKSNISLVFDFMETDLEVIIKDNSLVLTPSHIKAYMLMTLQG
LEYLHQHWILHRDLKPNNLLLDENGVLKLADFGLAKSFGSPNRAYTHQVV
TRWYRAPELLFGARMYGVGVDMWAVGCILAELLLRVPFLPGDSDLDQLTR
IFETLGTPTEEQWPDMCSLPDYVTFKSFPGIPLHHIFSAAGDDLLDLIQG
LFLFNPCARITATQALKMKYFSNRPGPTPGCQLPRP
Ligand information
Ligand IDX1W
InChIInChI=1S/C27H32N6O/c1-19(2)22-15-30-33-26(29-14-20-9-5-3-6-10-20)13-25(32-27(22)33)31-23-16-28-17-24(23)34-18-21-11-7-4-8-12-21/h3-13,15,19,23-24,28-29H,14,16-18H2,1-2H3,(H,31,32)/t23-,24+/m0/s1
InChIKeyOILLVYGGTARBHU-BJKOFHAPSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CC(C)c1cnn2c(NCc3ccccc3)cc(N[CH]4CNC[CH]4OCc5ccccc5)nc12
OpenEye OEToolkits 2.0.7CC(C)c1cnn2c1nc(cc2NCc3ccccc3)NC4CNCC4OCc5ccccc5
OpenEye OEToolkits 2.0.7CC(C)c1cnn2c1nc(cc2NCc3ccccc3)N[C@H]4CNC[C@H]4OCc5ccccc5
CACTVS 3.385CC(C)c1cnn2c(NCc3ccccc3)cc(N[C@H]4CNC[C@H]4OCc5ccccc5)nc12
FormulaC27 H32 N6 O
NameN5-[(3S,4R)-4-phenylmethoxypyrrolidin-3-yl]-N7-(phenylmethyl)-3-propan-2-yl-pyrazolo[1,5-a]pyrimidine-5,7-diamine
ChEMBL
DrugBank
ZINC
PDB chain8p76 Chain J Residue 401 [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]
PDB8p76 High-resolution cryo-EM of the human CDK-activating kinase for structure-based drug design
Resolution2.0 Å
Binding residue
(original residue number in PDB)		L18 G19 E20 A24 T25 V26 A39 F91 F93 M94 E95 T96
Binding residue
(residue number reindexed from 1)		L9 G10 E11 A15 T16 V17 A24 F67 F69 M70 E71 T72
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: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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8p76, PDBe:8p76, PDBj:8p76
PDBsum8p76
PubMed38480681
UniProtP50613|CDK7_HUMAN Cyclin-dependent kinase 7 (Gene Name=CDK7)

[Back to BioLiP]