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- PDB-4lm5: Crystal structure of Pim1 in complex with 2-{4-[(3-aminopropyl)am... -

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Basic information

Entry
Database: PDB / ID: 4lm5
TitleCrystal structure of Pim1 in complex with 2-{4-[(3-aminopropyl)amino]quinazolin-2-yl}phenol (resulting from displacement of SKF86002)
ComponentsSerine/threonine-protein kinase pim-1
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / co-crystallization / SKF86002 / fluorescence / inhibitor screening / kinase / TRANSFERASE-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 / 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 / regulation of hematopoietic stem cell proliferation / cellular detoxification / 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
2-{4-[(3-aminopropyl)amino]quinazolin-2-yl}phenol / Serine/threonine-protein kinase pim-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.25 Å
AuthorsParker, L.J. / Tanaka, A. / Handa, N. / Honda, K. / Tomabechi, Y. / Shirouzu, M. / Yokoyama, S.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Kinase crystal identification and ATP-competitive inhibitor screening using the fluorescent ligand SKF86002.
Authors: Parker, L.J. / Taruya, S. / Tsuganezawa, K. / Ogawa, N. / Mikuni, J. / Honda, K. / Tomabechi, Y. / Handa, N. / Shirouzu, M. / Yokoyama, S. / Tanaka, A.
History
DepositionJul 10, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 12, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / struct_conn / struct_ref_seq_dif
Item: _citation.country / _citation.journal_id_CSD ..._citation.country / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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)34,7745
Polymers34,2041
Non-polymers5714
Water2,000111
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)97.677, 97.677, 80.781
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 / PROTO-ONCOGENE SERINE/THREONINE-PROTEIN KINASE PIM-1


Mass: 34203.727 Da / Num. of mol.: 1 / Fragment: 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: Escherichia coli (E. coli)
References: UniProt: P11309, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-Q17 / 2-{4-[(3-aminopropyl)amino]quinazolin-2-yl}phenol


Mass: 294.351 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H18N4O
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 3.25 Å3/Da / Density % sol: 62.18 % / Mosaicity: 0.41 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 100MM CITRATE BUFFER PH 5.5, 200MM NACL, 1M NH4HPO4. Co-crystallised in the presence of 2mM SKF86002. Then these crystals were soaked with 2mM inhibitor dissolved in DMSO., VAPOR DIFFUSION, ...Details: 100MM CITRATE BUFFER PH 5.5, 200MM NACL, 1M NH4HPO4. Co-crystallised in the presence of 2mM SKF86002. Then these crystals were soaked with 2mM inhibitor dissolved in DMSO., VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 2, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.25→84.59 Å / Num. obs: 20902 / % possible obs: 100 % / Redundancy: 22.5 % / Rsym value: 0.066 / Net I/σ(I): 39.8
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
2.25-2.3722.10.4210.4121.86692330240.090.4210.4129.3100
2.37-2.5222.30.320.3122.46429328880.0680.320.31212.4100
2.52-2.6922.40.2260.2213.46041626990.0480.2260.22117.1100
2.69-2.922.50.1510.1485.15661525140.0320.1510.14824.5100
2.9-3.1822.60.0950.09385243523200.020.0950.09336.3100
3.18-3.5622.70.0570.05512.74762920990.0120.0570.05556.2100
3.56-4.1122.80.040.03916.94260418710.0080.040.03977.8100
4.11-5.0322.80.0330.03218.83587215710.0070.0330.03290.8100
5.03-7.1222.70.0340.03318.42788812290.0070.0340.03384.3100
7.12-29.72821.40.0340.03316.1147016870.0070.0340.03396.998.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 31.96 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å29.21 Å
Translation2.5 Å29.21 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
PHASER2.1.2phasing
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
CrystalCleardata collection
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UMW

3umw


Resolution: 2.25→29.728 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8834 / SU ML: 0.2 / σ(F): 1.36 / Phase error: 18.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1979 1053 5.05 %
Rwork0.1557 --
obs0.1578 20872 99.99 %
all-21925 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 98.83 Å2 / Biso mean: 39.9394 Å2 / Biso min: 16.61 Å2
Refinement stepCycle: LAST / Resolution: 2.25→29.728 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2156 0 40 111 2307
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132251
X-RAY DIFFRACTIONf_angle_d1.2663047
X-RAY DIFFRACTIONf_chiral_restr0.098321
X-RAY DIFFRACTIONf_plane_restr0.006392
X-RAY DIFFRACTIONf_dihedral_angle_d17.147825
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.2499-2.35230.22121430.166724452588
2.3523-2.47620.2161310.163424602591
2.4762-2.63130.20871260.166824802606
2.6313-2.83430.22221200.179624612581
2.8343-3.11930.2191430.17624762619
3.1193-3.570.22631320.164224652597
3.57-4.49530.18541300.131225022632
4.4953-29.7310.16011280.149625302658
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)
17.5798-2.3934-5.18753.80931.90493.81630.17110.338-0.6028-0.4212-0.1495-0.25870.4537-0.3910.03690.55170.0266-0.09960.1814-0.02260.388841.0366-7.8329-3.1164
23.47651.02380.13435.5721-2.84445.948-0.15310.148-0.2421-0.45080.33040.37010.0333-0.4576-0.2230.4589-0.0183-0.07380.1908-0.05550.276836.1101-1.5506-8.5726
32.89993.14151.98555.64383.37333.7558-0.0755-0.04-0.4274-0.20550.2046-0.2820.15210.0552-0.13120.39530.0645-0.01470.23260.05980.281143.18143.4301-3.5811
43.9546-0.54371.44671.3365-0.15362.87680.16630.0076-0.2517-0.2098-0.03090.08060.2865-0.028-0.12550.31010.0108-0.00630.15240.02930.186439.907915.2534-4.3195
56.8745-0.54042.34322.00741.68053.59110.0636-0.656-0.23060.0881-0.03120.23140.1632-0.5652-0.00410.2446-0.02520.02350.25320.05480.191830.679221.93335.4568
66.4699-0.12951.00872.6133-0.06827.121-0.1403-0.14290.4461-0.15470.0662-0.0245-0.3563-0.1440.04830.27280.0345-0.00470.1216-0.00870.212940.420630.21413.9444
75.781-1.2711-0.60217.567-3.32769.8333-0.2830.0108-0.1534-0.27260.1804-1.24710.63580.96540.10030.29160.0289-0.01850.5012-0.06070.395858.488918.32490.2396
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 35:49 )A35 - 49
2X-RAY DIFFRACTION2chain 'A' and (resseq 50:96 )A50 - 96
3X-RAY DIFFRACTION3chain 'A' and (resseq 97:140 )A97 - 140
4X-RAY DIFFRACTION4chain 'A' and (resseq 141:204 )A141 - 204
5X-RAY DIFFRACTION5chain 'A' and (resseq 205:250 )A205 - 250
6X-RAY DIFFRACTION6chain 'A' and (resseq 251:290 )A251 - 290
7X-RAY DIFFRACTION7chain 'A' and (resseq 291:305 )A291 - 305

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