Structure of PDB 6ya6 Chain A Binding Site BS01

Receptor Information
>6ya6 Chain A (length=344) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AGVKKDIEKLYEAVPQLSNVFKIEDKIGEGTFSSVYLATAQLQVGPEEKI
ALKHLIPTSHPIRIAAELQCLTVAGGQDNVMGVKYCFRKNDHVVIAMPYL
EHESFLDILNSLSFQEVREYMLNLFKALKRIHQFGIVHRDVKPSNFLYNR
RLKKYALVDFGLAQGTHDTKIELLKFVQPASLTCDCYATDKVCSICLSRR
QQVAPRAGTPGFRAPEVLTKCPNQTTAIDMWSAGVIFLSLLSGRYPFYKA
SDDLTALAQIMTIRGSRETIQAAKTFGKSILCSKEVPAQDLRKLCERLRG
AGAGGWNEVPDEAYDLLDKLLDLNPASRITAEEALLHPFFKDMS
Ligand information
Ligand ID0SX
InChIInChI=1S/C14H12ClN3O2/c15-7-3-4-10-8(6-7)11-12(20-10)14(19)18-13(17-11)9-2-1-5-16-9/h3-4,6,9,16H,1-2,5H2,(H,17,18,19)/t9-/m0/s1
InChIKeyJJWLXRKVUJDJKG-VIFPVBQESA-N
SMILES
SoftwareSMILES
ACDLabs 12.01Clc4cc3c(oc1c3N=C(NC1=O)C2NCCC2)cc4
OpenEye OEToolkits 1.7.6c1cc2c(cc1Cl)c3c(o2)C(=O)NC(=N3)[C@@H]4CCCN4
CACTVS 3.370Clc1ccc2oc3C(=O)NC(=Nc3c2c1)[CH]4CCCN4
CACTVS 3.370Clc1ccc2oc3C(=O)NC(=Nc3c2c1)[C@@H]4CCCN4
OpenEye OEToolkits 1.7.6c1cc2c(cc1Cl)c3c(o2)C(=O)NC(=N3)C4CCCN4
FormulaC14 H12 Cl N3 O2
Name8-chloro-2-[(2S)-pyrrolidin-2-yl][1]benzofuro[3,2-d]pyrimidin-4(3H)-one
ChEMBLCHEMBL2030402
DrugBankDB12357
ZINCZINC000084668615
PDB chain6ya6 Chain A Residue 601 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6ya6 Structural Basis for the Activation and Target Site Specificity of CDC7 Kinase.
Resolution1.44 Å
Binding residue
(original residue number in PDB)		V72 A88 K90 M134 Y136 L137 N182 L184 V195 D196
Binding residue
(residue number reindexed from 1)		V35 A51 K53 M97 Y99 L100 N145 L147 V158 D159
Annotation score1
Binding affinityBindingDB: IC50=3.4nM
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 T209
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:6ya6, PDBe:6ya6, PDBj:6ya6
PDBsum6ya6
PubMed32521228
UniProtO00311|CDC7_HUMAN Cell division cycle 7-related protein kinase (Gene Name=CDC7)

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