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- PDB-31ru: Crystal structure of PIM1 kinase in complex with compound 20 -

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Basic information

Entry
Database: PDB / ID: 31ru
TitleCrystal structure of PIM1 kinase in complex with compound 20
Components
  • ALA-ARG-LYS-ARG-ARG-ARG-HIS-PRO-SER-GLY-PRO-PRO-THR-ALA
  • Serine/threonine-protein kinase pim-1
KeywordsTRANSFERASE / serine/threonine protein kinase / inhibitor / drug design
Function / homology
Function and homology information


regulation of transmembrane transporter activity / positive regulation of cardioblast proliferation / positive regulation of cyclin-dependent protein serine/threonine kinase activity / regulation of hematopoietic stem cell proliferation / vitamin D receptor signaling pathway / cellular detoxification / STAT5 activation downstream of FLT3 ITD mutants / transcription factor binding / positive regulation of protein serine/threonine kinase activity / ribosomal small subunit binding ...regulation of transmembrane transporter activity / positive regulation of cardioblast proliferation / positive regulation of cyclin-dependent protein serine/threonine kinase activity / regulation of hematopoietic stem cell proliferation / vitamin D receptor signaling pathway / cellular detoxification / STAT5 activation downstream of FLT3 ITD mutants / transcription factor binding / positive regulation of protein serine/threonine kinase activity / ribosomal small subunit binding / : / positive regulation of cardiac muscle cell proliferation / positive regulation of brown fat cell differentiation / Signaling by FLT3 fusion proteins / positive regulation of TORC1 signaling / regulation of mitotic cell cycle / negative regulation of innate immune response / protein serine/threonine kinase activator activity / cellular response to type II interferon / protein autophosphorylation / manganese ion binding / Interleukin-4 and Interleukin-13 signaling / protein phosphorylation / non-specific serine/threonine protein kinase / protein stabilization / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / nucleolus / nucleoplasm / ATP binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Serine/threonine-protein kinase pim-1/2/3 / : / 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
Similarity search - Domain/homology
: / Serine/threonine-protein kinase pim-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsZhubi, R. / Schroeder, M. / Kalampaliki, A. / Knapp, S. / Kraemer, A. / Structural Genomics Consortium
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
CitationJournal: to be published
Title: Crystal structure of PIM1 kinase in complex with compound 20
Authors: Zhubi, R. / Schroeder, M. / Kalampaliki, A. / Knapp, S. / Kraemer, A. / Structural Genomics Consortium
History
DepositionJun 18, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 1, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine/threonine-protein kinase pim-1
Q: ALA-ARG-LYS-ARG-ARG-ARG-HIS-PRO-SER-GLY-PRO-PRO-THR-ALA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8617
Polymers37,1832
Non-polymers6785
Water88349
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1950 Å2
ΔGint-22 kcal/mol
Surface area12690 Å2
Unit cell
Length a, b, c (Å)96.624, 96.624, 80.199
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AQ

#1: Protein Serine/threonine-protein kinase pim-1


Mass: 35590.500 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PIM1 / Production host: Escherichia coli (E. coli)
References: UniProt: P11309, non-specific serine/threonine protein kinase
#2: Protein/peptide ALA-ARG-LYS-ARG-ARG-ARG-HIS-PRO-SER-GLY-PRO-PRO-THR-ALA


Mass: 1592.850 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 4 types, 54 molecules

#3: Chemical ChemComp-A1KBF / 6-chloranyl-3-[4-(1~{H}-indol-3-yl)-1~{H}-pyrazol-5-yl]quinazolin-4-one


Mass: 361.784 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H12ClN5O / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 57.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 1M AmmSO4, 0,2M NaCl, 0.1M bis-tris 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99998 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 6, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99998 Å / Relative weight: 1
ReflectionResolution: 2.3→48.31 Å / Num. obs: 19015 / % possible obs: 100 % / Redundancy: 9.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.118 / Rpim(I) all: 0.041 / Rrim(I) all: 0.125 / Net I/σ(I): 11.7
Reflection shellResolution: 2.3→2.38 Å / Rmerge(I) obs: 1.328 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1843 / CC1/2: 0.831 / Rpim(I) all: 0.459 / Rrim(I) all: 1.406

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Processing

Software
NameVersionClassification
PHENIX(1.20_4459: ???)refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→48.31 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2281 961 5.07 %
Rwork0.1953 --
obs0.197 18969 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→48.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2215 0 44 49 2308
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082319
X-RAY DIFFRACTIONf_angle_d0.9143154
X-RAY DIFFRACTIONf_dihedral_angle_d6.408337
X-RAY DIFFRACTIONf_chiral_restr0.053336
X-RAY DIFFRACTIONf_plane_restr0.009440
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.420.33151390.25782540X-RAY DIFFRACTION100
2.42-2.570.27931320.24132557X-RAY DIFFRACTION100
2.57-2.770.26861450.24542559X-RAY DIFFRACTION100
2.77-3.050.2571360.22512569X-RAY DIFFRACTION100
3.05-3.490.2731330.21052582X-RAY DIFFRACTION100
3.49-4.40.20461330.17082578X-RAY DIFFRACTION100
4.4-48.310.18691430.16982623X-RAY DIFFRACTION100

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