data_JKM
#

_chem_comp.id                                   JKM
_chem_comp.name                                 
;1-[(2S,3aS,4S,6R,6aR)-2-hydroxy-6-(hydroxymethyl)-2-oxidotetrahydrofuro[3,4-d][1,3,2]dioxaphosphol-4-yl]pyrimidine-2,4(
1H,3H)-dione
;

_chem_comp.type                                 NON-POLYMER
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C9 H11 N2 O8 P"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        "Uridine 2',3'-cyclophosphate"
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2012-02-24
_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                       306.166
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    JKM
_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       4DVL
_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
JKM  P       P       P  0  1  N  N  N   9.890  20.249  12.688  -2.550  -1.596  -0.239  P       JKM   1  
JKM  N1      N1      N  0  1  N  N  N  10.913  24.275  15.576   1.746   0.308   0.304  N1      JKM   2  
JKM  C2      C2      C  0  1  N  N  N  12.397  24.474  15.466   2.216  -0.917   0.601  C2      JKM   3  
JKM  O2      O2      O  0  1  N  N  N  13.007  24.188  14.469   1.488  -1.722   1.148  O2      JKM   4  
JKM  N3      N3      N  0  1  N  N  N  13.071  25.027  16.584   3.481  -1.265   0.299  N3      JKM   5  
JKM  C4      C4      C  0  1  N  N  N  12.364  25.326  17.700   4.301  -0.383  -0.308  C4      JKM   6  
JKM  O4      O4      O  0  1  N  N  N  12.950  25.845  18.785   5.446  -0.697  -0.582  O4      JKM   7  
JKM  C5      C5      C  0  1  N  N  N  10.952  25.132  17.867   3.819   0.910  -0.625  C5      JKM   8  
JKM  C6      C6      C  0  1  N  N  N  10.282  24.635  16.794   2.546   1.231  -0.312  C6      JKM   9  
JKM  "C1'"   "C1'"   C  0  1  N  N  S   9.900  23.748  14.572   0.362   0.655   0.639  "C1'"   JKM  10  
JKM  "C2'"   "C2'"   C  0  1  N  N  S  10.172  22.494  13.730  -0.608  -0.240  -0.105  "C2'"   JKM  11  
JKM  "O2'"   "O2'"   O  0  1  N  N  N  10.096  21.176  14.141  -1.012  -1.513   0.336  "O2'"   JKM  12  
JKM  O20     O20     O  0  1  N  N  N   8.986  21.509  11.981  -2.831  -0.063  -0.777  O20     JKM  13  
JKM  O2P     O2P     O  0  1  N  N  N   8.796  19.121  13.020  -3.578  -1.984   0.938  O2P     JKM  14  
JKM  "C3'"   "C3'"   C  0  1  N  N  R   8.834  22.559  12.887  -1.905   0.638   0.029  "C3'"   JKM  15  
JKM  O3P     O3P     O  0  1  N  N  N  11.116  19.722  12.014  -2.641  -2.567  -1.352  O3P     JKM  16  
JKM  "C4'"   "C4'"   C  0  1  N  N  R   8.693  24.053  12.555  -1.344   1.996  -0.319  "C4'"   JKM  17  
JKM  "O4'"   "O4'"   O  0  1  N  N  N   9.437  24.709  13.589   0.032   1.984   0.145  "O4'"   JKM  18  
JKM  "C5'"   "C5'"   C  0  1  N  N  N   7.173  24.350  12.668  -2.133   3.094   0.398  "C5'"   JKM  19  
JKM  "O5'"   "O5'"   O  0  1  N  N  N   6.515  23.821  11.541  -1.666   4.374  -0.031  "O5'"   JKM  20  
JKM  H5      H5      H  0  1  N  N  N  10.450  25.368  18.794   4.461   1.629  -1.112  H5      JKM  21  
JKM  H6      H6      H  0  1  N  N  N   9.212  24.507  16.873   2.161   2.212  -0.547  H6      JKM  22  
JKM  "H1'"   "H1'"   H  0  1  N  N  N   9.015  23.493  15.174   0.200   0.589   1.715  "H1'"   JKM  23  
JKM  "H2'"   "H2'"   H  0  1  N  N  N  11.029  22.671  13.063  -0.328  -0.288  -1.157  "H2'"   JKM  24  
JKM  HO2P    HO2P    H  0  0  N  N  N   9.113  18.275  12.726  -4.499  -2.046   0.650  HO2P    JKM  25  
JKM  "H3'"   "H3'"   H  0  1  N  N  N   8.018  22.308  13.581  -2.243   0.644   1.065  "H3'"   JKM  26  
JKM  "H4'"   "H4'"   H  0  1  N  N  N   9.068  24.277  11.546  -1.377   2.152  -1.397  "H4'"   JKM  27  
JKM  "H5'"   "H5'"   H  0  1  N  N  N   6.773  23.883  13.581  -3.192   2.994   0.159  "H5'"   JKM  28  
JKM  "H5'A"  "H5'A"  H  0  0  N  N  N   7.012  25.437  12.712  -1.993   2.998   1.475  "H5'A"  JKM  29  
JKM  "HO5'"  "HO5'"  H  0  0  N  N  N   5.584  24.000  11.604  -2.123   5.119   0.383  "HO5'"  JKM  30  
JKM  HN3     HN3     H  0  1  N  N  N  14.056  25.194  16.549   3.804  -2.152   0.520  HN3     JKM  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
JKM  O20    P       SING  N  N   1  
JKM  O3P    P       DOUB  N  N   2  
JKM  P      O2P     SING  N  N   3  
JKM  P      "O2'"   SING  N  N   4  
JKM  "C1'"  N1      SING  N  N   5  
JKM  C2     N1      SING  N  N   6  
JKM  N1     C6      SING  N  N   7  
JKM  O2     C2      DOUB  N  N   8  
JKM  C2     N3      SING  N  N   9  
JKM  N3     C4      SING  N  N  10  
JKM  C4     C5      SING  N  N  11  
JKM  C4     O4      DOUB  N  N  12  
JKM  C6     C5      DOUB  N  N  13  
JKM  C5     H5      SING  N  N  14  
JKM  C6     H6      SING  N  N  15  
JKM  "O4'"  "C1'"   SING  N  N  16  
JKM  "C2'"  "C1'"   SING  N  N  17  
JKM  "C1'"  "H1'"   SING  N  N  18  
JKM  "C3'"  "C2'"   SING  N  N  19  
JKM  "C2'"  "O2'"   SING  N  N  20  
JKM  "C2'"  "H2'"   SING  N  N  21  
JKM  O20    "C3'"   SING  N  N  22  
JKM  O2P    HO2P    SING  N  N  23  
JKM  "C4'"  "C3'"   SING  N  N  24  
JKM  "C3'"  "H3'"   SING  N  N  25  
JKM  "C4'"  "C5'"   SING  N  N  26  
JKM  "C4'"  "O4'"   SING  N  N  27  
JKM  "C4'"  "H4'"   SING  N  N  28  
JKM  "O5'"  "C5'"   SING  N  N  29  
JKM  "C5'"  "H5'"   SING  N  N  30  
JKM  "C5'"  "H5'A"  SING  N  N  31  
JKM  "O5'"  "HO5'"  SING  N  N  32  
JKM  N3     HN3     SING  N  N  33  
#   #
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
JKM  SMILES            ACDLabs               12.01  "O=C1C=CN(C(=O)N1)C2OC(C3OP(=O)(O)OC23)CO"  
JKM  InChI             InChI                 1.03   "InChI=1S/C9H11N2O8P/c12-3-4-6-7(19-20(15,16)18-6)8(17-4)11-2-1-5(13)10-9(11)14/h1-2,4,6-8,12H,3H2,(H,15,16)(H,10,13,14)/t4-,6-,7+,8+/m1/s1"  
JKM  InChIKey          InChI                 1.03   HWDMHJDYMFRXOX-GVYWOMJSSA-N  
JKM  SMILES_CANONICAL  CACTVS                3.370  "OC[C@H]1O[C@@H]([C@H]2O[P](O)(=O)O[C@H]12)N3C=CC(=O)NC3=O"  
JKM  SMILES            CACTVS                3.370  "OC[CH]1O[CH]([CH]2O[P](O)(=O)O[CH]12)N3C=CC(=O)NC3=O"  
JKM  SMILES_CANONICAL  "OpenEye OEToolkits"  1.7.6  "C1=CN(C(=O)NC1=O)[C@@H]2[C@@H]3[C@@H]([C@H](O2)CO)O[P@@](=O)(O3)O"  
JKM  SMILES            "OpenEye OEToolkits"  1.7.6  "C1=CN(C(=O)NC1=O)C2C3C(C(O2)CO)OP(=O)(O3)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
JKM  "SYSTEMATIC NAME"  ACDLabs               12.01  "1-[(2S,3aS,4S,6R,6aR)-2-hydroxy-6-(hydroxymethyl)-2-oxidotetrahydrofuro[3,4-d][1,3,2]dioxaphosphol-4-yl]pyrimidine-2,4(1H,3H)-dione"  
JKM  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  1.7.6  "1-[(2S,3aS,4S,6R,6aR)-6-(hydroxymethyl)-2-oxidanyl-2-oxidanylidene-3a,4,6,6a-tetrahydrofuro[3,4-d][1,3,2]dioxaphosphol-4-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
JKM  "Create component"  2012-02-24  RCSB  
JKM  "Modify synonyms"   2020-06-05  PDBE  
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     JKM
_pdbx_chem_comp_synonyms.name        "Uridine 2',3'-cyclophosphate"
_pdbx_chem_comp_synonyms.provenance  ?
_pdbx_chem_comp_synonyms.type        ?
##
