data_5MD
#

_chem_comp.id                                   5MD
_chem_comp.name                                 "2'-deoxy-1-methyl-pseudouridine"
_chem_comp.type                                 "DNA LINKING"
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C10 H14 N2 O5"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        "5-METHYL-2'-DEOXYPSEUDOURIDINE"
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2000-07-26
_chem_comp.pdbx_modified_date                   2020-06-17
_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                       242.229
_chem_comp.one_letter_code                      N
_chem_comp.three_letter_code                    5MD
_chem_comp.pdbx_model_coordinates_details       ?
_chem_comp.pdbx_model_coordinates_missing_flag  N
_chem_comp.pdbx_ideal_coordinates_details       ?
_chem_comp.pdbx_ideal_coordinates_missing_flag  N
_chem_comp.pdbx_model_coordinates_db_code       1F8Y
_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
5MD  "O5'"   "O5'"   O  0  1  N  N  N  56.676   -7.839  -22.105   2.029  -1.350  -3.670  "O5'"   5MD   1  
5MD  "C5'"   "C5'"   C  0  1  N  N  N  55.930   -6.833  -22.853   1.212  -0.178  -3.643  "C5'"   5MD   2  
5MD  "C4'"   "C4'"   C  0  1  N  N  R  56.276   -5.429  -22.312  -0.069  -0.467  -2.860  "C4'"   5MD   3  
5MD  "O4'"   "O4'"   O  0  1  N  N  N  57.683   -5.311  -22.274   0.249  -0.806  -1.498  "O4'"   5MD   4  
5MD  "C1'"   "C1'"   C  0  1  N  N  R  58.215   -4.739  -23.496  -0.818  -0.289  -0.676  "C1'"   5MD   5  
5MD  C1      C1      C  0  1  N  N  N  58.796   -5.719  -24.526  -0.355  -0.117   0.747  C1      5MD   6  
5MD  C6      C6      C  0  1  N  N  N  58.800   -7.048  -24.247  -1.012  -0.725   1.758  C6      5MD   7  
5MD  C2      C2      C  0  1  N  N  N  59.300   -5.242  -25.832   0.772   0.685   1.042  C2      5MD   8  
5MD  O2      O2      O  0  1  N  N  N  59.488   -4.103  -26.233   1.380   1.244   0.147  O2      5MD   9  
5MD  N3      N3      N  0  1  N  N  N  59.726   -6.251  -26.648   1.167   0.825   2.324  N3      5MD  10  
5MD  C4      C4      C  0  1  N  N  N  59.727   -7.588  -26.380   0.491   0.211   3.313  C4      5MD  11  
5MD  O4      O4      O  0  1  N  N  N  59.980   -8.335  -27.287   0.859   0.347   4.464  O4      5MD  12  
5MD  N5      N5      N  0  1  N  N  N  59.254   -7.979  -25.148  -0.578  -0.557   3.045  N5      5MD  13  
5MD  C5      C5      C  0  1  N  N  N  59.254   -9.381  -24.752  -1.291  -1.217   4.142  C5      5MD  14  
5MD  "C3'"   "C3'"   C  0  1  N  N  S  55.818   -4.279  -23.144  -0.958   0.790  -2.825  "C3'"   5MD  15  
5MD  "O3'"   "O3'"   O  0  1  N  N  N  55.639   -3.141  -22.324  -2.221   0.531  -3.439  "O3'"   5MD  16  
5MD  "C2'"   "C2'"   C  0  1  N  N  N  57.016   -3.969  -23.998  -1.139   1.085  -1.316  "C2'"   5MD  17  
5MD  "H5'"   H5*     H  0  1  N  N  N  56.463   -8.702  -22.437   2.824  -1.124  -4.172  "H5'"   5MD  18  
5MD  "H5'1"  "1H5'"  H  0  0  N  N  N  56.097   -6.914  -23.952   0.957   0.111  -4.663  "H5'1"  5MD  19  
5MD  "H5'2"  "2H5'"  H  0  0  N  N  N  54.832   -7.029  -22.844   1.757   0.633  -3.161  "H5'2"  5MD  20  
5MD  "H4'"   "H4'"   H  0  1  N  N  N  55.756   -5.367  -21.327  -0.610  -1.290  -3.327  "H4'"   5MD  21  
5MD  "H1'"   "H1'"   H  0  1  N  N  N  59.128   -4.128  -23.308  -1.688  -0.945  -0.719  "H1'"   5MD  22  
5MD  H6      H6      H  0  1  N  N  N  58.425   -7.379  -23.264  -1.874  -1.341   1.552  H6      5MD  23  
5MD  HN3     HN3     H  0  1  N  N  N  60.084   -5.974  -27.562   1.939   1.373   2.534  HN3     5MD  24  
5MD  H51     1H5     H  0  1  N  N  N  59.622  -10.137  -25.483  -0.808  -0.972   5.088  H51     5MD  25  
5MD  H52     2H5     H  0  1  N  N  N  59.823   -9.489  -23.799  -2.325  -0.873   4.163  H52     5MD  26  
5MD  H53     3H5     H  0  1  N  N  N  58.227   -9.665  -24.421  -1.269  -2.296   3.993  H53     5MD  27  
5MD  "H3'"   "H3'"   H  0  1  N  N  N  54.875   -4.510  -23.693  -0.458   1.624  -3.319  "H3'"   5MD  28  
5MD  "H3'A"  H3*     H  0  0  N  N  N  55.347   -2.408  -22.853  -2.753   1.332  -3.335  "H3'A"  5MD  29  
5MD  "H2'1"  "1H2'"  H  0  0  N  N  N  57.216   -2.873  -24.057  -2.164   1.385  -1.098  "H2'1"  5MD  30  
5MD  "H2'2"  "2H2'"  H  0  0  N  N  N  56.819   -4.156  -25.079  -0.433   1.844  -0.980  "H2'2"  5MD  31  
#   #
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
5MD  "O5'"  "C5'"   SING  N  N   1  
5MD  "O5'"  "H5'"   SING  N  N   2  
5MD  "C5'"  "C4'"   SING  N  N   3  
5MD  "C5'"  "H5'1"  SING  N  N   4  
5MD  "C5'"  "H5'2"  SING  N  N   5  
5MD  "C4'"  "O4'"   SING  N  N   6  
5MD  "C4'"  "C3'"   SING  N  N   7  
5MD  "C4'"  "H4'"   SING  N  N   8  
5MD  "O4'"  "C1'"   SING  N  N   9  
5MD  "C1'"  C1      SING  N  N  10  
5MD  "C1'"  "C2'"   SING  N  N  11  
5MD  "C1'"  "H1'"   SING  N  N  12  
5MD  C1     C6      DOUB  N  N  13  
5MD  C1     C2      SING  N  N  14  
5MD  C6     N5      SING  N  N  15  
5MD  C6     H6      SING  N  N  16  
5MD  C2     O2      DOUB  N  N  17  
5MD  C2     N3      SING  N  N  18  
5MD  N3     C4      SING  N  N  19  
5MD  N3     HN3     SING  N  N  20  
5MD  C4     O4      DOUB  N  N  21  
5MD  C4     N5      SING  N  N  22  
5MD  N5     C5      SING  N  N  23  
5MD  C5     H51     SING  N  N  24  
5MD  C5     H52     SING  N  N  25  
5MD  C5     H53     SING  N  N  26  
5MD  "C3'"  "O3'"   SING  N  N  27  
5MD  "C3'"  "C2'"   SING  N  N  28  
5MD  "C3'"  "H3'"   SING  N  N  29  
5MD  "O3'"  "H3'A"  SING  N  N  30  
5MD  "C2'"  "H2'1"  SING  N  N  31  
5MD  "C2'"  "H2'2"  SING  N  N  32  
#   #
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
5MD  SMILES            ACDLabs               10.04  "O=C1N(C=C(C(=O)N1)C2OC(CO)C(O)C2)C"  
5MD  SMILES_CANONICAL  CACTVS                3.341  "CN1C=C([C@H]2C[C@H](O)[C@@H](CO)O2)C(=O)NC1=O"  
5MD  SMILES            CACTVS                3.341  "CN1C=C([CH]2C[CH](O)[CH](CO)O2)C(=O)NC1=O"  
5MD  SMILES_CANONICAL  "OpenEye OEToolkits"  1.5.0  "CN1C=C(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)CO)O"  
5MD  SMILES            "OpenEye OEToolkits"  1.5.0  "CN1C=C(C(=O)NC1=O)C2CC(C(O2)CO)O"  
5MD  InChI             InChI                 1.03   "InChI=1S/C10H14N2O5/c1-12-3-5(9(15)11-10(12)16)7-2-6(14)8(4-13)17-7/h3,6-8,13-14H,2,4H2,1H3,(H,11,15,16)/t6-,7+,8+/m0/s1"  
5MD  InChIKey          InChI                 1.03   AMDJRICBYOAHBZ-XLPZGREQSA-N  
#   #
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
5MD  "SYSTEMATIC NAME"  ACDLabs               10.04  "(1R)-1,4-anhydro-2-deoxy-1-(1-methyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)-D-erythro-pentitol"  
5MD  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  1.5.0  "5-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-1-methyl-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
5MD  "Create component"   2000-07-26  RCSB  
5MD  "Modify descriptor"  2011-06-04  RCSB  
5MD  "Modify name"        2018-01-16  RCSB  
5MD  "Modify synonyms"    2020-06-05  PDBE  
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     5MD
_pdbx_chem_comp_synonyms.name        "5-METHYL-2'-DEOXYPSEUDOURIDINE"
_pdbx_chem_comp_synonyms.provenance  ?
_pdbx_chem_comp_synonyms.type        ?
##
