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- PDB-4hxx: Pyridinylpyrimidines selectively inhibit human methionine aminope... -

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Basic information

Entry
Database: PDB / ID: 4hxx
TitlePyridinylpyrimidines selectively inhibit human methionine aminopeptidase-1
ComponentsMethionine aminopeptidase 1
Keywordshydrolase/hydrolase inhibitor / Aminopeptidases / Pyrimidines / Pyrimidyl group / Pyridinylpyrimidine / cell cycle / hydrolase-hydrolase inhibitor complex
Function / homology
Function and homology information


N-terminal protein amino acid modification / peptidyl-methionine modification / methionyl aminopeptidase / initiator methionyl aminopeptidase activity / metalloexopeptidase activity / metalloaminopeptidase activity / protein maturation / aminopeptidase activity / cytosolic ribosome / platelet aggregation ...N-terminal protein amino acid modification / peptidyl-methionine modification / methionyl aminopeptidase / initiator methionyl aminopeptidase activity / metalloexopeptidase activity / metalloaminopeptidase activity / protein maturation / aminopeptidase activity / cytosolic ribosome / platelet aggregation / Inactivation, recovery and regulation of the phototransduction cascade / regulation of translation / proteolysis / metal ion binding / cytosol / cytoplasm
Similarity search - Function
MYND-like zinc finger / zf-MYND-like zinc finger, mRNA-binding / Zinc finger C6H2-type profile. / Methionine aminopeptidase subfamily 1 signature. / Peptidase M24A, methionine aminopeptidase, subfamily 1 / Peptidase M24, methionine aminopeptidase / Creatine Amidinohydrolase / Creatinase/methionine aminopeptidase superfamily / Peptidase M24 / Metallopeptidase family M24 ...MYND-like zinc finger / zf-MYND-like zinc finger, mRNA-binding / Zinc finger C6H2-type profile. / Methionine aminopeptidase subfamily 1 signature. / Peptidase M24A, methionine aminopeptidase, subfamily 1 / Peptidase M24, methionine aminopeptidase / Creatine Amidinohydrolase / Creatinase/methionine aminopeptidase superfamily / Peptidase M24 / Metallopeptidase family M24 / Creatinase/aminopeptidase-like / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Chem-1AY / : / : / Methionine aminopeptidase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.09 Å
AuthorsGabelli, S.B. / Zhang, F. / Liu, J. / Amzel, L.M.
CitationJournal: Bioorg.Med.Chem. / Year: 2013
Title: Pyridinylpyrimidines selectively inhibit human methionine aminopeptidase-1.
Authors: Zhang, P. / Yang, X. / Zhang, F. / Gabelli, S.B. / Wang, R. / Zhang, Y. / Bhat, S. / Chen, X. / Furlani, M. / Amzel, L.M. / Liu, J.O. / Ma, D.
History
DepositionNov 12, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2013Group: Database references
Revision 1.2May 15, 2013Group: Database references
Revision 1.3Apr 2, 2014Group: Other
Revision 1.4Nov 15, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.5Nov 20, 2019Group: Derived calculations / Category: pdbx_struct_conn_angle / struct_conn
Revision 1.6Feb 28, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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

Downloads & links

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Assembly

Deposited unit
A: Methionine aminopeptidase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0938
Polymers34,1791
Non-polymers9147
Water2,846158
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.500, 77.403, 48.068
Angle α, β, γ (deg.)90.000, 90.920, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Methionine aminopeptidase 1 / MAP 1 / MetAP 1 / Peptidase M 1


Mass: 34178.906 Da / Num. of mol.: 1 / Fragment: unp residues 81-384
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Strain: BL21 / Gene: KIAA0094, METAP1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P53582, methionyl aminopeptidase

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Non-polymers , 5 types, 165 molecules

#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Co
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-1AY / (1R)-N~2~-[5-chloro-2-(5-chloropyridin-2-yl)-6-methylpyrimidin-4-yl]-1-phenyl-N~1~-(4-phenylbutyl)ethane-1,2-diamine


Mass: 506.469 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H29Cl2N5
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / 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: 2.58 Å3/Da / Density % sol: 52.42 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 14-20 % PEG monomethyl ether 2000, 100 mM MES, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ DW / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 26, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.09→50 Å / Num. obs: 20262 / % possible obs: 97.9 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.117 / Χ2: 7.941 / Net I/σ(I): 14.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.09-2.1630.4917801.973186.6
2.16-2.253.30.42219192.376194.3
2.25-2.353.40.36720483.186199.3
2.35-2.483.60.34220564.3831100
2.48-2.633.60.27820715.719199.9
2.63-2.843.60.23120688.3011100
2.84-3.123.60.193206912.2791100
3.12-3.573.60.138205314.0161100
3.57-4.53.60.099208414.365199.7
4.5-503.60.06621149.185199.3

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
StructureStudiodata collection
RefinementResolution: 2.09→25.33 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.929 / WRfactor Rfree: 0.2579 / WRfactor Rwork: 0.1901 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8006 / SU B: 5.707 / SU ML: 0.153 / SU R Cruickshank DPI: 0.2206 / SU Rfree: 0.203 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.221 / ESU R Free: 0.203 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2579 1033 5.1 %RANDOM
Rwork0.1901 19193 --
obs0.1936 20226 97.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 108.47 Å2 / Biso mean: 43.0235 Å2 / Biso min: 17.93 Å2
Baniso -1Baniso -2Baniso -3
1-1.78 Å20 Å21.5 Å2
2---3.67 Å20 Å2
3---1.93 Å2
Refinement stepCycle: LAST / Resolution: 2.09→25.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2396 0 49 158 2603
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0212490
X-RAY DIFFRACTIONr_angle_refined_deg1.5511.9673382
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6035303
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.48523.13115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.19915404
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7281520
X-RAY DIFFRACTIONr_chiral_restr0.1070.2361
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021922
X-RAY DIFFRACTIONr_nbd_refined0.2170.21283
X-RAY DIFFRACTIONr_nbtor_refined0.3030.21660
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1770.2150
X-RAY DIFFRACTIONr_metal_ion_refined0.1020.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2090.234
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1850.24
X-RAY DIFFRACTIONr_mcbond_it0.9111.51515
X-RAY DIFFRACTIONr_mcangle_it1.6122456
X-RAY DIFFRACTIONr_scbond_it2.5431026
X-RAY DIFFRACTIONr_scangle_it3.8844.5926
LS refinement shellResolution: 2.09→2.144 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 73 -
Rwork0.267 1196 -
all-1269 -
obs--85.22 %

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