Structure of PDB 8pt3 Chain A Binding Site BS01

Receptor Information

>8pt3 Chain A (length=344) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

GPEMVRGQVFDVGPRYTNLSYIGEGAYGMVCSAYDNVNKVRVAIKKISPF
EHQTYCQRTLREIKILLRFRHENIIGINDIIRAPTIEQMKDVYIVQDLME
TDLYKLLKTQHLSNDHICYFLYQILRGLKYIHSANVLHRDLKPSNLLLNT
TCDLKICDFGLARVADPFLTEYVATRWYRAPEIMLNSKGYTKSIDIWSVG
CILAEMLSNRPIFPGKHYLDQLNHILGILGSPSQEDLNCIINLKARNYLL
SLPHKNKVPWNRLFPNADSKALDLLDKMLTFNPHKRIEVEQALAHPYLEQ
YYDPSDEPIAEAPFKFDMELDDLPKEKLKELIFEETARFQPGYR

Ligand information

Ligand ID

D7O

InChI

InChI=1S/C16H22O5/c1-9-6-16(14(19)20-5)7-10(9)12(17)11(8-16)13(18)21-15(2,3)4/h10-11H,1,6-8H2,2-5H3/t10-,11+,16+/m1/s1

InChIKey

ILHZGEBKECHEND-GDLVEWKHSA-N

SMILES

Software	SMILES
OpenEye OEToolkits 2.0.7	CC(C)(C)OC(=O)[C@H]1C[C@]2(C[C@@H](C1=O)C(=C)C2)C(=O)OC
CACTVS 3.385	COC(=O)[C]12C[CH](C(=C)C1)C(=O)[CH](C2)C(=O)OC(C)(C)C
OpenEye OEToolkits 2.0.7	CC(C)(C)OC(=O)C1CC2(CC(C1=O)C(=C)C2)C(=O)OC
CACTVS 3.385	COC(=O)[C@]12C[C@H](C(=C)C1)C(=O)[C@H](C2)C(=O)OC(C)(C)C

Formula

C16 H22 O5

Name

~{O}3-~{tert}-butyl ~{O}1-methyl (1~{S},3~{S},5~{R})-6-methylidene-4-oxidanylidene-bicyclo[3.2.1]octane-1,3-dicarboxylate

ChEMBL

DrugBank

ZINC

PDB chain

8pt3 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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Structure summary

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PDB	8pt3 Targeting a key protein-protein interaction surface on mitogen-activated protein kinases by a Michael acceptor-based cyclic warhead scaffold
Resolution	1.8 Å
Binding residue (original residue number in PDB)	Q119 D124 H125 F129 C161
Binding residue (residue number reindexed from 1)	Q110 D115 H116 F120 C152
Annotation score	1

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

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External links

PDB	RCSB:8pt3, PDBe:8pt3, PDBj:8pt3
PDBsum	8pt3
PubMed
UniProt	P28482\|MK01_HUMAN Mitogen-activated protein kinase 1 (Gene Name=MAPK1)

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