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- PDB-4qpa: Crystal Structure of ERK2 in complex with 7-(1-benzyl-1H-pyrazol-... -

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Basic information

Entry
Database: PDB / ID: 4qpa
TitleCrystal Structure of ERK2 in complex with 7-(1-benzyl-1H-pyrazol-4-yl)-2-(pyridin-4-yl)-5H-pyrrolo[2,3-b]pyrazine
ComponentsMitogen-activated protein kinase 1
Keywordstransferase/transferase inhibitor / Kinase / transferase-transferase inhibitor complex
Function / homology
Function and homology information


phospho-PLA2 pathway / Signaling by MAPK mutants / Suppression of apoptosis / RAF-independent MAPK1/3 activation / Signaling by Activin / Gastrin-CREB signalling pathway via PKC and MAPK / cardiac neural crest cell development involved in heart development / caveolin-mediated endocytosis / cytosine metabolic process / ERKs are inactivated ...phospho-PLA2 pathway / Signaling by MAPK mutants / Suppression of apoptosis / RAF-independent MAPK1/3 activation / Signaling by Activin / Gastrin-CREB signalling pathway via PKC and MAPK / cardiac neural crest cell development involved in heart development / caveolin-mediated endocytosis / cytosine metabolic process / ERKs are inactivated / response to epidermal growth factor / Signaling by MAP2K mutants / Signaling by NODAL / RSK activation / Golgi Cisternae Pericentriolar Stack Reorganization / regulation of cellular pH / positive regulation of macrophage proliferation / outer ear morphogenesis / Regulation of the apoptosome activity / regulation of Golgi inheritance / 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 / regulation of stress-activated MAPK cascade / IFNG signaling activates MAPKs / Frs2-mediated activation / positive regulation of macrophage chemotaxis / lung morphogenesis / ERBB2-ERBB3 signaling pathway / response to exogenous dsRNA / regulation of cytoskeleton organization / face development / Activation of the AP-1 family of transcription factors / androgen receptor signaling pathway / ERK/MAPK targets / RUNX2 regulates osteoblast differentiation / pseudopodium / Recycling pathway of L1 / progesterone receptor signaling pathway / positive regulation of telomere capping / MAPK1 (ERK2) activation / negative regulation of cell differentiation / Bergmann glial cell differentiation / thyroid gland development / Advanced glycosylation endproduct receptor signaling / steroid hormone mediated signaling pathway / RHO GTPases Activate NADPH Oxidases / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / Regulation of HSF1-mediated heat shock response / regulation of ossification / RHO GTPases Activate WASPs and WAVEs / MAP kinase activity / mitogen-activated protein kinase / phosphatase binding / Signal attenuation / Estrogen-stimulated signaling through PRKCZ / Nuclear events stimulated by ALK signaling in cancer / stress-activated MAPK cascade / Schwann cell development / Growth hormone receptor signaling / lipopolysaccharide-mediated signaling pathway / positive regulation of telomerase activity / ERK1 and ERK2 cascade / cellular response to cadmium ion / cellular response to amino acid starvation / positive regulation of telomere maintenance via telomerase / myelination / NPAS4 regulates expression of target genes / NCAM signaling for neurite out-growth / phosphotyrosine residue binding / ESR-mediated signaling / RNA polymerase II CTD heptapeptide repeat kinase activity / insulin-like growth factor receptor signaling pathway / thymus development / response to nicotine / positive regulation of peptidyl-threonine phosphorylation / Regulation of PTEN gene transcription / Signal transduction by L1 / long-term synaptic potentiation / caveola / Negative regulation of FGFR3 signaling / Downregulation of SMAD2/3:SMAD4 transcriptional activity / FCERI mediated MAPK activation / Negative regulation of FGFR2 signaling / Negative regulation of FGFR4 signaling / FCGR3A-mediated phagocytosis / Negative regulation of FGFR1 signaling / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / B cell receptor signaling pathway / Spry regulation of FGF signaling / peptidyl-threonine phosphorylation / Signaling by high-kinase activity BRAF mutants / regulation of protein stability / MAP2K and MAPK activation / Oncogene Induced Senescence / mitotic spindle / Regulation of actin dynamics for phagocytic cup formation
Similarity search - Function
Mitogen-activated protein (MAP) kinase, ERK1/2 / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain ...Mitogen-activated protein (MAP) kinase, ERK1/2 / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; 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
Chem-35W / Mitogen-activated protein kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 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

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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)85,9604
Polymers85,2562
Non-polymers7052
Water0
1
A: Mitogen-activated protein kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9802
Polymers42,6281
Non-polymers3521
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Mitogen-activated protein kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9802
Polymers42,6281
Non-polymers3521
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)82.703, 82.703, 275.892
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-35W / 7-(1-benzyl-1H-pyrazol-4-yl)-2-(pyridin-4-yl)-5H-pyrrolo[2,3-b]pyrazine


Mass: 352.392 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H16N6

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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: 2.77 Å3/Da / Density % sol: 55.54 %

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 20, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.85→50 Å / Num. all: 23316 / Num. obs: 23246 / % possible obs: 99.7 % / 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
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.85→49.348 Å / SU ML: 0.37 / σ(F): 1.43 / Phase error: 24.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2526 1077 5.06 %random
Rwork0.2118 ---
obs0.2138 23225 99.71 %-
all-23316 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.85→49.348 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5540 0 54 0 5594
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045731
X-RAY DIFFRACTIONf_angle_d0.9067769
X-RAY DIFFRACTIONf_dihedral_angle_d13.3272153
X-RAY DIFFRACTIONf_chiral_restr0.071846
X-RAY DIFFRACTIONf_plane_restr0.004993
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8501-2.91640.34021520.31892635X-RAY DIFFRACTION99
2.9164-2.98930.32761530.30042697X-RAY DIFFRACTION100
2.9893-3.07020.31451480.26812715X-RAY DIFFRACTION100
3.0702-3.16050.28561440.25012673X-RAY DIFFRACTION100
3.1605-3.26250.29441370.24822674X-RAY DIFFRACTION100
3.2625-3.37910.27011390.23522688X-RAY DIFFRACTION100
3.3791-3.51430.27171560.22822672X-RAY DIFFRACTION100
3.5143-3.67420.23131350.20812724X-RAY DIFFRACTION100
3.6742-3.86790.25511680.18962664X-RAY DIFFRACTION100
3.8679-4.11010.23491420.18782724X-RAY DIFFRACTION100
4.1101-4.42720.24821680.19032666X-RAY DIFFRACTION100
4.4272-4.87240.22331610.17122710X-RAY DIFFRACTION100
4.8724-5.57660.21331290.19382700X-RAY DIFFRACTION100
5.5766-7.02270.26051100.2232714X-RAY DIFFRACTION100
7.0227-49.35490.21531120.19552718X-RAY DIFFRACTION99
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)
10.4801-0.20110.18720.43280.12060.9102-0.089-0.00160.01550.18860.102-0.28580.42250.0118-0.00540.39970.1413-0.06260.26650.01430.38973.3381-61.9083-53.4756
21.4007-0.1520.61541.36750.92273.1129-0.1495-0.04360.00170.00610.03630.1004-0.3674-0.442-0.01280.36330.0119-0.03060.3883-0.02720.336-12.2833-42.0216-62.8573
32.24090.44640.59962.52290.82631.4141-0.9293-0.3895-0.2569-0.2531.06210.5844-0.11970.58750.0584-0.02270.64390.13450.35470.1940.3728-21.3914-28.8278-18.5307
42.2544-0.33270.30181.8743-0.40911.7254-0.126-0.14010.12210.01090.0183-0.1543-0.02040.1963-0.00040.20120.03310.01550.2552-0.020.26765.0257-31.7709-27.5464
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 10:108 OR RESID 335:355 ) )A10 - 108
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 10:108 OR RESID 335:355 ) )A335 - 355
3X-RAY DIFFRACTION2( CHAIN A AND RESID 109:334 )A109 - 334
4X-RAY DIFFRACTION3( CHAIN B AND ( RESID 10:108 OR RESID 335:358 ) )B10 - 108
5X-RAY DIFFRACTION3( CHAIN B AND ( RESID 10:108 OR RESID 335:358 ) )B335 - 358
6X-RAY DIFFRACTION4( CHAIN B AND RESID 109:334 )B109 - 334

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