Structure of PDB 2ym5 Chain A Binding Site BS01

Receptor Information
>2ym5 Chain A (length=248) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DWDLVQTLGEVQLAVNRVTEEAVAVKIVDMNIKKEICINKMLNHENVVKF
YGHRREIQYLFLEYCSGGELFDRIEPDIGMPEPDAQRFFHQLMAGVVYLH
GIGITHRDIKPENLLLDERDNLKISDFGLATVFRYNNRERLLNKMCGTLP
YVAPELLKRREFHAEPVDVWSCGIVLTAMLAGELPWDQPSDSCQEYSDWK
EKKTYLNPWKKIDSAPLALLHKILVENPSARITIPDIKKDRWYNKPLK
Ligand information
Ligand IDYM5
InChIInChI=1S/C18H21N5O2/c19-7-14-9-23(4-5-25-14)18-16-15(8-20-17(16)21-11-22-18)13-3-1-2-12(6-13)10-24/h1-3,6,8,11,14,24H,4-5,7,9-10,19H2,(H,20,21,22)/t14-/m0/s1
InChIKeyXYTDDDZEIXYDNO-AWEZNQCLSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.9.2c1cc(cc(c1)c2c[nH]c3c2c(ncn3)N4CCOC(C4)CN)CO
OpenEye OEToolkits 1.9.2c1cc(cc(c1)c2c[nH]c3c2c(ncn3)N4CCO[C@H](C4)CN)CO
CACTVS 3.385NC[CH]1CN(CCO1)c2ncnc3[nH]cc(c4cccc(CO)c4)c23
ACDLabs 12.01n1cnc4c(c1N2CC(OCC2)CN)c(c3cccc(c3)CO)cn4
CACTVS 3.385NC[C@H]1CN(CCO1)c2ncnc3[nH]cc(c4cccc(CO)c4)c23
FormulaC18 H21 N5 O2
Name(3-{4-[(2S)-2-(AMINOMETHYL)MORPHOLIN-4-YL]-7H-PYRROLO[2,3-D]PYRIMIDIN-5-YL}PHENYL)METHANOL
ChEMBL
DrugBank
ZINCZINC000082155053
PDB chain2ym5 Chain A Residue 1271 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB2ym5 Structure-Guided Evolution of Potent and Selective Chk1 Inhibitors Through Scaffold Morphing.
Resolution2.03 Å
Binding residue
(original residue number in PDB)		V23 A36 E85 Y86 C87 E91 L137 S147
Binding residue
(residue number reindexed from 1)		V11 A24 E63 Y64 C65 E69 L115 S125
Annotation score1
Binding affinityMOAD: ic50=0.43uM
PDBbind-CN: -logKd/Ki=6.37,IC50=0.43uM
BindingDB: IC50=430nM
Enzymatic activity
Catalytic site (original residue number in PDB) D130 K132 E134 N135 D148 T170
Catalytic site (residue number reindexed from 1) D108 K110 E112 N113 D126 T148
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:2ym5, PDBe:2ym5, PDBj:2ym5
PDBsum2ym5
PubMed22111927
UniProtO14757|CHK1_HUMAN Serine/threonine-protein kinase Chk1 (Gene Name=CHEK1)

[Back to BioLiP]