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- PDB-2c1b: Structure of cAMP-dependent protein kinase complexed with (4R,2S)... -

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Basic information

Entry
Database: PDB / ID: 2c1b
TitleStructure of cAMP-dependent protein kinase complexed with (4R,2S)-5'-(4-(4-Chlorobenzyloxy)pyrrolidin-2-ylmethanesulfonyl)isoquinoline
Components
  • CAMP-DEPENDENT PROTEIN KINASE
  • CAMP-DEPENDENT PROTEIN KINASE INHIBITOR
KeywordsTRANSFERASE/INHIBITOR / COMPLEX (TRANSFERASE-INHIBITOR) / ATP-BINDING / CAMP / PHOSPHORYLATION / TRANSFERASE / SERINE/THREONINE-PROTEIN KINASE / PROTEIN KINASE INHIBITOR / TRANSFERASE-INHIBITOR complex
Function / homology
Function and homology information


CD209 (DC-SIGN) signaling / HDL assembly / Regulation of insulin secretion / Rap1 signalling / Ion homeostasis / 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 ...CD209 (DC-SIGN) signaling / HDL assembly / Regulation of insulin secretion / Rap1 signalling / Ion homeostasis / 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 / RET signaling / AURKA Activation by TPX2 / Interleukin-3, Interleukin-5 and GM-CSF signaling / Recruitment of NuMA to mitotic centrosomes / VEGFA-VEGFR2 Pathway / negative regulation of cAMP-dependent protein kinase activity / negative regulation of cAMP/PKA signal transduction / PKA activation / MAPK6/MAPK4 signaling / GLI3 is processed to GLI3R by the proteasome / Regulation of PLK1 Activity at G2/M Transition / Hedgehog 'off' state / cAMP-dependent protein kinase inhibitor activity / cAMP-dependent protein kinase / cAMP-dependent protein kinase activity / cAMP-dependent protein kinase complex / AMP-activated protein kinase activity / negative regulation of protein import into nucleus / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / Vasopressin regulates renal water homeostasis via Aquaporins / Mitochondrial protein degradation / protein kinase A regulatory subunit binding / protein kinase A catalytic subunit binding / mesoderm formation / sperm flagellum / negative regulation of TORC1 signaling / regulation of G2/M transition of mitotic cell cycle / protein kinase A signaling / acrosomal vesicle / neuromuscular junction / cellular response to heat / peptidyl-serine phosphorylation / protein kinase activity / protein phosphorylation / protein domain specific binding / protein serine kinase activity / protein serine/threonine kinase activity / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / mitochondrion / ATP binding / nucleus / plasma membrane / 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. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; 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. / 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-CQP / cAMP-dependent protein kinase catalytic subunit alpha / cAMP-dependent protein kinase inhibitor alpha
Similarity search - Component
Biological speciesBOS TAURUS (cattle)
HOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsCollins, I. / Caldwell, J. / Fonseca, T. / Donald, A. / Bavetsias, V. / Hunter, L.J. / Garrett, M.D. / Rowlands, M.G. / Aherne, G.W. / Davies, T.G. ...Collins, I. / Caldwell, J. / Fonseca, T. / Donald, A. / Bavetsias, V. / Hunter, L.J. / Garrett, M.D. / Rowlands, M.G. / Aherne, G.W. / Davies, T.G. / Berdini, V. / Woodhead, S.J. / Seavers, L.C.A. / Wyatt, P.G. / Workman, P. / McDonald, E.
CitationJournal: Bioorg. Med. Chem. / Year: 2006
Title: Structure-based design of isoquinoline-5-sulfonamide inhibitors of protein kinase B.
Authors: Collins, I. / Caldwell, J. / Fonseca, T. / Donald, A. / Bavetsias, V. / Hunter, L.J. / Garrett, M.D. / Rowlands, M.G. / Aherne, G.W. / Davies, T.G. / Berdini, V. / Woodhead, S.J. / Davis, D. ...Authors: Collins, I. / Caldwell, J. / Fonseca, T. / Donald, A. / Bavetsias, V. / Hunter, L.J. / Garrett, M.D. / Rowlands, M.G. / Aherne, G.W. / Davies, T.G. / Berdini, V. / Woodhead, S.J. / Davis, D. / Seavers, L.C. / Wyatt, P.G. / Workman, P. / McDonald, E.
History
DepositionSep 12, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 2, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 28, 2018Group: Database references / Structure summary / Category: audit_author / citation / citation_author
Item: _audit_author.name / _citation.journal_abbrev ..._audit_author.name / _citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name
Revision 1.4Oct 16, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CAMP-DEPENDENT PROTEIN KINASE
I: CAMP-DEPENDENT PROTEIN KINASE INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4963
Polymers43,0642
Non-polymers4321
Water8,071448
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)73.310, 75.160, 80.052
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsTHE CAMP-DEPENDENT PROTEIN KINASE IS A MONOMER ININ THE ABSENCE OF THE REGULATORY SUBUNIT . IN THISENTRY THIS IS ANNOTATED AS A DIMER SINCE THIS ISIN COMPLEX WITH PEPTIDE CHAIN I.

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Components

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


Mass: 40837.609 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BOS TAURUS (cattle) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P00517, EC: 2.7.1.37
#2: Protein/peptide CAMP-DEPENDENT PROTEIN KINASE INHIBITOR / ALPHA FORM / PKI-ALPHA / CAMP-DEPENDENT PROTEIN KINASE INHIBITOR / MUSCLE/BRAIN ISOFORM


Mass: 2226.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P61925
#3: Chemical ChemComp-CQP / (4R,2S)-5'-(4-(4-CHLOROBENZYLOXY)PYRROLIDIN-2-YLMETHANESULFONYL)ISOQUINOLINE


Mass: 431.936 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H22ClN3O3S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 448 / 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: 2.56 Å3/Da / Density % sol: 51.96 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→34 Å / Num. obs: 29832 / % possible obs: 98 % / Observed criterion σ(I): 2 / Redundancy: 3 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 14
Reflection shellResolution: 2→2.11 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.12 / Mean I/σ(I) obs: 6.3 / % possible all: 90.4

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Processing

SoftwareName: REFMAC / Version: 5.1.29 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→34.02 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.923 / SU B: 3.081 / SU ML: 0.088 / Cross valid method: THROUGHOUT / ESU R: 0.159 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.211 1511 5.1 %RANDOM
Rwork0.16 ---
obs0.162 28290 97.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 18.18 Å2
Baniso -1Baniso -2Baniso -3
1-0.4 Å20 Å20 Å2
2--0.46 Å20 Å2
3----0.87 Å2
Refinement stepCycle: LAST / Resolution: 2→34.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2939 0 29 448 3416
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223046
X-RAY DIFFRACTIONr_bond_other_d0.0020.022715
X-RAY DIFFRACTIONr_angle_refined_deg1.3111.9584113
X-RAY DIFFRACTIONr_angle_other_deg0.78336329
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7335355
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.080.2427
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023327
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02662
X-RAY DIFFRACTIONr_nbd_refined0.2370.2603
X-RAY DIFFRACTIONr_nbd_other0.240.23231
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0830.21755
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.2350
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1990.25
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2540.229
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1740.216
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.41451773
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.49462862
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.47161273
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.8117.51251
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: 2→2.05 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.234 111
Rwork0.155 1769

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