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- PDB-7oow: Crystal structure of PIM1 in complex with ARC-1415 -

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Basic information

Entry
Database: PDB / ID: 7oow
TitleCrystal structure of PIM1 in complex with ARC-1415
Components
  • INHIBITOR ARC-1415
  • Serine/threonine-protein kinase pim-1
KeywordsTRANSFERASE / PIM1 / inhibitor / kinase / kinase substrate / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


positive regulation of cardioblast proliferation / regulation of hematopoietic stem cell proliferation / vitamin D receptor signaling pathway / cellular detoxification / 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 / negative regulation of innate immune response ...positive regulation of cardioblast proliferation / regulation of hematopoietic stem cell proliferation / vitamin D receptor signaling pathway / cellular detoxification / 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 / negative regulation of innate immune response / Signaling by FLT3 fusion proteins / positive regulation of brown fat cell differentiation / positive regulation of TORC1 signaling / 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 / non-specific serine/threonine protein kinase / protein stabilization / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / negative regulation of apoptotic process / nucleolus / 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 / : / 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
: / polypeptide(D) / Serine/threonine-protein kinase pim-1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsChaikuad, A. / Dixon-Clarke, S.E. / Nonga, O.E. / Uri, A. / Bullock, A. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: Molecules / Year: 2021
Title: Crystal Structure-Guided Design of Bisubstrate Inhibitors and Photoluminescent Probes for Protein Kinases of the PIM Family.
Authors: Nonga, O.E. / Lavogina, D. / Enkvist, E. / Kestav, K. / Chaikuad, A. / Dixon-Clarke, S.E. / Bullock, A.N. / Kopanchuk, S. / Ivan, T. / Ekambaram, R. / Viht, K. / Knapp, S. / Uri, A.
History
DepositionMay 28, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 4, 2021Provider: repository / Type: Initial release
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr2_label_atom_id
Revision 2.1Jan 31, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 2.2Apr 10, 2024Group: Derived calculations / Source and taxonomy / Structure summary
Category: entity_src_gen / pdbx_molecule ...entity_src_gen / pdbx_molecule / pdbx_molecule_features / pdbx_struct_assembly / pdbx_struct_assembly_prop
Item: _entity_src_gen.gene_src_common_name / _pdbx_molecule.prd_id ..._entity_src_gen.gene_src_common_name / _pdbx_molecule.prd_id / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly_prop.value

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine/threonine-protein kinase pim-1
B: INHIBITOR ARC-1415
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1787
Polymers36,9052
Non-polymers2735
Water3,855214
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2990 Å2
ΔGint18 kcal/mol
Surface area13220 Å2
Unit cell
Length a, b, c (Å)98.614, 98.614, 80.729
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: 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: Polypeptide(D) INHIBITOR ARC-1415


Type: Peptide-like / Class: Inhibitor / Mass: 1314.620 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: BIRD: PRD_002339
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 214 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.18 Å3/Da / Density % sol: 61.37 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 15%(w/v) PEG 10000, 0.2M magnesium chloride, 0.1M tris pH 7.9

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 25, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.95→42.7 Å / Num. obs: 32555 / % possible obs: 99.9 % / Redundancy: 5.1 % / CC1/2: 0.995 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.052 / Rrim(I) all: 0.12 / Net I/av σ(I): 11 / Net I/σ(I): 11
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.95-2.0250.9483.131960.7340.4941.12199.9
7.55-42.75.10.095770.990.0410.09998.8

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
REFMAC5.8.0257refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2j2i

2j2i


Resolution: 1.95→42.7 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.958 / SU B: 5.134 / SU ML: 0.075 / SU R Cruickshank DPI: 0.111 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.111 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1838 1547 4.8 %RANDOM
Rwork0.1602 ---
obs0.1614 30996 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 101.65 Å2 / Biso mean: 33.68 Å2 / Biso min: 13.19 Å2
Baniso -1Baniso -2Baniso -3
1-0.47 Å20.24 Å2-0 Å2
2--0.47 Å20 Å2
3----1.53 Å2
Refinement stepCycle: final / Resolution: 1.95→42.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2217 0 110 214 2541
Biso mean--50.06 40.43 -
Num. residues----273
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0132384
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172193
X-RAY DIFFRACTIONr_angle_refined_deg1.4121.6513221
X-RAY DIFFRACTIONr_angle_other_deg1.3121.6315067
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7355272
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.80921.314137
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.56715377
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5761520
X-RAY DIFFRACTIONr_chiral_restr0.0750.2283
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022742
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02538
LS refinement shellResolution: 1.95→2.001 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 120 -
Rwork0.232 2249 -
all-2369 -
obs--99.71 %
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)
12.08150.678-0.68682.66880.591.45170.1345-0.03670.1160.141-0.0346-0.2455-0.27730.2853-0.09990.0866-0.0837-0.01010.1016-0.00990.062672.15455.67621.724
20.40550.13990.0540.59050.23770.85570.0491-0.02540.0084-0.0313-0.0178-0.0183-0.0271-0.0097-0.03130.0156-0.00070.00740.0409-0.00460.005954.68342.45914.931
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A33 - 86
2X-RAY DIFFRACTION2A87 - 305

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