Structure of PDB 4qtd Chain A Binding Site BS01

Receptor Information
>4qtd Chain A (length=355) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RDNNFYSVEIGDSTFTVLKRYQNLKPIGSGAQGIVCAAYDAILERNVAIK
KLSRPFQNQTHAKRAYRELVLMKCVNHKNIIGLLNVFTPQKSLEEFQDVY
IVMELMDANLCQVIQMELDHERMSYLLYQMLCGIKHLHSAGIIHRDLKPS
NIVVKSDCTLKILDFGLARTSFMMTPYVVTRYYRAPEVILGMGYKENVDL
WSVGCIMGEMVCHKILFPGRDYIDQWNKVIEQLGTPCPEFMKKLQPTVRT
YVENRPKYAGYSFEKLFPDVLFPADSEHNKLKASQARDLLSKMLVIDASK
RISVDEALQHPYINVWYDPSEAEAPPPKIPDKQLDEREHTIEEWKELIYK
EVMDL
Ligand information
Ligand ID38Z
InChIInChI=1S/C33H33N9O2/c43-30(42-18-16-41(17-19-42)27-5-2-24(3-6-27)32-35-11-1-12-36-32)22-40-15-10-25(21-40)33(44)37-26-4-7-29-28(20-26)31(39-38-29)23-8-13-34-14-9-23/h1-9,11-14,20,25H,10,15-19,21-22H2,(H,37,44)(H,38,39)/t25-/m1/s1
InChIKeyHDAJDNHIBCDLQF-RUZDIDTESA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6c1cnc(nc1)c2ccc(cc2)N3CCN(CC3)C(=O)CN4CCC(C4)C(=O)Nc5ccc6c(c5)c([nH]n6)c7ccncc7
OpenEye OEToolkits 1.7.6c1cnc(nc1)c2ccc(cc2)N3CCN(CC3)C(=O)CN4CC[C@H](C4)C(=O)Nc5ccc6c(c5)c([nH]n6)c7ccncc7
CACTVS 3.385O=C(CN1CC[CH](C1)C(=O)Nc2ccc3n[nH]c(c4ccncc4)c3c2)N5CCN(CC5)c6ccc(cc6)c7ncccn7
CACTVS 3.385O=C(CN1CC[C@H](C1)C(=O)Nc2ccc3n[nH]c(c4ccncc4)c3c2)N5CCN(CC5)c6ccc(cc6)c7ncccn7
ACDLabs 12.01O=C(N3CCN(c2ccc(c1ncccn1)cc2)CC3)CN7CCC(C(=O)Nc5cc6c(c4ccncc4)nnc6cc5)C7
FormulaC33 H33 N9 O2
Name(3R)-1-(2-oxo-2-{4-[4-(pyrimidin-2-yl)phenyl]piperazin-1-yl}ethyl)-N-[3-(pyridin-4-yl)-2H-indazol-5-yl]pyrrolidine-3-carboxamide
ChEMBLCHEMBL3590107
DrugBank
ZINCZINC000096174209
PDB chain4qtd Chain A Residue 424 [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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PDB4qtd A unique inhibitor binding site in ERK1/2 is associated with slow binding kinetics.
Resolution1.5 Å
Binding residue
(original residue number in PDB)		V40 A53 M108 L110 M111 D112 A113 N114 C116 Q117 Q120 S155 N156 L168
Binding residue
(residue number reindexed from 1)		V35 A48 M103 L105 M106 D107 A108 N109 C111 Q112 Q115 S150 N151 L163
Annotation score1
Binding affinityMOAD: ic50=1080nM
PDBbind-CN: -logKd/Ki=5.97,IC50=1080nM
Enzymatic activity
Catalytic site (original residue number in PDB) D151 K153 N156 D169 T188
Catalytic site (residue number reindexed from 1) D146 K148 N151 D164 T180
Enzyme Commision number 2.7.11.24: mitogen-activated protein kinase.
Gene Ontology
Molecular Function
GO:0004672 protein kinase activity
GO:0004707 MAP 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:4qtd, PDBe:4qtd, PDBj:4qtd
PDBsum4qtd
PubMed25195011
UniProtP45983|MK08_HUMAN Mitogen-activated protein kinase 8 (Gene Name=MAPK8)

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