Structure of PDB 2ydk Chain A Binding Site BS01

Receptor Information
>2ydk Chain A (length=263) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VPFVEDWDLVQTLGEGAYGEVQLAVNRVTEEAVAVKIVDMKRENIKKEIC
INKMLNHENVVKFYGHRREGNIQYLFLEYCSGGELFDRIEPDIGMPEPDA
QRFFHQLMAGVVYLHGIGITHRDIKPENLLLDERDNLKISDFGLATVFRY
NNRERLLNKMCGTLPYVAPELLKRREFHAEPVDVWSCGIVLTAMLAGELP
WDQPSDSCQEYSDWKEKKTYLNPWKKIDSAPLALLHKILVENPSARITIP
DIKKDRWYNKPLK
Ligand information
Ligand IDYDK
InChIInChI=1S/C17H20N4O2S/c18-17(23)21-16-13(15(22)20-12-7-4-8-19-10-12)9-14(24-16)11-5-2-1-3-6-11/h1-3,5-6,9,12,19H,4,7-8,10H2,(H,20,22)(H3,18,21,23)/t12-/m0/s1
InChIKeyUXZRCIBKIDILEF-LBPRGKRZSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=C(Nc2sc(cc2C(=O)NC1CCCNC1)c3ccccc3)N
CACTVS 3.370NC(=O)Nc1sc(cc1C(=O)N[CH]2CCCNC2)c3ccccc3
OpenEye OEToolkits 1.7.0c1ccc(cc1)c2cc(c(s2)NC(=O)N)C(=O)NC3CCCNC3
OpenEye OEToolkits 1.7.0c1ccc(cc1)c2cc(c(s2)NC(=O)N)C(=O)N[C@H]3CCCNC3
CACTVS 3.370NC(=O)Nc1sc(cc1C(=O)N[C@H]2CCCNC2)c3ccccc3
FormulaC17 H20 N4 O2 S
Name2-(CARBAMOYLAMINO)-5-PHENYL-N-[(3S)-PIPERIDIN-3-YL]THIOPHENE-3-CARBOXAMIDE
ChEMBLCHEMBL487273
DrugBank
ZINCZINC000045498140
PDB chain2ydk Chain A Residue 1277 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2ydk 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.
Resolution1.9 Å
Binding residue
(original residue number in PDB)		L15 A36 E85 Y86 C87 G90 E134 N135 L137 D148
Binding residue
(residue number reindexed from 1)		L13 A34 E78 Y79 C80 G83 E127 N128 L130 D141
Annotation score1
Binding affinityMOAD: ic50=0.007uM
PDBbind-CN: -logKd/Ki=8.15,IC50=7nM
BindingDB: IC50=7nM,EC50=20nM
Enzymatic activity
Catalytic site (original residue number in PDB) D130 K132 E134 N135 D148 T170
Catalytic site (residue number reindexed from 1) D123 K125 E127 N128 D141 T163
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

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Molecular Function
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Biological Process
External links
PDB RCSB:2ydk, PDBe:2ydk, PDBj:2ydk
PDBsum2ydk
PubMed22551018
UniProtO14757|CHK1_HUMAN Serine/threonine-protein kinase Chk1 (Gene Name=CHEK1)

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