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- PDB-7zun: Crystal structure of PIM1 in complex with a Pyrrolo-Pyrazinone co... -

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Basic information

Entry
Database: PDB / ID: 7zun
TitleCrystal structure of PIM1 in complex with a Pyrrolo-Pyrazinone compound
ComponentsIsoform 2 of Serine/threonine-protein kinase pim-1
KeywordsTRANSFERASE / PIM1 / ATP BINDING / KINASE INHIBITOR
Function / homologynon-specific serine/threonine protein kinase / Chem-JYO / Isoform 2 of Serine/threonine-protein kinase pim-1
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsCasale, E.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Chirality / Year: 2022
Title: Stereoselective synthesis of 3,4-dihydropyrrolo[1,2-a]pyrazin-1(2H)-one derivatives as PIM kinase inhibitors inspired from marine alkaloids.
Authors: Casuscelli, F. / Ardini, E. / Avanzi, N. / Badari, A. / Casale, E. / Disingrini, T. / Donati, D. / Ermoli, A. / Felder, E.R. / Galvani, A. / Isacchi, A. / Menichincheri, M. / Montemartini, M. ...Authors: Casuscelli, F. / Ardini, E. / Avanzi, N. / Badari, A. / Casale, E. / Disingrini, T. / Donati, D. / Ermoli, A. / Felder, E.R. / Galvani, A. / Isacchi, A. / Menichincheri, M. / Montemartini, M. / Orrenius, C. / Piutti, C. / Salom, B. / Papeo, G.
History
DepositionMay 12, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 5, 2022Provider: repository / Type: Initial release
Revision 2.0Oct 12, 2022Group: Atomic model / Database references / Category: atom_site / citation
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Isoform 2 of Serine/threonine-protein kinase pim-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2512
Polymers35,8361
Non-polymers4151
Water82946
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.090, 95.090, 80.181
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Isoform 2 of Serine/threonine-protein kinase pim-1


Mass: 35835.691 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: residue SEP 261 is a PHOSPHOSERINE THE FIRST TWO RESIDUES AT THE N-TERMINAL GLY AND PRO ARE EXPRESSION TAG
Source: (gene. exp.) Homo sapiens (human) / Gene: PIM1 / Production host: Escherichia coli (E. coli)
References: UniProt: P11309-2, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-JYO / (4~{S})-4-(2-azanylethyl)-6-phenyl-7-[3-(trifluoromethyloxy)phenyl]-3,4-dihydropyrrolo[1,2-a]pyrazin-1-ol


Mass: 415.408 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H20F3N3O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.91 Å3/Da / Density % sol: 57.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.6 / Details: 20% PEG 3350K, 0.3 M NACL, 0.1 M TRIS-HCL PH 7.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 29, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.5→36.7 Å / Num. obs: 14258 / % possible obs: 99.3 % / Redundancy: 4.4 % / CC1/2: 0.996 / Rmerge(I) obs: 0.093 / Net I/σ(I): 11.4
Reflection shellResolution: 2.5→2.6 Å / Rmerge(I) obs: 0.47 / Num. unique obs: 6771 / CC1/2: 0.807 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YHS

1yhs


Resolution: 2.5→36.655 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.918 / SU B: 8.666 / SU ML: 0.189 / Cross valid method: FREE R-VALUE / ESU R: 0.317 / ESU R Free: 0.245
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.235 716 5.031 %
Rwork0.1744 13516 -
all0.177 --
obs-14232 99.15 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 47.926 Å2
Baniso -1Baniso -2Baniso -3
1-1.293 Å20.646 Å20 Å2
2--1.293 Å2-0 Å2
3----4.193 Å2
Refinement stepCycle: LAST / Resolution: 2.5→36.655 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2186 0 30 46 2262
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0132277
X-RAY DIFFRACTIONr_bond_other_d0.0030.0152095
X-RAY DIFFRACTIONr_angle_refined_deg1.3151.6543099
X-RAY DIFFRACTIONr_angle_other_deg1.2941.5864814
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.625268
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.73421.603131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.88215366
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2341518
X-RAY DIFFRACTIONr_chiral_restr0.0580.2279
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022555
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02547
X-RAY DIFFRACTIONr_nbd_refined0.2060.2421
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1930.21995
X-RAY DIFFRACTIONr_nbtor_refined0.1660.21083
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.2970
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.279
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0910.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.240.26
X-RAY DIFFRACTIONr_nbd_other0.2150.232
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.6060.24
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.6440.21
X-RAY DIFFRACTIONr_mcbond_it3.0465.0051078
X-RAY DIFFRACTIONr_mcbond_other3.0455.0021077
X-RAY DIFFRACTIONr_mcangle_it4.7527.4911344
X-RAY DIFFRACTIONr_mcangle_other4.7517.4941345
X-RAY DIFFRACTIONr_scbond_it3.2565.2941199
X-RAY DIFFRACTIONr_scbond_other3.2555.2941200
X-RAY DIFFRACTIONr_scangle_it5.1647.8171755
X-RAY DIFFRACTIONr_scangle_other5.1637.8161756
X-RAY DIFFRACTIONr_lrange_it7.31556.0722490
X-RAY DIFFRACTIONr_lrange_other7.31856.0592487
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.5650.333560.27985X-RAY DIFFRACTION99.4269
2.565-2.6350.336470.248978X-RAY DIFFRACTION99.418
2.635-2.7120.301620.233936X-RAY DIFFRACTION99.4024
2.712-2.7950.235530.231921X-RAY DIFFRACTION99.3878
2.795-2.8860.214470.202889X-RAY DIFFRACTION99.4687
2.886-2.9880.272260.19854X-RAY DIFFRACTION98.434
2.988-3.10.253520.184833X-RAY DIFFRACTION99.5501
3.1-3.2270.296230.181812X-RAY DIFFRACTION99.4048
3.227-3.370.262450.177768X-RAY DIFFRACTION99.5104
3.37-3.5340.233430.181735X-RAY DIFFRACTION99.8716
3.534-3.7250.215400.174696X-RAY DIFFRACTION100
3.725-3.950.223340.149670X-RAY DIFFRACTION99.0155
3.95-4.2220.188230.143634X-RAY DIFFRACTION99.848
4.222-4.560.21240.128592X-RAY DIFFRACTION99.0354
4.56-4.9930.199290.131532X-RAY DIFFRACTION98.0769
4.993-5.580.176350.156468X-RAY DIFFRACTION98.4344
5.58-6.4380.251420.172398X-RAY DIFFRACTION96.4912
6.438-7.8730.257200.176367X-RAY DIFFRACTION99.7423
7.873-11.0840.217110.144282X-RAY DIFFRACTION97.6667
11.084-360.19140.246166X-RAY DIFFRACTION96.0452

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