Structure of PDB 4i5m Chain A Binding Site BS01

Receptor Information
>4i5m Chain A (length=273) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RIIVDPTTGKRYSRGKTLGKGGFAKCYEMTDLTNNKVYAAKIIPHSRVSK
PHQREKIDKEIELHRILHHKHVVQFYHYFEDKENIYILLEYCSRRSMAHI
LKARKVLTEPEVRYYLRQIVSGLKYLHEQEILHRDLKLGNFFINESMELK
VGDFGLAARLETPNYLSPEVLNKQGHGAESDIWALGCVMYTMLLGRPPFE
TTNLKETYRSIREARYTMPSSLLAPAKHLIASMLSKNPEDRPSLDDIIRH
DFFTQGFTPDRLSSSCCHTVPDF
Ligand information
Ligand IDR78
InChIInChI=1S/C28H39N7O3/c1-5-22-27(37)34(3)23-17-29-28(32-25(23)35(22)20-8-6-7-9-20)31-21-11-10-18(16-24(21)38-4)26(36)30-19-12-14-33(2)15-13-19/h10-11,16-17,19-20,22H,5-9,12-15H2,1-4H3,(H,30,36)(H,29,31,32)/t22-/m1/s1
InChIKeyXQVVPGYIWAGRNI-JOCHJYFZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CC[C@@H]1C(=O)N(c2cnc(nc2N1C3CCCC3)Nc4ccc(cc4OC)C(=O)NC5CCN(CC5)C)C
OpenEye OEToolkits 1.5.0CCC1C(=O)N(c2cnc(nc2N1C3CCCC3)Nc4ccc(cc4OC)C(=O)NC5CCN(CC5)C)C
CACTVS 3.341CC[CH]1N(C2CCCC2)c3nc(Nc4ccc(cc4OC)C(=O)NC5CCN(C)CC5)ncc3N(C)C1=O
ACDLabs 10.04O=C5N(c1c(nc(nc1)Nc3ccc(C(=O)NC2CCN(C)CC2)cc3OC)N(C4CCCC4)C5CC)C
CACTVS 3.341CC[C@H]1N(C2CCCC2)c3nc(Nc4ccc(cc4OC)C(=O)NC5CCN(C)CC5)ncc3N(C)C1=O
FormulaC28 H39 N7 O3
Name4-{[(7R)-8-cyclopentyl-7-ethyl-5-methyl-6-oxo-5,6,7,8-tetrahydropteridin-2-yl]amino}-3-methoxy-N-(1-methylpiperidin-4-yl)benzamide
ChEMBLCHEMBL513909
DrugBankDB16107
ZINCZINC000013986815
PDB chain4i5m Chain A Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4i5m Selective and brain-permeable polo-like kinase-2 (Plk-2) inhibitors that reduce alpha-synuclein phosphorylation in rat brain.
Resolution1.801 Å
Binding residue
(original residue number in PDB)		K57 L59 K61 C67 A80 K82 L130 E131 Y132 C133 S134 R136 F183
Binding residue
(residue number reindexed from 1)		K16 L18 K20 C26 A39 K41 L89 E90 Y91 C92 S93 R95 F142
Annotation score1
Binding affinityMOAD: ic50=0.0088uM
PDBbind-CN: -logKd/Ki=8.06,IC50=8.8nM
BindingDB: IC50=14nM,Ki=<1nM,Kd=0.810000nM
Enzymatic activity
Catalytic site (original residue number in PDB) D176 K178 G180 N181 D194 T214
Catalytic site (residue number reindexed from 1) D135 K137 G139 N140 D153 T162
Enzyme Commision number 2.7.11.21: polo kinase.
Gene Ontology
Molecular Function
GO:0004672 protein kinase activity
GO:0005524 ATP binding
Biological Process
GO:0006468 protein phosphorylation

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Molecular Function
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Biological Process
External links
PDB RCSB:4i5m, PDBe:4i5m, PDBj:4i5m
PDBsum4i5m
PubMed23794260
UniProtQ9NYY3|PLK2_HUMAN Serine/threonine-protein kinase PLK2 (Gene Name=PLK2)

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