data_EDV
#

_chem_comp.id                                   EDV
_chem_comp.name                                 "1-(2-deoxy-2-methyl-beta-D-arabinofuranosyl)-5-ethynylpyrimidine-2,4(1H,3H)-dione"
_chem_comp.type                                 NON-POLYMER
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C12 H14 N2 O5"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        "(2'S)-2'-DEOXY-2'-METHYL-5-ETHYNYLURIDINE"
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2014-02-12
_chem_comp.pdbx_modified_date                   2021-03-01
_chem_comp.pdbx_ambiguous_flag                  N
_chem_comp.pdbx_release_status                  REL
_chem_comp.pdbx_replaced_by                     ?
_chem_comp.pdbx_replaces                        ?
_chem_comp.formula_weight                       266.250
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    EDV
_chem_comp.pdbx_model_coordinates_details       ?
_chem_comp.pdbx_model_coordinates_missing_flag  N
_chem_comp.pdbx_ideal_coordinates_details       Corina
_chem_comp.pdbx_ideal_coordinates_missing_flag  N
_chem_comp.pdbx_model_coordinates_db_code       4OQX
_chem_comp.pdbx_subcomponent_list               ?
_chem_comp.pdbx_processing_site                 RCSB
#   #
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.alt_atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.charge
_chem_comp_atom.pdbx_align
_chem_comp_atom.pdbx_aromatic_flag
_chem_comp_atom.pdbx_leaving_atom_flag
_chem_comp_atom.pdbx_stereo_config
_chem_comp_atom.model_Cartn_x
_chem_comp_atom.model_Cartn_y
_chem_comp_atom.model_Cartn_z
_chem_comp_atom.pdbx_model_Cartn_x_ideal
_chem_comp_atom.pdbx_model_Cartn_y_ideal
_chem_comp_atom.pdbx_model_Cartn_z_ideal
_chem_comp_atom.pdbx_component_atom_id
_chem_comp_atom.pdbx_component_comp_id
_chem_comp_atom.pdbx_ordinal
EDV  O01  O01  O  0  1  N  N  N  51.215  23.252  53.490  -3.720  -2.443   1.225  O01  EDV   1  
EDV  C03  C03  C  0  1  N  N  N  50.233  24.086  52.875  -3.572  -1.658   0.040  C03  EDV   2  
EDV  C06  C06  C  0  1  N  N  R  50.172  25.489  53.525  -2.880  -0.338   0.385  C06  EDV   3  
EDV  O08  O08  O  0  1  N  N  N  48.882  25.939  53.086  -1.499  -0.571   0.738  O08  EDV   4  
EDV  C09  C09  C  0  1  N  N  S  50.118  25.617  55.113  -2.821   0.579  -0.857  C09  EDV   5  
EDV  O11  O11  O  0  1  N  N  N  50.420  26.959  55.480  -3.878   1.540  -0.820  O11  EDV   6  
EDV  C13  C13  C  0  1  N  N  S  48.660  25.369  55.495  -1.448   1.278  -0.742  C13  EDV   7  
EDV  C15  C15  C  0  1  N  N  N  48.395  23.884  55.598  -0.569   0.933  -1.946  C15  EDV   8  
EDV  C16  C16  C  0  1  N  N  R  47.992  26.080  54.265  -0.840   0.701   0.555  C16  EDV   9  
EDV  N18  N18  N  0  1  N  N  N  46.602  25.674  53.825   0.604   0.509   0.400  N18  EDV  10  
EDV  C19  C19  C  0  1  N  N  N  45.512  26.352  54.257   1.433   1.539   0.637  C19  EDV  11  
EDV  O20  O20  O  0  1  N  N  N  45.622  27.286  55.049   0.964   2.609   0.975  O20  EDV  12  
EDV  N21  N21  N  0  1  N  N  N  44.221  25.998  53.813   2.766   1.421   0.512  N21  EDV  13  
EDV  C23  C23  C  0  1  N  N  N  44.043  24.941  52.900   3.314   0.246   0.139  C23  EDV  14  
EDV  O24  O24  O  0  1  N  N  N  42.918  24.616  52.504   4.521   0.132   0.024  O24  EDV  15  
EDV  C25  C25  C  0  1  N  N  N  45.155  24.259  52.452   2.425  -0.894  -0.126  C25  EDV  16  
EDV  C26  C26  C  0  1  N  N  N  46.433  24.614  52.893   1.079  -0.714   0.024  C26  EDV  17  
EDV  C28  C28  C  0  1  N  N  N  44.927  23.219  51.555   2.956  -2.165  -0.520  C28  EDV  18  
EDV  C29  C29  C  0  1  N  N  N  44.725  22.393  50.839   3.391  -3.206  -0.843  C29  EDV  19  
EDV  H1   H1   H  0  1  N  N  N  51.221  22.403  53.064  -4.152  -3.296   1.081  H1   EDV  20  
EDV  H2   H2   H  0  1  N  N  N  50.481  24.199  51.809  -2.969  -2.206  -0.684  H2   EDV  21  
EDV  H3   H3   H  0  1  N  N  N  49.248  23.606  52.973  -4.554  -1.454  -0.385  H3   EDV  22  
EDV  H4   H4   H  0  1  N  N  N  50.981  26.123  53.133  -3.403   0.161   1.201  H4   EDV  23  
EDV  H5   H5   H  0  1  N  N  N  50.787  24.881  55.582  -2.876  -0.013  -1.771  H5   EDV  24  
EDV  H6   H6   H  0  1  N  N  N  50.390  27.044  56.426  -4.763   1.152  -0.828  H6   EDV  25  
EDV  H7   H7   H  0  1  N  N  N  48.400  25.888  56.429  -1.575   2.357  -0.660  H7   EDV  26  
EDV  H8   H8   H  0  1  N  N  N  48.903  23.481  56.487  -1.057   1.270  -2.861  H8   EDV  27  
EDV  H9   H9   H  0  1  N  N  N  47.312  23.710  55.684   0.396   1.429  -1.845  H9   EDV  28  
EDV  H10  H10  H  0  1  N  N  N  48.777  23.380  54.698  -0.420  -0.146  -1.990  H10  EDV  29  
EDV  H11  H11  H  0  1  N  N  N  47.948  27.150  54.514  -1.048   1.360   1.398  H11  EDV  30  
EDV  H12  H12  H  0  1  N  N  N  43.425  26.502  54.149   3.337   2.185   0.691  H12  EDV  31  
EDV  H13  H13  H  0  1  N  N  N  47.296  24.080  52.524   0.396  -1.529  -0.162  H13  EDV  32  
EDV  H14  H14  H  0  1  N  N  N  44.532  21.605  50.156   3.781  -4.137  -1.132  H14  EDV  33  
#   #
loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.value_order
_chem_comp_bond.pdbx_aromatic_flag
_chem_comp_bond.pdbx_stereo_config
_chem_comp_bond.pdbx_ordinal
EDV  C29  C28  TRIP  N  N   1  
EDV  C28  C25  SING  N  N   2  
EDV  C25  C26  DOUB  N  N   3  
EDV  C25  C23  SING  N  N   4  
EDV  O24  C23  DOUB  N  N   5  
EDV  C03  O01  SING  N  N   6  
EDV  C03  C06  SING  N  N   7  
EDV  C26  N18  SING  N  N   8  
EDV  C23  N21  SING  N  N   9  
EDV  O08  C06  SING  N  N  10  
EDV  O08  C16  SING  N  N  11  
EDV  C06  C09  SING  N  N  12  
EDV  N21  C19  SING  N  N  13  
EDV  N18  C19  SING  N  N  14  
EDV  N18  C16  SING  N  N  15  
EDV  C19  O20  DOUB  N  N  16  
EDV  C16  C13  SING  N  N  17  
EDV  C09  O11  SING  N  N  18  
EDV  C09  C13  SING  N  N  19  
EDV  C13  C15  SING  N  N  20  
EDV  O01  H1   SING  N  N  21  
EDV  C03  H2   SING  N  N  22  
EDV  C03  H3   SING  N  N  23  
EDV  C06  H4   SING  N  N  24  
EDV  C09  H5   SING  N  N  25  
EDV  O11  H6   SING  N  N  26  
EDV  C13  H7   SING  N  N  27  
EDV  C15  H8   SING  N  N  28  
EDV  C15  H9   SING  N  N  29  
EDV  C15  H10  SING  N  N  30  
EDV  C16  H11  SING  N  N  31  
EDV  N21  H12  SING  N  N  32  
EDV  C26  H13  SING  N  N  33  
EDV  C29  H14  SING  N  N  34  
#   #
loop_
_pdbx_chem_comp_descriptor.comp_id
_pdbx_chem_comp_descriptor.type
_pdbx_chem_comp_descriptor.program
_pdbx_chem_comp_descriptor.program_version
_pdbx_chem_comp_descriptor.descriptor
EDV  SMILES            ACDLabs               12.01  "O=C1NC(=O)N(C=C1C#C)C2OC(C(O)C2C)CO"  
EDV  InChI             InChI                 1.03   "InChI=1S/C12H14N2O5/c1-3-7-4-14(12(18)13-10(7)17)11-6(2)9(16)8(5-15)19-11/h1,4,6,8-9,11,15-16H,5H2,2H3,(H,13,17,18)/t6-,8+,9-,11+/m0/s1"  
EDV  InChIKey          InChI                 1.03   HBALXYGFMJGYHQ-GTQWGBSQSA-N  
EDV  SMILES_CANONICAL  CACTVS                3.385  "C[C@H]1[C@H](O)[C@@H](CO)O[C@H]1N2C=C(C#C)C(=O)NC2=O"  
EDV  SMILES            CACTVS                3.385  "C[CH]1[CH](O)[CH](CO)O[CH]1N2C=C(C#C)C(=O)NC2=O"  
EDV  SMILES_CANONICAL  "OpenEye OEToolkits"  1.7.6  "C[C@H]1[C@@H]([C@H](O[C@H]1N2C=C(C(=O)NC2=O)C#C)CO)O"  
EDV  SMILES            "OpenEye OEToolkits"  1.7.6  "CC1C(C(OC1N2C=C(C(=O)NC2=O)C#C)CO)O"  
#   #
loop_
_pdbx_chem_comp_identifier.comp_id
_pdbx_chem_comp_identifier.type
_pdbx_chem_comp_identifier.program
_pdbx_chem_comp_identifier.program_version
_pdbx_chem_comp_identifier.identifier
EDV  "SYSTEMATIC NAME"  ACDLabs               12.01  "1-(2-deoxy-2-methyl-beta-D-arabinofuranosyl)-5-ethynylpyrimidine-2,4(1H,3H)-dione"  
EDV  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  1.7.6  "5-ethynyl-1-[(2R,3S,4S,5R)-5-(hydroxymethyl)-3-methyl-4-oxidanyl-oxolan-2-yl]pyrimidine-2,4-dione"  
#   #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
EDV  "Create component"  2014-02-12  RCSB  
EDV  "Modify synonyms"   2014-02-18  RCSB  
EDV  "Initial release"   2014-08-13  RCSB  
EDV  "Modify synonyms"   2021-03-01  PDBE  
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     EDV
_pdbx_chem_comp_synonyms.name        "(2'S)-2'-DEOXY-2'-METHYL-5-ETHYNYLURIDINE"
_pdbx_chem_comp_synonyms.provenance  ?
_pdbx_chem_comp_synonyms.type        ?
##
