Structure of PDB 4o6e Chain A Binding Site BS01

Receptor Information
>4o6e Chain A (length=328) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MVRGQVFDVGPRYTNLSYIGEGAYGMVCSAYDNVNKVRVAIKKISPFEHQ
TYCQRTLREIKILLRFRHENIIGINDIIRAPTIEQMKDVYIVQDLMETDL
YKLLKTQHLSNDHICYFLYQILRGLKYIHSANVLHRDLKPSNLLLNTTCD
LKICDFGLARVADPVATRWYRAPEIMLNYTKSIDIWSVGCILAEMLSNRP
IFPGKHYLDQLNHILGILGSPSQEDLNCIINLKARNYLLSLPHKNKVPWN
RLFPNADSKALDLLDKMLTFNPHKRIEVEQALAHPYLEQYYDPSDEPIAE
APFKELDDLPKEKLKELIFEETARFQPG
Ligand information
Ligand ID2SH
InChIInChI=1S/C21H25ClFN5O3/c22-16-9-13(1-2-17(16)23)19(12-29)27-21(30)28-6-3-14-10-24-20(26-18(14)11-28)25-15-4-7-31-8-5-15/h1-2,9-10,15,19,29H,3-8,11-12H2,(H,27,30)(H,24,25,26)/t19-/m1/s1
InChIKeyQTZUMCMRRPENJM-LJQANCHMSA-N
SMILES
SoftwareSMILES
CACTVS 3.385OC[C@@H](NC(=O)N1CCc2cnc(NC3CCOCC3)nc2C1)c4ccc(F)c(Cl)c4
OpenEye OEToolkits 1.7.6c1cc(c(cc1[C@@H](CO)NC(=O)N2CCc3cnc(nc3C2)NC4CCOCC4)Cl)F
CACTVS 3.385OC[CH](NC(=O)N1CCc2cnc(NC3CCOCC3)nc2C1)c4ccc(F)c(Cl)c4
ACDLabs 12.01Fc1ccc(cc1Cl)C(NC(=O)N3Cc2nc(ncc2CC3)NC4CCOCC4)CO
OpenEye OEToolkits 1.7.6c1cc(c(cc1C(CO)NC(=O)N2CCc3cnc(nc3C2)NC4CCOCC4)Cl)F
FormulaC21 H25 Cl F N5 O3
NameN-[(1S)-1-(3-chloro-4-fluorophenyl)-2-hydroxyethyl]-2-(tetrahydro-2H-pyran-4-ylamino)-5,8-dihydropyrido[3,4-d]pyrimidine-7(6H)-carboxamide
ChEMBLCHEMBL3298414
DrugBank
ZINCZINC000098208260
PDB chain4o6e Chain A Residue 401 [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]
PDB4o6e Discovery of 5,6,7,8-tetrahydropyrido[3,4-d]pyrimidine inhibitors of Erk2.
Resolution1.95 Å
Binding residue
(original residue number in PDB)		E33 G34 G37 V39 A52 K54 Q105 M108 E109 T110 K114 N154 L156 D167
Binding residue
(residue number reindexed from 1)		E21 G22 G25 V27 A40 K42 Q93 M96 E97 T98 K102 N142 L144 D155
Annotation score1
Binding affinityMOAD: ic50=1nM
PDBbind-CN: -logKd/Ki=9.00,IC50=1nM
BindingDB: IC50=1.000000nM,Ki=0.400000nM
Enzymatic activity
Catalytic site (original residue number in PDB) D149 K151 S153 N154 D167 T190
Catalytic site (residue number reindexed from 1) D137 K139 S141 N142 D155 T167
Enzyme Commision number 2.7.11.24: mitogen-activated protein kinase.
Gene Ontology
Molecular Function
GO:0001784 phosphotyrosine residue binding
GO:0003677 DNA binding
GO:0004672 protein kinase activity
GO:0004674 protein serine/threonine kinase activity
GO:0004707 MAP kinase activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0008353 RNA polymerase II CTD heptapeptide repeat kinase activity
GO:0016301 kinase activity
GO:0019902 phosphatase binding
GO:0042802 identical protein binding
GO:0106310 protein serine kinase activity
Biological Process
GO:0000165 MAPK cascade
GO:0006357 regulation of transcription by RNA polymerase II
GO:0006468 protein phosphorylation
GO:0006915 apoptotic process
GO:0006935 chemotaxis
GO:0006974 DNA damage response
GO:0007165 signal transduction
GO:0007166 cell surface receptor signaling pathway
GO:0007268 chemical synaptic transmission
GO:0007507 heart development
GO:0007611 learning or memory
GO:0008286 insulin receptor signaling pathway
GO:0009887 animal organ morphogenesis
GO:0010759 positive regulation of macrophage chemotaxis
GO:0010800 positive regulation of peptidyl-threonine phosphorylation
GO:0014032 neural crest cell development
GO:0014044 Schwann cell development
GO:0016310 phosphorylation
GO:0018105 peptidyl-serine phosphorylation
GO:0018107 peptidyl-threonine phosphorylation
GO:0019858 cytosine metabolic process
GO:0030278 regulation of ossification
GO:0030521 androgen receptor signaling pathway
GO:0030641 regulation of cellular pH
GO:0030878 thyroid gland development
GO:0031647 regulation of protein stability
GO:0031663 lipopolysaccharide-mediated signaling pathway
GO:0032206 positive regulation of telomere maintenance
GO:0032496 response to lipopolysaccharide
GO:0032872 regulation of stress-activated MAPK cascade
GO:0033554 cellular response to stress
GO:0033598 mammary gland epithelial cell proliferation
GO:0034198 cellular response to amino acid starvation
GO:0035094 response to nicotine
GO:0035556 intracellular signal transduction
GO:0038127 ERBB signaling pathway
GO:0038133 ERBB2-ERBB3 signaling pathway
GO:0042473 outer ear morphogenesis
GO:0042552 myelination
GO:0043330 response to exogenous dsRNA
GO:0043401 steroid hormone receptor signaling pathway
GO:0045542 positive regulation of cholesterol biosynthetic process
GO:0045596 negative regulation of cell differentiation
GO:0048009 insulin-like growth factor receptor signaling pathway
GO:0048538 thymus development
GO:0050847 progesterone receptor signaling pathway
GO:0050852 T cell receptor signaling pathway
GO:0050853 B cell receptor signaling pathway
GO:0051403 stress-activated MAPK cascade
GO:0051493 regulation of cytoskeleton organization
GO:0060020 Bergmann glial cell differentiation
GO:0060291 long-term synaptic potentiation
GO:0060324 face development
GO:0060425 lung morphogenesis
GO:0060440 trachea formation
GO:0060716 labyrinthine layer blood vessel development
GO:0061308 cardiac neural crest cell development involved in heart development
GO:0070371 ERK1 and ERK2 cascade
GO:0070849 response to epidermal growth factor
GO:0071356 cellular response to tumor necrosis factor
GO:0072584 caveolin-mediated endocytosis
GO:0090170 regulation of Golgi inheritance
GO:0120041 positive regulation of macrophage proliferation
GO:2000641 regulation of early endosome to late endosome transport
Cellular Component
GO:0005576 extracellular region
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005739 mitochondrion
GO:0005769 early endosome
GO:0005770 late endosome
GO:0005788 endoplasmic reticulum lumen
GO:0005794 Golgi apparatus
GO:0005813 centrosome
GO:0005819 spindle
GO:0005829 cytosol
GO:0005856 cytoskeleton
GO:0005886 plasma membrane
GO:0005901 caveola
GO:0005925 focal adhesion
GO:0016020 membrane
GO:0031143 pseudopodium
GO:0035578 azurophil granule lumen
GO:0045202 synapse
GO:0070161 anchoring junction
GO:0072686 mitotic spindle
GO:1904813 ficolin-1-rich granule lumen

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4o6e, PDBe:4o6e, PDBj:4o6e
PDBsum4o6e
PubMed24813737
UniProtP28482|MK01_HUMAN Mitogen-activated protein kinase 1 (Gene Name=MAPK1)

[Back to BioLiP]