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- PDB-3vbq: Exploitation of hydrogen bonding constraints and flat hydrophobic... -

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Basic information

Entry
Database: PDB / ID: 3vbq
TitleExploitation of hydrogen bonding constraints and flat hydrophobic energy landscapes in Pim-1 kinase needle screening and inhibitor design
ComponentsSerine/threonine-protein kinase pim-1
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Pim1 / Rossmann Fold / 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 / ribosomal small subunit binding / transcription factor 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 / ribosomal small subunit binding / transcription factor 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 / positive regulation of brown fat cell differentiation / negative regulation of innate immune response / 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-0F5 / Serine/threonine-protein kinase pim-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsLiu, J.
CitationJournal: J.Med.Chem. / Year: 2012
Title: Implications of promiscuous Pim-1 kinase fragment inhibitor hydrophobic interactions for fragment-based drug design.
Authors: Good, A.C. / Liu, J. / Hirth, B. / Asmussen, G. / Xiang, Y. / Biemann, H.P. / Bishop, K.A. / Fremgen, T. / Fitzgerald, M. / Gladysheva, T. / Jain, A. / Jancsics, K. / Metz, M. / Papoulis, A. ...Authors: Good, A.C. / Liu, J. / Hirth, B. / Asmussen, G. / Xiang, Y. / Biemann, H.P. / Bishop, K.A. / Fremgen, T. / Fitzgerald, M. / Gladysheva, T. / Jain, A. / Jancsics, K. / Metz, M. / Papoulis, A. / Skerlj, R. / Stepp, J.D. / Wei, R.R.
History
DepositionJan 2, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2012Provider: repository / Type: Initial release
Revision 1.1May 16, 2012Group: Database references
Revision 2.0Feb 19, 2020Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_entity_nonpoly / struct_ref_seq_dif
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _chem_comp.name / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details
Revision 2.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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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)34,8772
Polymers34,4811
Non-polymers3951
Water2,756153
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)97.709, 97.709, 81.174
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

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


Mass: 34481.094 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 / Production host: Escherichia coli (E. coli)
References: UniProt: P11309, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-0F5 / (5~{Z})-5-[[3-[6-[(4-azanylcyclohexyl)amino]pyrazin-2-yl]phenyl]methylidene]-1,3-thiazolidine-2,4-dione


Mass: 395.478 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H21N5O2S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 153 / 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: 3.24 Å3/Da / Density % sol: 62.08 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.4
Details: 0.1M Imidazole, 1M Sodium acetate , pH 6.4, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1
DetectorType: ADSC QUANTUM 210 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.85→85 Å / Num. all: 37698 / Num. obs: 37698 / % possible obs: 100 % / Observed criterion σ(F): 0.1 / Observed criterion σ(I): 0.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→84.62 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.959 / SU B: 4.615 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.1 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.20618 1882 5 %RANDOM
Rwork0.17616 ---
all0.20618 35819 --
obs0.17775 35759 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.392 Å2
Baniso -1Baniso -2Baniso -3
1-0.74 Å20.37 Å20 Å2
2--0.74 Å20 Å2
3----1.11 Å2
Refinement stepCycle: LAST / Resolution: 1.85→84.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2209 0 28 153 2390
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.022309
X-RAY DIFFRACTIONr_angle_refined_deg2.2341.963136
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5725272
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.10723.109119
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.89915379
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8091521
X-RAY DIFFRACTIONr_chiral_restr0.1970.2331
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0211798
LS refinement shellResolution: 1.849→1.897 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 143 -
Rwork0.266 2560 -
obs--99.78 %
Refinement TLS params.Method: refined / Origin x: -30.9229 Å / Origin y: -27.3963 Å / Origin z: 0.6877 Å
111213212223313233
T0.0468 Å20.0203 Å20.0184 Å2-0.0398 Å2-0.0051 Å2--0.0207 Å2
L0.814 °2-0.0504 °20.203 °2-0.468 °2-0.032 °2--1.0756 °2
S-0.0362 Å °-0.0035 Å °-0.0187 Å °-0.0477 Å °0.0236 Å °-0.029 Å °0.0146 Å °0.1262 Å °0.0126 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A35 - 305
2X-RAY DIFFRACTION1A555
3X-RAY DIFFRACTION1A1 - 27
4X-RAY DIFFRACTION1A327 - 452

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