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- PDB-3k45: Alternate Binding Modes Observed for the E- and Z-isomers of 2,4-... -

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Basic information

Entry
Database: PDB / ID: 3k45
TitleAlternate Binding Modes Observed for the E- and Z-isomers of 2,4-Diaminofuro[2,3d]pyrimidines as Ternary Complexes with NADPH and Mouse Dihydrofolate Reductase
ComponentsDihydrofolate reductase
KeywordsOXIDOREDUCTASE / PROTEIN LIGAND COFACTOR TERNARY COMPLEX / NADP / ONE-CARBON METABOLISM
Function / homology
Function and homology information


Metabolism of folate and pterines / regulation of removal of superoxide radicals / dihydrofolic acid binding / tetrahydrobiopterin biosynthetic process / tetrahydrofolate metabolic process / response to methotrexate / tetrahydrofolate interconversion / axon regeneration / dihydrofolate metabolic process / folic acid metabolic process ...Metabolism of folate and pterines / regulation of removal of superoxide radicals / dihydrofolic acid binding / tetrahydrobiopterin biosynthetic process / tetrahydrofolate metabolic process / response to methotrexate / tetrahydrofolate interconversion / axon regeneration / dihydrofolate metabolic process / folic acid metabolic process / dihydrofolate reductase / dihydrofolate reductase activity / tetrahydrofolate biosynthetic process / positive regulation of nitric-oxide synthase activity / response to nicotine / NADP binding / mRNA binding / mitochondrion / nucleus / cytosol / cytoplasm
Similarity search - Function
Dihydrofolate Reductase, subunit A / Dihydrofolate Reductase, subunit A / Dihydrofolate reductase / Dihydrofolate reductase conserved site / Dihydrofolate reductase (DHFR) domain signature. / Dihydrofolate reductase domain / Dihydrofolate reductase / Dihydrofolate reductase (DHFR) domain profile. / Dihydrofolate reductase-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-51P / Chem-NDP / Dihydrofolate reductase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsCody, V.
CitationJournal: Bioorg.Med.Chem. / Year: 2009
Title: Design, synthesis, and X-ray crystal structures of 2,4-diaminofuro[2,3-d]pyrimidines as multireceptor tyrosine kinase and dihydrofolate reductase inhibitors.
Authors: Gangjee, A. / Li, W. / Lin, L. / Zeng, Y. / Ihnat, M. / Warnke, L.A. / Green, D.W. / Cody, V. / Pace, J. / Queener, S.F.
History
DepositionOct 5, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.3Sep 6, 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: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5323
Polymers21,4901
Non-polymers1,0422
Water3,261181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.358, 61.094, 43.304
Angle α, β, γ (deg.)90.00, 117.13, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Dihydrofolate reductase


Mass: 21489.818 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Dhfr / Plasmid: PPH70D / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): JM105 / References: UniProt: P00375, dihydrofolate reductase
#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Chemical ChemComp-51P / 5-[(1Z)-2-(2-methoxyphenyl)prop-1-en-1-yl]furo[2,3-d]pyrimidine-2,4-diamine


Mass: 296.324 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H16N4O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 181 / 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: 2.27 Å3/Da / Density % sol: 45.71 %
Crystal growpH: 8.3
Details: 200 MM TRIS, PH 8.3, 85 MM NA CACODYLATE, 25% PEG 4K, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 23, 2007
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→17.82 Å / Num. obs: 24297 / % possible obs: 98.5 % / Observed criterion σ(I): 1 / Redundancy: 2.4 % / Biso Wilson estimate: 33.2 Å2 / Rmerge(I) obs: 0.074 / Rsym value: 0.7 / Net I/σ(I): 8.2
Reflection shellResolution: 1.6→1.64 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 3.3 / Rsym value: 0.49 / % possible all: 95.3

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.2.0019refinement
d*TREKdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2FZJ

2fzj


Resolution: 1.6→17.82 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.939 / SU B: 5.834 / SU ML: 0.091 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.174 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.242 1227 5.1 %RANDOM
Rwork0.196 ---
obs0.198 23070 95.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 33.86 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.6→17.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1489 0 69 181 1739
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221724
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8432.0652365
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8445201
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.82524.42970
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.87615291
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.799159
X-RAY DIFFRACTIONr_chiral_restr0.120.2250
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021292
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2040.2828
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3160.21161
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.2162
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.260.240
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1340.222
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3071.51011
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.94821598
X-RAY DIFFRACTIONr_scbond_it2.7193837
X-RAY DIFFRACTIONr_scangle_it3.5844.5767
X-RAY DIFFRACTIONr_rigid_bond_restr2.00431848
X-RAY DIFFRACTIONr_sphericity_free5.63181
X-RAY DIFFRACTIONr_sphericity_bonded3.36831670
LS refinement shellResolution: 1.6→1.64 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.449 77 -
Rwork0.304 1645 -
obs--91.94 %

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