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- PDB-6ayd: Pim1 complexed with N-(6-(4-hydroxyphenyl)-1H-indazol-3-yl)cyclop... -

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Basic information

Entry
Database: PDB / ID: 6ayd
TitlePim1 complexed with N-(6-(4-hydroxyphenyl)-1H-indazol-3-yl)cyclopropanecarboxamide
ComponentsSerine/threonine-protein kinase pim-1
KeywordsTransferase/Transferase Inhibitor / Kinase / Transferase-Transferase Inhibitor complex
Function / homology
Function and homology information


positive regulation of cardioblast proliferation / cellular detoxification / regulation of hematopoietic stem cell proliferation / vitamin D receptor signaling pathway / STAT5 activation downstream of FLT3 ITD mutants / transcription factor binding / ribosomal small subunit binding / positive regulation of cyclin-dependent protein serine/threonine kinase activity / positive regulation of cardiac muscle cell proliferation / positive regulation of TORC1 signaling ...positive regulation of cardioblast proliferation / cellular detoxification / regulation of hematopoietic stem cell proliferation / vitamin D receptor signaling pathway / STAT5 activation downstream of FLT3 ITD mutants / transcription factor binding / ribosomal small subunit binding / positive regulation of cyclin-dependent protein serine/threonine kinase activity / positive regulation of cardiac muscle cell proliferation / positive regulation of TORC1 signaling / Signaling by FLT3 fusion proteins / negative regulation of innate immune response / positive regulation of brown fat cell differentiation / protein serine/threonine kinase activator activity / regulation of transmembrane transporter activity / positive regulation of protein serine/threonine kinase activity / negative regulation of DNA-binding transcription factor activity / cellular response to type II interferon / manganese ion binding / Interleukin-4 and Interleukin-13 signaling / protein autophosphorylation / protein stabilization / non-specific serine/threonine protein kinase / cell cycle / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / nucleolus / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / nucleoplasm / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Serine/threonine-protein kinase pim-1/2/3 / 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 ...Serine/threonine-protein kinase pim-1/2/3 / 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-C2J / Serine/threonine-protein kinase pim-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsShewchuk, L.M. / Henley, Z.A.
CitationJournal: ACS Med Chem Lett / Year: 2017
Title: From PIM1 to PI3K delta via GSK3 beta : Target Hopping through the Kinome.
Authors: Henley, Z.A. / Bax, B.D. / Inglesby, L.M. / Champigny, A. / Gaines, S. / Faulder, P. / Le, J. / Thomas, D.A. / Washio, Y. / Baldwin, I.R.
History
DepositionSep 8, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 27, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)38,3552
Polymers38,0621
Non-polymers2931
Water61334
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)97.300, 97.300, 80.221
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 Serine/threonine-protein kinase pim-1


Mass: 38062.148 Da / Num. of mol.: 1 / Fragment: UNP residues 1-312 / Mutation: R250G
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: Chemical ChemComp-C2J / N-[6-(4-hydroxyphenyl)-2H-indazol-3-yl]cyclopropanecarboxamide


Mass: 293.320 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H15N3O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H2O

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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: 2.88 Å3/Da / Density % sol: 57.29 %
Crystal growTemperature: 277 K / Method: vapor diffusion
Details: 1M succinate pH 7.0, 0.1M BisTrisPropane, 1% 1,6-hexanediol

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 9, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 3→20 Å / Num. obs: 7834 / % possible obs: 94 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 15
Reflection shellResolution: 3→3.078 Å / Rmerge(I) obs: 0.54 / Num. unique obs: 385 / % possible all: 63

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Processing

Software
NameVersionClassification
REFMAC5.8.0124refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BIK

2bik


Resolution: 3→20 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.885 / SU B: 36.658 / SU ML: 0.314 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.383
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2297 379 4.6 %RANDOM
Rwork0.1676 ---
obs0.1707 7834 94.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 134.48 Å2 / Biso mean: 73.88 Å2 / Biso min: 23.83 Å2
Baniso -1Baniso -2Baniso -3
1-1.45 Å20.72 Å20 Å2
2--1.45 Å2-0 Å2
3----4.69 Å2
Refinement stepCycle: final / Resolution: 3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2193 0 22 34 2249
Biso mean--60.49 45.91 -
Num. residues----272
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0192283
X-RAY DIFFRACTIONr_bond_other_d0.0030.022130
X-RAY DIFFRACTIONr_angle_refined_deg1.4391.9573104
X-RAY DIFFRACTIONr_angle_other_deg0.96534883
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0855273
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.87523.246114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.68115370
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5851519
X-RAY DIFFRACTIONr_chiral_restr0.0770.2330
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212587
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02564
LS refinement shellResolution: 3→3.078 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.17 14 -
Rwork0.285 385 -
all-399 -
obs--62.74 %
Refinement TLS params.Method: refined / Origin x: -8.681 Å / Origin y: -40.228 Å / Origin z: -0.63 Å
111213212223313233
T0.1068 Å2-0.0238 Å20.0379 Å2-0.0912 Å2-0.015 Å2--0.0338 Å2
L0.91 °2-0.63 °20.488 °2-0.8004 °2-0.6434 °2--1.6492 °2
S0.1976 Å °-0.0638 Å °-0.0301 Å °0.0072 Å °-0.0117 Å °0.1171 Å °-0.1025 Å °0.0051 Å °-0.1858 Å °

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