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- PDB-4qp3: Crystal Structure of ERK2 in complex with (S)-2-((9H-purin-6-yl)a... -

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Basic information

Entry
Database: PDB / ID: 4qp3
TitleCrystal Structure of ERK2 in complex with (S)-2-((9H-purin-6-yl)amino)-3-phenylpropan-1-ol
ComponentsMitogen-activated protein kinase 1
Keywordstransferase/transferase inhibitor / Kinase / transferase-transferase inhibitor complex
Function / homology
Function and homology information


phospho-PLA2 pathway / interleukin-34-mediated signaling pathway / Signaling by MAPK mutants / RAF-independent MAPK1/3 activation / Suppression of apoptosis / Gastrin-CREB signalling pathway via PKC and MAPK / Signaling by Activin / cardiac neural crest cell development involved in heart development / caveolin-mediated endocytosis / cytosine metabolic process ...phospho-PLA2 pathway / interleukin-34-mediated signaling pathway / Signaling by MAPK mutants / RAF-independent MAPK1/3 activation / Suppression of apoptosis / Gastrin-CREB signalling pathway via PKC and MAPK / Signaling by Activin / cardiac neural crest cell development involved in heart development / caveolin-mediated endocytosis / cytosine metabolic process / response to epidermal growth factor / Signaling by NODAL / ERKs are inactivated / Signaling by MAP2K mutants / RSK activation / Golgi Cisternae Pericentriolar Stack Reorganization / Regulation of the apoptosome activity / positive regulation of macrophage proliferation / regulation of cellular pH / outer ear morphogenesis / Signaling by LTK in cancer / regulation of Golgi inheritance / positive regulation of peptidyl-threonine phosphorylation / ERBB signaling pathway / labyrinthine layer blood vessel development / mammary gland epithelial cell proliferation / trachea formation / Negative feedback regulation of MAPK pathway / regulation of early endosome to late endosome transport / IFNG signaling activates MAPKs / regulation of stress-activated MAPK cascade / Frs2-mediated activation / positive regulation of macrophage chemotaxis / ERBB2-ERBB3 signaling pathway / Activation of the AP-1 family of transcription factors / regulation of cytoskeleton organization / ERK/MAPK targets / RUNX2 regulates osteoblast differentiation / response to exogenous dsRNA / MAPK1 (ERK2) activation / pseudopodium / lung morphogenesis / face development / positive regulation of telomere maintenance / Bergmann glial cell differentiation / Recycling pathway of L1 / thyroid gland development / Advanced glycosylation endproduct receptor signaling / peptidyl-threonine phosphorylation / regulation of ossification / MAP kinase activity / negative regulation of cell differentiation / RHO GTPases Activate NADPH Oxidases / Regulation of HSF1-mediated heat shock response / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / mitogen-activated protein kinase / RHO GTPases Activate WASPs and WAVEs / Signal attenuation / phosphatase binding / Growth hormone receptor signaling / Estrogen-stimulated signaling through PRKCZ / Schwann cell development / stress-activated MAPK cascade / Nuclear events stimulated by ALK signaling in cancer / NPAS4 regulates expression of target genes / ERK1 and ERK2 cascade / phosphotyrosine residue binding / myelination / Transcriptional and post-translational regulation of MITF-M expression and activity / NCAM signaling for neurite out-growth / RNA polymerase II CTD heptapeptide repeat kinase activity / insulin-like growth factor receptor signaling pathway / cellular response to amino acid starvation / ESR-mediated signaling / lipopolysaccharide-mediated signaling pathway / thymus development / Regulation of PTEN gene transcription / Signal transduction by L1 / B cell receptor signaling pathway / response to nicotine / FCGR3A-mediated phagocytosis / FCERI mediated MAPK activation / Negative regulation of FGFR3 signaling / Negative regulation of FGFR2 signaling / Negative regulation of FGFR4 signaling / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Negative regulation of FGFR1 signaling / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / positive regulation of cholesterol biosynthetic process / Spry regulation of FGF signaling / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / Oncogene Induced Senescence / caveola / regulation of protein stability / Regulation of actin dynamics for phagocytic cup formation / epidermal growth factor receptor signaling pathway / long-term synaptic potentiation / chemotaxis / Interferon gamma signaling
Similarity search - Function
Mitogen-activated protein (MAP) kinase, ERK1/2 / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / : / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. ...Mitogen-activated protein (MAP) kinase, ERK1/2 / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / : / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
(2S)-3-phenyl-2-(9H-purin-6-ylamino)propan-1-ol / Mitogen-activated protein kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.599 Å
AuthorsYin, J. / Wang, W.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2015
Title: Fragment-based discovery of potent ERK2 pyrrolopyrazine inhibitors.
Authors: Burdick, D.J. / Wang, S. / Heise, C. / Pan, B. / Drummond, J. / Yin, J. / Goeser, L. / Magnuson, S. / Blaney, J. / Moffat, J. / Wang, W. / Chen, H.
History
DepositionJun 22, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 16, 2015Group: Database references
Revision 1.2Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mitogen-activated protein kinase 1
B: Mitogen-activated protein kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,7944
Polymers85,2562
Non-polymers5392
Water2,918162
1
A: Mitogen-activated protein kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8972
Polymers42,6281
Non-polymers2691
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Mitogen-activated protein kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8972
Polymers42,6281
Non-polymers2691
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)83.083, 83.083, 277.013
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Mitogen-activated protein kinase 1 / MAP kinase 1 / MAPK 1 / ERT1 / Extracellular signal-regulated kinase 2 / ERK-2 / MAP kinase isoform ...MAP kinase 1 / MAPK 1 / ERT1 / Extracellular signal-regulated kinase 2 / ERK-2 / MAP kinase isoform p42 / p42-MAPK / Mitogen-activated protein kinase 2 / MAP kinase 2 / MAPK 2


Mass: 42627.828 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAPK1, ERK2, PRKM1, PRKM2 / Production host: Escherichia coli (E. coli)
References: UniProt: P28482, mitogen-activated protein kinase
#2: Chemical ChemComp-36Q / (2S)-3-phenyl-2-(9H-purin-6-ylamino)propan-1-ol


Mass: 269.302 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H15N5O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 56.13 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 10% PEG3350, 0.2 M proline, and 0.1 M HEPES pH7.5, in a 24-well Linbro plates incubated at 4C, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 30, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 2.599→50 Å / Num. all: 30999 / Num. obs: 28860 / % possible obs: 93.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2

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Processing

Software
NameVersionClassification
BOSdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.599→29.831 Å / SU ML: 0.36 / σ(F): 1.34 / Phase error: 26.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2675 1439 5 %random
Rwork0.2214 ---
all0.2237 30999 --
obs0.2237 28853 93.08 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.599→29.831 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5501 0 40 162 5703
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035673
X-RAY DIFFRACTIONf_angle_d0.8777687
X-RAY DIFFRACTIONf_dihedral_angle_d13.1462142
X-RAY DIFFRACTIONf_chiral_restr0.071840
X-RAY DIFFRACTIONf_plane_restr0.003984
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5991-2.6920.35871280.28992807X-RAY DIFFRACTION97
2.692-2.79970.36751390.26362776X-RAY DIFFRACTION97
2.7997-2.9270.29581440.25992754X-RAY DIFFRACTION96
2.927-3.08110.2951550.2572753X-RAY DIFFRACTION95
3.0811-3.2740.31291460.24412731X-RAY DIFFRACTION95
3.274-3.52640.26241560.22182721X-RAY DIFFRACTION94
3.5264-3.88060.27591610.20482696X-RAY DIFFRACTION93
3.8806-4.44050.23131520.19062696X-RAY DIFFRACTION91
4.4405-5.58860.23711460.19982679X-RAY DIFFRACTION89
5.5886-29.83260.24861120.22372728X-RAY DIFFRACTION85
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0221-0.0009-0.00190.00680.00720.0008-0.1374-0.2039-0.10950.14570.13770.08840.00670.03270.01960.20370.4170.09990.39390.1380.2084-21.2044-28.6158-18.6225
20.10680.0261-0.00570.0405-0.02920.1135-0.1627-0.0295-0.0464-0.06530.01210.02110.01440.0862-0.1795-0.05150.1140.08310.0665-0.03970.09455.087-31.9684-27.9562
30.02580.00050.00590.0038-0.01550.0237-0.0226-0.0626-0.04960.13890.0289-0.12580.0618-0.0029-0.00390.39510.0305-0.19240.25850.08290.34712.6232-62.4405-53.518
40.04950.01690.03520.05960.02490.1088-0.0457-0.062-0.03210.04510.0114-0.0685-0.0626-0.2771-0.01860.1359-0.0189-0.0090.2203-0.04780.1344-12.3262-42.0944-63.0292
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 10:108 OR RESID 335:358 ) )A10 - 108
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 10:108 OR RESID 335:358 ) )A335 - 358
3X-RAY DIFFRACTION2( CHAIN A AND RESID 109:334 )A109 - 334
4X-RAY DIFFRACTION3( CHAIN B AND ( RESID 10:108 OR RESID 335:355 ) )B10 - 108
5X-RAY DIFFRACTION3( CHAIN B AND ( RESID 10:108 OR RESID 335:355 ) )B335 - 355
6X-RAY DIFFRACTION4( CHAIN B AND RESID 109:334 )B109 - 334

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