Structure of PDB 6ckx Chain A Binding Site BS02

Receptor Information
>6ckx Chain A (length=293) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RCVDKFDIIGIIGEGTYGQVYKAKDKDTGELVALKKVRLDNEKEGFPITA
IREIKILRQLIHRSVVNMKEIVTDKGAFYLVFEYMDHDLMGLLESGLVHF
SEDHIKSFMKQLMEGLEYCHKKNFLHRDIKCSNILLNNSGQIKLADFGLA
RLYNSEESRPYTNKVITLWYRPPELLLGEERYTPAIDVWSCGCILGELFT
KKPIFQANLELAQLELISRLCGSPCPAVWPDVIKLPYFNTMKPKKQYRRR
LREEFSFIPSAALDLLDHMLTLDPSKRCTAEQTLQSDFLKDVE
Ligand information
Ligand ID8M1
InChIInChI=1S/C26H28N6O/c1-18(33)32(23-11-7-19(8-12-23)21-16-28-31(2)17-21)24-13-9-22(10-14-24)29-26-27-15-20-5-3-4-6-25(20)30-26/h3-8,11-12,15-17,22,24H,9-10,13-14H2,1-2H3,(H,27,29,30)/t22-,24-
InChIKeyFNRJTMUROZAOIB-HCGLCNNCSA-N
SMILES
SoftwareSMILES
CACTVS 3.385Cn1cc(cn1)c2ccc(cc2)N([C@@H]3CC[C@H](CC3)Nc4ncc5ccccc5n4)C(C)=O
ACDLabs 12.01C3(CCC(Nc2ncc1ccccc1n2)CC3)N(c4ccc(cc4)c5cnn(C)c5)C(C)=O
OpenEye OEToolkits 2.0.6CC(=O)N(c1ccc(cc1)c2cnn(c2)C)C3CCC(CC3)Nc4ncc5ccccc5n4
CACTVS 3.385Cn1cc(cn1)c2ccc(cc2)N([CH]3CC[CH](CC3)Nc4ncc5ccccc5n4)C(C)=O
FormulaC26 H28 N6 O
NameN-[4-(1-methyl-1H-pyrazol-4-yl)phenyl]-N-{trans-4-[(quinazolin-2-yl)amino]cyclohexyl}acetamide
ChEMBLCHEMBL4159417
DrugBank
ZINC
PDB chain6ckx Chain A Residue 1102 [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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PDB6ckx Discovery of 3-Benzyl-1-( trans-4-((5-cyanopyridin-2-yl)amino)cyclohexyl)-1-arylurea Derivatives as Novel and Selective Cyclin-Dependent Kinase 12 (CDK12) Inhibitors.
Resolution2.8 Å
Binding residue
(original residue number in PDB)		I733 G734 A754 F813 M816 H818 D819 L866
Binding residue
(residue number reindexed from 1)		I12 G13 A33 F82 M85 H87 D88 L135
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=7.89,IC50=0.013uM
BindingDB: IC50=13nM
Enzymatic activity
Catalytic site (original residue number in PDB) D859 K861 N864 D877 S889 T898
Catalytic site (residue number reindexed from 1) D128 K130 N133 D146 S158 T167
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:0005524 ATP binding
Biological Process
GO:0006468 protein phosphorylation

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:6ckx, PDBe:6ckx, PDBj:6ckx
PDBsum6ckx
PubMed30067358
UniProtQ9NYV4|CDK12_HUMAN Cyclin-dependent kinase 12 (Gene Name=CDK12)

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