Structure of PDB 3zdu Chain A Binding Site BS01

Receptor Information
>3zdu Chain A (length=297) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MEMYETLGKVGEGSYGTVMKCKHKNTGQIVAIKIFYNKIAMREIKFLKQF
HHENLVNLIEVFRQKKKIHLVFEFIDHTVLDELQHYCHGLESKRLRKYLF
QILRAIDYLHSNNIIHRDIKPENILVSQSGITKLCDFGFARTDIYDDEVA
TRWYRAPELVLKDTSYGKPVDIWALGCMIIEMATGNPYLPSSSDLDLLHK
IVLKVGNLSPHLQNIFSKSPIFAGVVLPQVQHPKNARKKYPKLNGLLADI
VHACLQIDPADRISSSDLLHHEYFTRDGFIEKFMPELKAKLLQEAKV
Ligand information
Ligand ID38R
InChIInChI=1S/C20H21N7/c21-11-9-14-5-7-16(8-6-14)23-20-22-12-10-18(25-20)24-19-13-17(26-27-19)15-3-1-2-4-15/h5-8,10,12-13,15H,1-4,9H2,(H3,22,23,24,25,26,27)
InChIKeyVKAOLAKWGBXOCQ-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.9.2c1cc(ccc1CC#N)Nc2nccc(n2)Nc3cc(n[nH]3)C4CCCC4
CACTVS 3.385N#CCc1ccc(Nc2nccc(Nc3[nH]nc(c3)C4CCCC4)n2)cc1
ACDLabs 12.01N#CCc1ccc(cc1)Nc2nccc(n2)Nc3cc(nn3)C4CCCC4
FormulaC20 H21 N7
Name[4-({4-[(3-cyclopentyl-1H-pyrazol-5-yl)amino]pyrimidin-2-yl}amino)phenyl]acetonitrile
ChEMBL
DrugBank
ZINCZINC000095920754
PDB chain3zdu Chain A Residue 350 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3zdu CDKL Family Kinases Have Evolved Distinct Structural Features and Ciliary Function.
Resolution2.2 Å
Binding residue
(original residue number in PDB)		V18 A31 K33 F79 E80 F81 I82 T85 E129 L132 C142 D143
Binding residue
(residue number reindexed from 1)		V18 A31 K33 F72 E73 F74 I75 T78 E122 L125 C135 D136
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) D125 K127 N130 D143 I156 T163
Catalytic site (residue number reindexed from 1) D118 K120 N123 D136 I144 T151
Enzyme Commision number 2.7.11.22: cyclin-dependent 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:3zdu, PDBe:3zdu, PDBj:3zdu
PDBsum3zdu
PubMed29420175
UniProtQ8IVW4|CDKL3_HUMAN Cyclin-dependent kinase-like 3 (Gene Name=CDKL3)

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