Structure of PDB 7nxj Chain C Binding Site BS01

Receptor Information
>7nxj Chain C (length=323) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
IDWGKRCVDKFDIIGIIGEGTYGQVYKARDKDTGEMVALKKVRLDNEKEG
FPITAIREIKILRQLTHQSIINMKEIVTDKEDALDFKKDKGAFYLVFEYM
DHDLMGLLESGLVHFNENHIKSFMRQLMEGLDYCHKKNFLHRDIKCSNIL
LNNRGQIKLADFGLARLYSSEESRPYTNKVITLWYRPPELLLGEERYTPA
IDVWSCGCILGELFTKKPIFQANQELAQLELISRICGSPCPAVWPDVIKL
PYFNTMKPKKQYRRKLREEFVFIPAAALDLFDYMLALDPSKRCTAEQALQ
CEFLRDVEPSKMPPPDLPLWQDC
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 chain7nxj 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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PDB7nxj Structure-activity relationship study of THZ531 derivatives enables the discovery of BSJ-01-175 as a dual CDK12/13 covalent inhibitor with efficacy in Ewing sarcoma.
Resolution2.36 Å
Binding residue
(original residue number in PDB)		I708 I711 V719 K721 A732 K734 I765 F791 Y793 M794 H796 D797 L844 D855 C1017
Binding residue
(residue number reindexed from 1)		I14 I17 V25 K27 A38 K40 I71 F97 Y99 M100 H102 D103 L150 D161 C323
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) D837 K839 S841 N842 D855 S867 T876
Catalytic site (residue number reindexed from 1) D143 K145 S147 N148 D161 S173 T182
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:7nxj, PDBe:7nxj, PDBj:7nxj
PDBsum7nxj
PubMed33945934
UniProtQ14004|CDK13_HUMAN Cyclin-dependent kinase 13 (Gene Name=CDK13)

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