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Structure of PDB 2ydi Chain A Binding Site BS01

Receptor Information
>2ydi Chain A (length=279) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AVPFVEDWDLVQTLGEGAYGEVQLAVNRVTEEAVAVKIVDMKRAVDCPEN
IKKEICINKMLNHENVVKFYGHRREGNIQYLFLEYCSGGELFDRIEPDIG
MPEPDAQRFFHQLMAGVVYLHGIGITHRDIKPENLLLDERDNLKISDFGL
ATVFRYNNRERLLNKMCGTLPYVAPELLKRREFHAEPVDVWSCGIVLTAM
LAGELPWDQPSDSCQEYSDWKEKKTYLNPWKKIDSAPLALLHKILVENPS
ARITIPDIKKDRWYNKPLKKGAKRPRVTS
Ligand information
Ligand IDYDI
InChIInChI=1S/C16H20N4O3S/c1-20(2)7-8-23-11-5-3-10(4-6-11)13-9-12(14(17)21)15(24-13)19-16(18)22/h3-6,9H,7-8H2,1-2H3,(H2,17,21)(H3,18,19,22)
InChIKeyRFSVVCBVIFWEMZ-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0CN(C)CCOc1ccc(cc1)c2cc(c(s2)NC(=O)N)C(=O)N
ACDLabs 12.01O=C(Nc1sc(cc1C(=O)N)c2ccc(OCCN(C)C)cc2)N
CACTVS 3.370CN(C)CCOc1ccc(cc1)c2sc(NC(N)=O)c(c2)C(N)=O
FormulaC16 H20 N4 O3 S
Name5-[4-(2-DIMETHYLAMINOETHYLOXY)PHENYL]-2-UREIDO-THIOPHENE-3-CARBOXAMIDE
ChEMBLCHEMBL452021
DrugBank
ZINCZINC000034021557
PDB chain2ydi Chain A Residue 1282 [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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PDB2ydi Discovery of Checkpoint Kinase Inhibitor (S)-5-(3-Fluorophenyl)-N-(Piperidin-3-Yl)-3-Ureidothiophene-2-Carboxamide (Azd7762) by Structure-Based Design and Optimization of Thiophenecarboxamide Ureas.
Resolution1.6 Å
Binding residue
(original residue number in PDB)		L15 A36 E85 Y86 C87 S88 G90 L137
Binding residue
(residue number reindexed from 1)		L14 A35 E84 Y85 C86 S87 G89 L136
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=6.82,IC50=0.15uM
BindingDB: IC50=150nM
Enzymatic activity
Catalytic site (original residue number in PDB) D130 K132 E134 N135 D148 T170
Catalytic site (residue number reindexed from 1) D129 K131 E133 N134 D147 T169
Enzyme Commision number 2.7.11.1: non-specific serine/threonine protein kinase.
Gene Ontology
Molecular Function
GO:0004672 protein kinase activity
GO:0004674 protein serine/threonine kinase activity
GO:0005524 ATP binding
Biological Process
GO:0000077 DNA damage checkpoint signaling
GO:0006468 protein phosphorylation

View graph for
Molecular Function
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Biological Process
External links
PDB RCSB:2ydi, PDBe:2ydi, PDBj:2ydi
PDBsum2ydi
PubMed22551018
UniProtO14757|CHK1_HUMAN Serine/threonine-protein kinase Chk1 (Gene Name=CHEK1)

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