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- PDB-2vo7: Structure of PKA complexed with 4-(4-Chlorobenzyl)-1-(7H-pyrrolo(... -

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Basic information

Entry
Database: PDB / ID: 2vo7
TitleStructure of PKA complexed with 4-(4-Chlorobenzyl)-1-(7H-pyrrolo(2,3- d)pyrimidin-4-yl)piperidin-4-ylamine
Components
  • CAMP-DEPENDENT PROTEIN KINASE INHIBITOR ALPHA
  • CAMP-DEPENDENT PROTEIN KINASE, ALPHA-CATALYTIC SUBUNIT
KeywordsTRANSFERASE / LIPOPROTEIN / ATP-BINDING / PHOSPHOPROTEIN / SERINE/THREONINE-PROTEIN KINASE / NUCLEOTIDE-BINDING / PROTEIN KINASE INHIBITOR / CAMP / KINASE / NUCLEUS / MYRISTATE / CYTOPLASM
Function / homology
Function and homology information


CD209 (DC-SIGN) signaling / HDL assembly / Regulation of insulin secretion / Rap1 signalling / Ion homeostasis / negative regulation of cAMP-dependent protein kinase activity / PKA activation in glucagon signalling / DARPP-32 events / CREB1 phosphorylation through the activation of Adenylate Cyclase / GPER1 signaling ...CD209 (DC-SIGN) signaling / HDL assembly / Regulation of insulin secretion / Rap1 signalling / Ion homeostasis / negative regulation of cAMP-dependent protein kinase activity / PKA activation in glucagon signalling / DARPP-32 events / CREB1 phosphorylation through the activation of Adenylate Cyclase / GPER1 signaling / Factors involved in megakaryocyte development and platelet production / Loss of Nlp from mitotic centrosomes / Recruitment of mitotic centrosome proteins and complexes / Loss of proteins required for interphase microtubule organization from the centrosome / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 / RET signaling / Recruitment of NuMA to mitotic centrosomes / Interleukin-3, Interleukin-5 and GM-CSF signaling / VEGFA-VEGFR2 Pathway / PKA activation / Regulation of PLK1 Activity at G2/M Transition / MAPK6/MAPK4 signaling / GLI3 is processed to GLI3R by the proteasome / Hedgehog 'off' state / cAMP-dependent protein kinase inhibitor activity / histone H1-4S35 kinase activity / cAMP-dependent protein kinase / regulation of protein processing / dorsal/ventral neural tube patterning / cAMP-dependent protein kinase activity / cellular response to parathyroid hormone stimulus / protein localization to lipid droplet / negative regulation of protein import into nucleus / regulation of bicellular tight junction assembly / cAMP-dependent protein kinase complex / interleukin-2-mediated signaling pathway / Mitochondrial protein degradation / sperm capacitation / regulation of osteoblast differentiation / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / cellular response to cold / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / Vasopressin regulates renal water homeostasis via Aquaporins / protein kinase A regulatory subunit binding / negative regulation of glycolytic process through fructose-6-phosphate / ciliary base / protein kinase A catalytic subunit binding / intracellular potassium ion homeostasis / TORC1 signaling / mesoderm formation / plasma membrane raft / axoneme / sperm flagellum / postsynaptic modulation of chemical synaptic transmission / regulation of G2/M transition of mitotic cell cycle / negative regulation of cAMP/PKA signal transduction / negative regulation of TORC1 signaling / protein serine/threonine/tyrosine kinase activity / protein export from nucleus / cellular response to glucagon stimulus / cellular response to nutrient levels / positive regulation of gluconeogenesis / positive regulation of phagocytosis / acrosomal vesicle / regulation of proteasomal protein catabolic process / positive regulation of protein export from nucleus / neural tube closure / cellular response to glucose stimulus / negative regulation of smoothened signaling pathway / neuromuscular junction / positive regulation of cholesterol biosynthetic process / mRNA processing / positive regulation of insulin secretion / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / manganese ion binding / cellular response to heat / adenylate cyclase-activating G protein-coupled receptor signaling pathway / protein kinase activity / postsynapse / regulation of cell cycle / nuclear speck / protein domain specific binding / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / ubiquitin protein ligase binding / protein kinase binding / perinuclear region of cytoplasm / glutamatergic synapse / magnesium ion binding / negative regulation of transcription by RNA polymerase II / mitochondrion / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
cAMP-dependent protein kinase inhibitor / cAMP-dependent protein kinase inhibitor / cAMP-dependent protein kinase catalytic subunit / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 ...cAMP-dependent protein kinase inhibitor / cAMP-dependent protein kinase inhibitor / cAMP-dependent protein kinase catalytic subunit / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / 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
Chem-M05 / cAMP-dependent protein kinase catalytic subunit alpha / cAMP-dependent protein kinase inhibitor alpha
Similarity search - Component
Biological speciesBOS TAURUS (domestic cattle)
HOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsCaldwell, J.J. / Davies, T.G. / Donald, A. / McHardy, T. / Rowlands, M.G. / Aherne, G.W. / Hunter, L.K. / Taylor, K. / Ruddle, R. / Raynaud, F.I. ...Caldwell, J.J. / Davies, T.G. / Donald, A. / McHardy, T. / Rowlands, M.G. / Aherne, G.W. / Hunter, L.K. / Taylor, K. / Ruddle, R. / Raynaud, F.I. / Verdonk, M. / Workman, P. / Garrett, M.D. / Collins, I.
CitationJournal: J.Med.Chem. / Year: 2008
Title: Identification of 4-(4-Aminopiperidin-1-Yl)-7H-Pyrrolo[2,3-D]Pyrimidines as Selective Inhibitors of Protein Kinase B Through Fragment Elaboration.
Authors: Caldwell, J.J. / Davies, T.G. / Donald, A. / Mchardy, T. / Rowlands, M.G. / Aherne, G.W. / Hunter, L.K. / Taylor, K. / Ruddle, R. / Raynaud, F.I. / Verdonk, M. / Workman, P. / Garrett, M.D. / Collins, I.
History
DepositionFeb 8, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 8, 2008Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2015Group: Data collection / Derived calculations ...Data collection / Derived calculations / Non-polymer description / Other / Version format compliance
Revision 1.2Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _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: CAMP-DEPENDENT PROTEIN KINASE, ALPHA-CATALYTIC SUBUNIT
I: CAMP-DEPENDENT PROTEIN KINASE INHIBITOR ALPHA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7504
Polymers43,0642
Non-polymers6862
Water6,161342
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2360 Å2
ΔGint-7.3 kcal/mol
Surface area19790 Å2
MethodPQS
Unit cell
Length a, b, c (Å)72.488, 75.143, 80.203
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein CAMP-DEPENDENT PROTEIN KINASE, ALPHA-CATALYTIC SUBUNIT / PROTEIN KINASE A / PKA C-ALPHA


Mass: 40837.609 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BOS TAURUS (domestic cattle) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P00517, cAMP-dependent protein kinase
#2: Protein/peptide CAMP-DEPENDENT PROTEIN KINASE INHIBITOR ALPHA / PKI / PKI-ALPHA / CAMP- DEPENDENT PROTEIN KINASE INHIBITOR / MUSCLE/BRAIN ISOFORM


Mass: 2226.411 Da / Num. of mol.: 1 / Fragment: RESIDUES 6-25 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P61925
#3: Chemical ChemComp-M05 / 4-(4-chlorobenzyl)-1-(7H-pyrrolo[2,3-d]pyrimidin-4-yl)piperidin-4-aminium


Mass: 342.846 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H21ClN5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 342 / 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

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Sample preparation

CrystalDensity Matthews: 2.33 Å3/Da / Density % sol: 46.89 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: RIGAKU CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.98→33 Å / Num. obs: 28363 / % possible obs: 95.9 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.04
Reflection shellResolution: 1.98→2.1 Å / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 4.2 / % possible all: 86.9

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Processing

SoftwareName: REFMAC / Version: 5.2.0019I / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.98→33.36 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.922 / SU B: 3.771 / SU ML: 0.109 / Cross valid method: THROUGHOUT / ESU R: 0.181 / ESU R Free: 0.169 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. BROKEN DENSITY FOR PHE 54 OF THE GLYCINE LOOP. SOME INDICATIONS OF ALTERNATIVE CONFORMATIONS WERE PRESENT FOR THIS REGION BUT WERE POORLY ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. BROKEN DENSITY FOR PHE 54 OF THE GLYCINE LOOP. SOME INDICATIONS OF ALTERNATIVE CONFORMATIONS WERE PRESENT FOR THIS REGION BUT WERE POORLY DEFINED. ONLY THE DOMINANT CONFORMATION HAS BEEN BUILT.
RfactorNum. reflection% reflectionSelection details
Rfree0.241 1509 5.1 %RANDOM
Rwork0.188 ---
obs0.191 28363 96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 22 Å2
Baniso -1Baniso -2Baniso -3
1-1.24 Å20 Å20 Å2
2---0.03 Å20 Å2
3----1.21 Å2
Refinement stepCycle: LAST / Resolution: 1.98→33.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2943 0 48 342 3333
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0223081
X-RAY DIFFRACTIONr_bond_other_d0.0020.022155
X-RAY DIFFRACTIONr_angle_refined_deg1.3911.9484167
X-RAY DIFFRACTIONr_angle_other_deg0.8922.9815218
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1465357
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.21523.608153
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.58215.082551
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6261518
X-RAY DIFFRACTIONr_chiral_restr0.0930.2429
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023362
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02670
X-RAY DIFFRACTIONr_nbd_refined0.2060.2631
X-RAY DIFFRACTIONr_nbd_other0.1980.22277
X-RAY DIFFRACTIONr_nbtor_refined0.1860.21506
X-RAY DIFFRACTIONr_nbtor_other0.0860.21529
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1190.276
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1350.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3340.221
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1580.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.08751781
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.10962879
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.10361300
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it0.1287.51287
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.98→2.03 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.324 101
Rwork0.235 1814

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