Structure of PDB 5acb Chain C Binding Site BS01

Receptor Information
>5acb Chain C (length=325) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ESDWGKRCVDKFDIIGIIGEGTYGQVYKAKDKDTGELVALKKVRLDNEKE
GFPITAIREIKILRQLIHRSVVNMKEIVTDKQDALDFKKDKGAFYLVFEY
MDHDLMGLLESGLVHFSEDHIKSFMKQLMEGLEYCHKKNFLHRDIKCSNI
LLNNSGQIKLADFGLARLYNSEESRPYTNKVITLWYRPPELLLGEERYTP
AIDVWSCGCILGELFTKKPIFQANLELAQLELISRLCGSPCPAVWPDVIK
LPYFNTMKPKKQYRRRLREEFSFIPSAALDLLDHMLTLDPSKRCTAEQTL
QSDFLKDVELSKMAPPDLPHWQDCH
Ligand information
Ligand ID5I1
InChIInChI=1S/C30H34ClN7O2/c1-37(2)15-6-10-27(39)34-21-13-11-20(12-14-21)29(40)38-16-5-7-22(19-38)35-30-33-18-25(31)28(36-30)24-17-32-26-9-4-3-8-23(24)26/h3-4,8-9,11-14,17-18,22,32H,5-7,10,15-16,19H2,1-2H3,(H,34,39)(H,33,35,36)/t22-/m1/s1
InChIKeyZVKCKFIOVYZRHX-JOCHJYFZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6CN(C)CCCC(=O)Nc1ccc(cc1)C(=O)N2CCC[C@H](C2)Nc3ncc(c(n3)c4c[nH]c5c4cccc5)Cl
CACTVS 3.385CN(C)CCCC(=O)Nc1ccc(cc1)C(=O)N2CCC[CH](C2)Nc3ncc(Cl)c(n3)c4c[nH]c5ccccc45
CACTVS 3.385CN(C)CCCC(=O)Nc1ccc(cc1)C(=O)N2CCC[C@H](C2)Nc3ncc(Cl)c(n3)c4c[nH]c5ccccc45
OpenEye OEToolkits 1.7.6CN(C)CCCC(=O)Nc1ccc(cc1)C(=O)N2CCCC(C2)Nc3ncc(c(n3)c4c[nH]c5c4cccc5)Cl
FormulaC30 H34 Cl N7 O2
NameN-[4-[(3R)-3-[[5-chloranyl-4-(1H-indol-3-yl)pyrimidin-2-yl]amino]piperidin-1-yl]carbonylphenyl]-4-(dimethylamino)butanamide
ChEMBL
DrugBank
ZINCZINC000584905065
PDB chain5acb Chain C Residue 2000 [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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PDB5acb Covalent Targeting of Remote Cysteine Residues to Develop Cdk12 and Cdk13 Inhibitors.
Resolution2.7 Å
Binding residue
(original residue number in PDB)		I733 V741 A754 K756 F813 M816 D819 L866 Q1037 C1039
Binding residue
(residue number reindexed from 1)		I18 V26 A39 K41 F98 M101 D104 L151 Q322 C324
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=6.80,IC50=158nM
Enzymatic activity
Catalytic site (original residue number in PDB) D859 K861 S863 N864 D877 S889 T898
Catalytic site (residue number reindexed from 1) D144 K146 S148 N149 D162 S174 T183
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

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Molecular Function
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Biological Process
External links
PDB RCSB:5acb, PDBe:5acb, PDBj:5acb
PDBsum5acb
PubMed27571479
UniProtQ9NYV4|CDK12_HUMAN Cyclin-dependent kinase 12 (Gene Name=CDK12)

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