Structure of PDB 6ya8 Chain A Binding Site BS01

Receptor Information
>6ya8 Chain A (length=340) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AGVKKDIEKLYEAVPQLSNVFKIEDKIGEGTFSSVYLATAQLQVGPEEKI
ALKHLIPTSHPIRIAAELQCLTVAGGQDNVMGVKYCFRKNDHVVIAMPYL
EHESFLDILNSLSFQEVREYMLNLFKALKRIHQFGIVHRDVKPSNFLYNR
RLKKYALVDFGLAQGTHDTKIELLKFVPASLTCDCYATDKVCSICLSRRQ
QVAPRAGTPGFRAPEVLTKCPNQTTAIDMWSAGVIFLSLLSGRYPFYKAS
DDLTALAQIMTIRGSRETIQAAKTFGKSILCSKEVPAQDLRKLCERLRGA
GGWNEVPDEAYDLLDKLLDLNPASRITAEEALLHPFFKDM
Ligand information
Ligand IDADP
InChIInChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyXTWYTFMLZFPYCI-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
FormulaC10 H15 N5 O10 P2
NameADENOSINE-5'-DIPHOSPHATE
ChEMBLCHEMBL14830
DrugBankDB16833
ZINCZINC000012360703
PDB chain6ya8 Chain A Residue 601 [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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PDB6ya8 Structural Basis for the Activation and Target Site Specificity of CDC7 Kinase.
Resolution1.79 Å
Binding residue
(original residue number in PDB)		S70 V72 A88 K90 M134 Y136 L137 H139 S181 L184 D196
Binding residue
(residue number reindexed from 1)		S33 V35 A51 K53 M97 Y99 L100 H102 S144 L147 D159
Annotation score5
Enzymatic activity
Catalytic site (original residue number in PDB) D177 K179 N182 D196 T376
Catalytic site (residue number reindexed from 1) D140 K142 N145 D159 T208
Enzyme Commision number 2.7.11.1: non-specific serine/threonine protein 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:6ya8, PDBe:6ya8, PDBj:6ya8
PDBsum6ya8
PubMed32521228
UniProtO00311|CDC7_HUMAN Cell division cycle 7-related protein kinase (Gene Name=CDC7)

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