Structure of PDB 2ydj Chain B Binding Site BS01

Receptor Information
>2ydj Chain B (length=253) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
WDLVQTLGEGAYGEVQLAVNRVTEEAVAVKIVDMNIKKEICINKMLNHEN
VVKFYGHRREGNIQYLFLEYCSGGELFDRIEPDIGMPEPDAQRFFHQLMA
GVVYLHGIGITHRDIKPENLLLDERDNLKISDFGLATVFRYNNRERLLNK
MCGTLPYVAPELLKRREFHAEPVDVWSCGIVLTAMLAGELPWDQPSDSCQ
EYSDWKEKKTYLNPWKKIDSAPLALLHKILVENPSARITIPDIKKDRWYN
KPL
Ligand information
Ligand IDYDJ
InChIInChI=1S/C17H19FN4O2S/c18-11-4-1-3-10(7-11)14-8-13(22-17(19)24)15(25-14)16(23)21-12-5-2-6-20-9-12/h1,3-4,7-8,12,20H,2,5-6,9H2,(H,21,23)(H3,19,22,24)/t12-/m0/s1
InChIKeyIAYGCINLNONXHY-LBPRGKRZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0c1cc(cc(c1)F)c2cc(c(s2)C(=O)N[C@H]3CCCNC3)NC(=O)N
OpenEye OEToolkits 1.7.0c1cc(cc(c1)F)c2cc(c(s2)C(=O)NC3CCCNC3)NC(=O)N
CACTVS 3.370NC(=O)Nc1cc(sc1C(=O)N[CH]2CCCNC2)c3cccc(F)c3
CACTVS 3.370NC(=O)Nc1cc(sc1C(=O)N[C@H]2CCCNC2)c3cccc(F)c3
ACDLabs 12.01O=C(c1sc(cc1NC(=O)N)c2cccc(F)c2)NC3CCCNC3
FormulaC17 H19 F N4 O2 S
Name5-(3-fluorophenyl)-N-[(3S)-3-piperidyl]-3-ureido-thiophene-2-carboxamide
ChEMBLCHEMBL2041933
DrugBankDB12242
ZINCZINC000033359230
PDB chain2ydj Chain B Residue 1270 [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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PDB2ydj 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.
Resolution1.85 Å
Binding residue
(original residue number in PDB)		L15 Y20 A36 E85 Y86 C87 G90 E134 N135 L137 D148
Binding residue
(residue number reindexed from 1)		L7 Y12 A28 E69 Y70 C71 G74 E118 N119 L121 D132
Annotation score1
Binding affinityMOAD: ic50=0.005uM
BindingDB: IC50=6.0nM,EC50=10nM
Enzymatic activity
Catalytic site (original residue number in PDB) D130 K132 E134 N135 D148 T170
Catalytic site (residue number reindexed from 1) D114 K116 E118 N119 D132 T154
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
View graph for
Biological Process
External links
PDB RCSB:2ydj, PDBe:2ydj, PDBj:2ydj
PDBsum2ydj
PubMed22551018
UniProtO14757|CHK1_HUMAN Serine/threonine-protein kinase Chk1 (Gene Name=CHEK1)

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