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- PDB-4enx: Crystal Structure of Pim-1 Kinase in complex with inhibitor (2E,5... -

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Basic information

Entry
Database: PDB / ID: 4enx
TitleCrystal Structure of Pim-1 Kinase in complex with inhibitor (2E,5Z)-2-(2-chlorophenylimino)-5-(4-hydroxy-3-nitrobenzylidene)thiazolidin-4-one
ComponentsSerine/threonine-protein kinase pim-1
KeywordsTRANSFERASE/INHIBITOR / Pim-1 kinase / TRANSFERASE-INHIBITOR complex
Function / homology
Function and homology information


positive regulation of cardioblast proliferation / regulation of hematopoietic stem cell proliferation / cellular detoxification / vitamin D receptor signaling pathway / STAT5 activation downstream of FLT3 ITD mutants / transcription factor binding / positive regulation of cyclin-dependent protein serine/threonine kinase activity / ribosomal small subunit binding / positive regulation of cardiac muscle cell proliferation / positive regulation of TORC1 signaling ...positive regulation of cardioblast proliferation / regulation of hematopoietic stem cell proliferation / cellular detoxification / vitamin D receptor signaling pathway / STAT5 activation downstream of FLT3 ITD mutants / transcription factor binding / positive regulation of cyclin-dependent protein serine/threonine kinase activity / ribosomal small subunit binding / 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 / 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 / cytoplasm / cytosol
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 ...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
PHOSPHATE ION / Chem-Z20 / Serine/threonine-protein kinase pim-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å
AuthorsParker, L.J. / Handa, N. / Yokoyama, S.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2012
Title: Flexibility of the P-loop of Pim-1 kinase: observation of a novel conformation induced by interaction with an inhibitor
Authors: Parker, L.J. / Watanabe, H. / Tsuganezawa, K. / Tomabechi, Y. / Handa, N. / Shirouzu, M. / Yuki, H. / Honma, T. / Ogawa, N. / Nagano, T. / Yokoyama, S. / Tanaka, A.
History
DepositionApr 13, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 8, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2012Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)34,6583
Polymers34,1881
Non-polymers4712
Water99155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)97.074, 97.074, 80.941
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: 34187.727 Da / Num. of mol.: 1 / Fragment: Protein kinase domain, UNP RESIDUES 120-404
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PIM1 / Plasmid: pCR2.1-TOPO / Production host: cell-free protein synthesis (unknown)
References: UniProt: P11309, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-Z20 / (2Z,5Z)-2-[(2-chlorophenyl)imino]-5-(4-hydroxy-3-nitrobenzylidene)-1,3-thiazolidin-4-one


Mass: 375.786 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H10ClN3O4S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 3.22 Å3/Da / Density % sol: 61.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 100mM Citrate buffer, pH 5.5, 200mM NaCl, 1M NH4HPO4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 31, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.8→31.782 Å / Num. all: 10791 / Num. obs: 10791 / % possible obs: 99.9 % / Redundancy: 22.7 % / Biso Wilson estimate: 60.77 Å2 / Rmerge(I) obs: 0.086 / Rsym value: 0.086 / Net I/σ(I): 40.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) allRmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.8-2.9522.60.3940.38523536915650.0820.3940.38510.1100
2.95-3.1322.60.2880.2822.73354614820.060.2880.28214100
3.13-3.3522.70.1850.1814.23147713860.0380.1850.18121.1100
3.35-3.6122.80.1150.1126.72973713070.0240.1150.11232.2100
3.61-3.9622.80.0750.07310.12728011940.0160.0750.07345.3100
3.96-4.4322.80.0540.05213.92465710830.0110.0540.05258.8100
4.43-5.1122.90.0430.04217220309640.0090.0430.04269.3100
5.11-6.2622.80.0470.04616.1185958160.010.0470.04666.8100
6.26-8.8522.50.0370.03619.5144066390.0080.0370.03678.5100
8.85-31.78220.60.0270.02622.373273550.0060.0270.02699.498.2

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.8 Å31.78 Å
Translation2.8 Å31.78 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.25data scaling
PHASER2.3.0phasing
PHENIX1.7.3_928refinement
PDB_EXTRACT3.11data extraction
CrystalCleardata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UMX

3umx


Resolution: 2.8→31.775 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8502 / SU ML: 0.31 / σ(F): 1.36 / Phase error: 22.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2326 544 5.05 %
Rwork0.1902 --
obs0.1923 10762 99.93 %
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 30.587 Å2 / ksol: 0.367 e/Å3
Displacement parametersBiso max: 99.29 Å2 / Biso mean: 43.2285 Å2 / Biso min: 16.49 Å2
Baniso -1Baniso -2Baniso -3
1-2.6182 Å20 Å2-0 Å2
2--2.6182 Å2-0 Å2
3----5.2364 Å2
Refinement stepCycle: LAST / Resolution: 2.8→31.775 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2160 0 30 55 2245
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062248
X-RAY DIFFRACTIONf_angle_d0.8913052
X-RAY DIFFRACTIONf_chiral_restr0.058322
X-RAY DIFFRACTIONf_plane_restr0.003395
X-RAY DIFFRACTIONf_dihedral_angle_d13.147820
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs
2.8003-3.08190.2981400.2558253426742534
3.0819-3.52740.27091430.2004254026832540
3.5274-4.44220.21251310.1657255626872556
4.4422-31.77710.19971300.1816258827182588
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
19.04240.34824.65526.36370.70156.87510.27220.79660.5995-0.4137-0.32210.5514-0.0060.3997-0.11170.70980.04070.04620.12640.02230.3293-42.93826.9813-2.5774
22.1783-2.66570.06116.3891-0.27534.9574-0.06510.0777-0.0791-0.1706-0.1727-0.5212-0.50851.02860.22410.4768-0.12010.07010.40190.00930.2905-30.52811.377-7.786
31.99931.3645-7.34526.8917-0.73387.2403-0.48261.6282-0.0096-1.04170.36320.10060.132-0.65520.18670.6199-0.01720.03480.3130.04120.267-39.2166-7.8137-11.8545
41.60071.00850.73674.1995-0.87212.23710.04140.02070.2091-0.08150.03150.1715-0.4065-0.046-0.10010.23120.04440.02070.1616-0.02180.2263-43.8645-8.909-1.2634
55.4289-0.7801-0.50692.07950.92573.41520.01880.03010.2513-0.0861-0.0499-0.0556-0.38710.19510.04990.335-0.03040.03340.13950.02730.1642-36.4423-12.4844-3.2554
66.9452-0.0862-4.63576.56732.22635.13850.0968-0.34990.15530.39180.1698-0.63540.09810.5274-0.29950.29480.0368-0.0470.4173-0.02960.2368-23.9609-20.98683.1335
76.1933-1.83420.31534.3987-2.63783.18590.0202-0.6228-0.09450.06550.2045-0.051-0.28270.4227-0.19220.2298-0.03730.0130.2627-0.03930.1952-34.2851-21.82198.8306
84.8393-0.04760.10783.4551-0.24055.31840.07610.0959-0.5176-0.32170.11590.02070.78790.0071-0.16230.28480.0317-0.04190.1368-0.01310.272-40.096-29.99135.2154
99.05054.4383-0.38275.31463.54038.1106-0.16410.32120.295-0.8478-0.09050.7306-0.7706-0.88430.36190.2420.088-0.04130.45460.13460.3718-58.4529-18.12591.5928
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 37:61)A37 - 61
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 62:87)A62 - 87
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 88:105)A88 - 105
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 106:160)A106 - 160
5X-RAY DIFFRACTION5CHAIN A AND (RESSEQ 161:204)A161 - 204
6X-RAY DIFFRACTION6CHAIN A AND (RESSEQ 205:219)A205 - 219
7X-RAY DIFFRACTION7CHAIN A AND (RESSEQ 220:250)A220 - 250
8X-RAY DIFFRACTION8CHAIN A AND (RESSEQ 251:290)A251 - 290
9X-RAY DIFFRACTION9CHAIN A AND (RESSEQ 291:305)A291 - 305

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