Structure of PDB 1ny3 Chain A Binding Site BS01

Receptor Information

>1ny3 Chain A (length=277) Species: 9606 (Homo sapiens)

FHVKSGLQIKKNAIIDDYKVTSQVLGLGINGKVLQIFNKRTQEKFALKML
QDCPKARREVELHWRASQCPHIVRIVDVYENLYAGRKCLLIVMECLDGGE
LFSRIQDTEREASEIMKSIGEAIQYLHSINIAHRDVKPENLLYTSKRPNA
ILKLTDFGFAKETTSHPYYVAPEVLGPEKYDKSCDMWSLGVIMYILLCGY
PPFYSGMKTRIRMGQYEFPNPEWSEVSEEVKMLIRNLLKTEPTQRMTITE
FMNHPWIMQSTKVPQTPLHTSRVLKED

Ligand information

• Ligand ID: ADP
• InChI: InChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
• InChIKey: XTWYTFMLZFPYCI-KQYNXXCUSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N
  CACTVS 3.341: Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
  ACDLabs 10.04: O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
  CACTVS 3.341: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
• Formula: C10 H15 N5 O10 P2
• Name: ADENOSINE-5'-DIPHOSPHATE
• ChEMBL: CHEMBL14830
• DrugBank: DB16833
• ZINC: ZINC000012360703
• PDB chain: 1ny3 Chain A Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1ny3 Catalytically active MAP KAP kinase 2 structures in complex with staurosporine and ADP reveal differences with the autoinhibited enzyme
• Resolution: 3.0 Å
• Binding residue (original residue number in PDB): L72 G73 I74 A91 K93 L141 D207
• Binding residue (residue number reindexed from 1): L27 G28 I29 A46 K48 L96 D156
• Annotation score: 5

Enzymatic activity

• Catalytic site (original residue number in PDB): D186 K188 E190 N191 D207 S216
• Catalytic site (residue number reindexed from 1): D135 K137 E139 N140 D156 S165
• 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:0004683 calcium/calmodulin-dependent protein kinase activity
• GO:0005515 protein binding
• GO:0005516 calmodulin binding
• GO:0005524 ATP binding
• GO:0009931 calcium-dependent protein serine/threonine kinase activity
• GO:0044024 histone H2AS1 kinase activity
• GO:0051019 mitogen-activated protein kinase binding
• GO:0106310 protein serine kinase activity

Biological Process

• GO:0000165 MAPK cascade
• GO:0002224 toll-like receptor signaling pathway
• GO:0006338 chromatin remodeling
• GO:0006468 protein phosphorylation
• GO:0006691 leukotriene metabolic process
• GO:0006954 inflammatory response
• GO:0006974 DNA damage response
• GO:0010803 regulation of tumor necrosis factor-mediated signaling pathway
• GO:0016310 phosphorylation
• GO:0018105 peptidyl-serine phosphorylation
• GO:0032496 response to lipopolysaccharide
• GO:0032675 regulation of interleukin-6 production
• GO:0032680 regulation of tumor necrosis factor production
• GO:0032760 positive regulation of tumor necrosis factor production
• GO:0034097 response to cytokine
• GO:0035556 intracellular signal transduction
• GO:0035924 cellular response to vascular endothelial growth factor stimulus
• GO:0038066 p38MAPK cascade
• GO:0043488 regulation of mRNA stability
• GO:0044351 macropinocytosis
• GO:0048010 vascular endothelial growth factor receptor signaling pathway
• GO:0048255 mRNA stabilization
• GO:0048839 inner ear development
• GO:0060907 positive regulation of macrophage cytokine production
• GO:0070935 3'-UTR-mediated mRNA stabilization
• GO:1900034 regulation of cellular response to heat

Cellular Component

• GO:0005634 nucleus
• GO:0005654 nucleoplasm
• GO:0005737 cytoplasm
• GO:0005813 centrosome
• GO:0005829 cytosol
• GO:0070062 extracellular exosome

External links

• PDB: RCSB:1ny3, PDBe:1ny3, PDBj:1ny3
• PDBsum: 1ny3
• PubMed: 12791252
• UniProt: P49137|MAPK2_HUMAN MAP kinase-activated protein kinase 2 (Gene Name=MAPKAPK2)