data_TD5
# 
_chem_comp.id                                    TD5 
_chem_comp.name                                  "(4~{R})-4-[3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-4-methyl-5-[2-[oxidanyl(phosphonooxy)phosphoryl]oxyethyl]-1,3-thiazol-3-ium-2-yl]-4-oxidanyl-butanoic acid" 
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C16 H25 N4 O10 P2 S" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    1 
_chem_comp.pdbx_initial_date                     2015-11-20 
_chem_comp.pdbx_modified_date                    2016-10-28 
_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                        527.403 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     TD5 
_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        5EJM 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  PDBJ 
# 
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 
TD5 S1     S1  S 0 1 Y N N -13.962 -8.702  -27.928 -1.406 1.942  -0.438 S1     TD5 1  
TD5 C2     C1  C 0 1 Y N N -14.514 -8.330  -26.317 -2.689 0.874  -0.068 C2     TD5 2  
TD5 N3     N1  N 1 1 Y N N -15.237 -9.389  -25.859 -2.313 0.020  0.823  N3     TD5 3  
TD5 C4     C2  C 0 1 Y N N -15.324 -10.439 -26.707 -1.076 0.119  1.266  C4     TD5 4  
TD5 C5     C3  C 0 1 Y N N -14.666 -10.291 -27.938 -0.368 1.110  0.717  C5     TD5 5  
TD5 C6     C4  C 0 1 N N N -14.577 -11.316 -29.109 1.065  1.456  1.030  C6     TD5 6  
TD5 C7     C5  C 0 1 N N N -15.297 -10.914 -30.441 1.993  0.680  0.093  C7     TD5 7  
TD5 O7     O1  O 0 1 N N N -14.965 -11.994 -31.257 3.352  1.008  0.391  O7     TD5 8  
TD5 PA     P1  P 0 1 N N N -15.111 -11.794 -32.817 4.601  0.373  -0.403 PA     TD5 9  
TD5 PB     P2  P 0 1 N N N -12.464 -10.750 -33.168 7.507  0.377  0.182  PB     TD5 10 
TD5 "N1'"  N2  N 0 1 Y N N -19.600 -10.064 -24.310 -2.079 -3.422 -1.273 "N1'"  TD5 11 
TD5 C11    C6  C 0 1 N N R -14.212 -7.071  -25.528 -4.059 0.923  -0.693 C11    TD5 12 
TD5 C13    C7  C 0 1 N N N -12.433 -6.548  -23.648 -6.278 2.070  -0.645 C13    TD5 13 
TD5 O1A    O2  O 0 1 N N N -14.840 -13.122 -33.535 4.522  -1.104 -0.348 O1A    TD5 14 
TD5 O1B    O3  O 0 1 N N N -11.917 -10.638 -31.750 8.320  0.906  1.466  O1B    TD5 15 
TD5 "C2'"  C8  C 0 1 Y N N -20.168 -8.998  -24.915 -2.720 -4.516 -0.915 "C2'"  TD5 16 
TD5 O2A    O4  O 0 1 N N N -16.479 -11.274 -33.100 4.562  0.856  -1.939 O2A    TD5 17 
TD5 O2B    O5  O 0 1 N N N -12.031 -9.577  -34.022 7.554  -1.102 0.143  O2B    TD5 18 
TD5 "N3'"  N3  N 0 1 Y N N -19.400 -8.043  -25.422 -3.520 -4.541 0.132  "N3'"  TD5 19 
TD5 O3A    O6  O 0 1 N N N -14.065 -10.680 -33.244 5.975  0.863  0.278  O3A    TD5 20 
TD5 O3B    O7  O 0 1 N N N -11.986 -12.029 -33.840 8.174  0.971  -1.158 O3B    TD5 21 
TD5 "C4'"  C9  C 0 1 Y N N -18.041 -8.101  -25.317 -3.707 -3.451 0.869  "C4'"  TD5 22 
TD5 "N4'"  N4  N 0 1 N N N -17.374 -7.086  -25.834 -4.549 -3.481 1.970  "N4'"  TD5 23 
TD5 "C5'"  C10 C 0 1 Y N N -17.427 -9.201  -24.692 -3.042 -2.274 0.517  "C5'"  TD5 24 
TD5 "C6'"  C11 C 0 1 Y N N -18.254 -10.187 -24.188 -2.215 -2.295 -0.588 "C6'"  TD5 25 
TD5 "C7'"  C12 C 0 1 N N N -15.893 -9.383  -24.527 -3.223 -1.013 1.323  "C7'"  TD5 26 
TD5 OL1    O8  O 0 1 N N N -13.692 -6.106  -26.448 -3.933 1.095  -2.106 OL1    TD5 27 
TD5 OL2    O9  O 0 1 N N N -12.391 -6.045  -21.333 -8.341 3.405  -0.400 OL2    TD5 28 
TD5 OL3    O10 O 0 1 N N N -13.480 -7.831  -21.895 -6.517 3.990  0.701  OL3    TD5 29 
TD5 CLB    C13 C 0 1 N N N -13.019 -7.572  -24.654 -4.847 2.095  -0.104 CLB    TD5 30 
TD5 CLC    C14 C 0 1 N N N -12.791 -6.831  -22.218 -7.054 3.225  -0.065 CLC    TD5 31 
TD5 CM2    C15 C 0 1 N N N -21.734 -8.892  -25.046 -2.534 -5.773 -1.725 CM2    TD5 32 
TD5 CM4    C16 C 0 1 N N N -16.116 -11.728 -26.337 -0.506 -0.811 2.306  CM4    TD5 33 
TD5 H6     H1  H 0 1 N N N -15.019 -12.261 -28.761 1.219  2.526  0.890  H6     TD5 34 
TD5 H6A    H2  H 0 1 N N N -13.512 -11.472 -29.338 1.286  1.189  2.063  H6A    TD5 35 
TD5 H7A    H3  H 0 1 N N N -14.905 -9.968  -30.843 1.839  -0.390 0.233  H7A    TD5 36 
TD5 H7     H4  H 0 1 N N N -16.385 -10.831 -30.303 1.773  0.947  -0.940 H7     TD5 37 
TD5 H1     H5  H 0 1 N N N -15.062 -6.721  -24.923 -4.586 -0.009 -0.486 H1     TD5 38 
TD5 H13    H6  H 0 1 N N N -11.337 -6.560  -23.740 -6.258 2.155  -1.731 H13    TD5 39 
TD5 H13A   H7  H 0 0 N N N -12.812 -5.549  -23.909 -6.757 1.133  -0.362 H13A   TD5 40 
TD5 H2     H8  H 0 1 N N N -11.402 -9.844  -31.671 9.252  0.650  1.475  H2     TD5 41 
TD5 H3     H9  H 0 1 N N N -16.932 -11.873 -33.681 4.610  1.815  -2.051 H3     TD5 42 
TD5 H4     H10 H 0 1 N N N -11.524 -11.813 -34.642 8.178  1.937  -1.201 H4     TD5 43 
TD5 "HN4'" H11 H 0 0 N N N -18.018 -6.429  -26.227 -4.939 -4.320 2.258  "HN4'" TD5 44 
TD5 HN4A   H12 H 0 0 N N N -16.838 -6.640  -25.117 -4.747 -2.663 2.451  HN4A   TD5 45 
TD5 "H6'"  H13 H 0 1 N N N -17.831 -11.052 -23.699 -1.684 -1.404 -0.890 "H6'"  TD5 46 
TD5 "H7'A" H14 H 0 0 N N N -15.692 -10.337 -24.017 -3.002 -1.217 2.370  "H7'A" TD5 47 
TD5 "H7'"  H15 H 0 1 N N N -15.490 -8.554  -23.926 -4.253 -0.667 1.229  "H7'"  TD5 48 
TD5 HOL1   H16 H 0 0 N N N -13.491 -5.302  -25.984 -3.473 1.905  -2.364 HOL1   TD5 49 
TD5 H5     H17 H 0 1 N N N -12.691 -6.345  -20.483 -8.797 4.159  -0.003 H5     TD5 50 
TD5 HLB    H18 H 0 1 N N N -13.365 -8.445  -24.081 -4.867 2.010  0.982  HLB    TD5 51 
TD5 HLBA   H19 H 0 0 N N N -12.209 -7.877  -25.333 -4.368 3.033  -0.387 HLBA   TD5 52 
TD5 HM2B   H20 H 0 0 N N N -21.996 -7.968  -25.582 -1.697 -6.344 -1.323 HM2B   TD5 53 
TD5 HM2    H21 H 0 1 N N N -22.115 -9.760  -25.604 -3.441 -6.374 -1.676 HM2    TD5 54 
TD5 HM2A   H22 H 0 0 N N N -22.185 -8.874  -24.043 -2.328 -5.509 -2.763 HM2A   TD5 55 
TD5 HM4A   H23 H 0 0 N N N -15.444 -12.441 -25.836 -0.106 -1.701 1.818  HM4A   TD5 56 
TD5 HM4B   H24 H 0 0 N N N -16.944 -11.468 -25.661 0.293  -0.305 2.847  HM4B   TD5 57 
TD5 HM4    H25 H 0 1 N N N -16.520 -12.186 -27.252 -1.291 -1.101 3.004  HM4    TD5 58 
# 
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 
TD5 O2B   PB     DOUB N N 1  
TD5 O3B   PB     SING N N 2  
TD5 O1A   PA     DOUB N N 3  
TD5 O3A   PB     SING N N 4  
TD5 O3A   PA     SING N N 5  
TD5 PB    O1B    SING N N 6  
TD5 O2A   PA     SING N N 7  
TD5 PA    O7     SING N N 8  
TD5 O7    C7     SING N N 9  
TD5 C7    C6     SING N N 10 
TD5 C6    C5     SING N N 11 
TD5 C5    S1     SING Y N 12 
TD5 C5    C4     DOUB Y N 13 
TD5 S1    C2     SING Y N 14 
TD5 C4    CM4    SING N N 15 
TD5 C4    N3     SING Y N 16 
TD5 OL1   C11    SING N N 17 
TD5 C2    N3     DOUB Y N 18 
TD5 C2    C11    SING N N 19 
TD5 N3    "C7'"  SING N N 20 
TD5 "N4'" "C4'"  SING N N 21 
TD5 C11   CLB    SING N N 22 
TD5 "N3'" "C4'"  DOUB Y N 23 
TD5 "N3'" "C2'"  SING Y N 24 
TD5 "C4'" "C5'"  SING Y N 25 
TD5 CM2   "C2'"  SING N N 26 
TD5 "C2'" "N1'"  DOUB Y N 27 
TD5 "C5'" "C7'"  SING N N 28 
TD5 "C5'" "C6'"  DOUB Y N 29 
TD5 CLB   C13    SING N N 30 
TD5 "N1'" "C6'"  SING Y N 31 
TD5 C13   CLC    SING N N 32 
TD5 CLC   OL3    DOUB N N 33 
TD5 CLC   OL2    SING N N 34 
TD5 C6    H6     SING N N 35 
TD5 C6    H6A    SING N N 36 
TD5 C7    H7A    SING N N 37 
TD5 C7    H7     SING N N 38 
TD5 C11   H1     SING N N 39 
TD5 C13   H13    SING N N 40 
TD5 C13   H13A   SING N N 41 
TD5 O1B   H2     SING N N 42 
TD5 O2A   H3     SING N N 43 
TD5 O3B   H4     SING N N 44 
TD5 "N4'" "HN4'" SING N N 45 
TD5 "N4'" HN4A   SING N N 46 
TD5 "C6'" "H6'"  SING N N 47 
TD5 "C7'" "H7'A" SING N N 48 
TD5 "C7'" "H7'"  SING N N 49 
TD5 OL1   HOL1   SING N N 50 
TD5 OL2   H5     SING N N 51 
TD5 CLB   HLB    SING N N 52 
TD5 CLB   HLBA   SING N N 53 
TD5 CM2   HM2B   SING N N 54 
TD5 CM2   HM2    SING N N 55 
TD5 CM2   HM2A   SING N N 56 
TD5 CM4   HM4A   SING N N 57 
TD5 CM4   HM4B   SING N N 58 
TD5 CM4   HM4    SING N N 59 
# 
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 
TD5 InChI            InChI                1.03  "InChI=1S/C16H24N4O10P2S/c1-9-13(5-6-29-32(27,28)30-31(24,25)26)33-16(12(21)3-4-14(22)23)20(9)8-11-7-18-10(2)19-15(11)17/h7,12,21H,3-6,8H2,1-2H3,(H5-,17,18,19,22,23,24,25,26,27,28)/p+1/t12-/m1/s1" 
TD5 InChIKey         InChI                1.03  ZWUKRGPVMMTMAF-GFCCVEGCSA-O                                                                                                                                                                          
TD5 SMILES_CANONICAL CACTVS               3.385 "Cc1ncc(C[n+]2c(C)c(CCO[P](O)(=O)O[P](O)(O)=O)sc2[C@H](O)CCC(O)=O)c(N)n1"                                                                                                                            
TD5 SMILES           CACTVS               3.385 "Cc1ncc(C[n+]2c(C)c(CCO[P](O)(=O)O[P](O)(O)=O)sc2[CH](O)CCC(O)=O)c(N)n1"                                                                                                                             
TD5 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.4 "Cc1c(sc([n+]1Cc2cnc(nc2N)C)[C@@H](CCC(=O)O)O)CCOP(=O)(O)OP(=O)(O)O"                                                                                                                                 
TD5 SMILES           "OpenEye OEToolkits" 2.0.4 "Cc1c(sc([n+]1Cc2cnc(nc2N)C)C(CCC(=O)O)O)CCOP(=O)(O)OP(=O)(O)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 
TD5 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.4 "(4~{R})-4-[3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-4-methyl-5-[2-[oxidanyl(phosphonooxy)phosphoryl]oxyethyl]-1,3-thiazol-3-ium-2-yl]-4-oxidanyl-butanoic acid" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
TD5 "Create component" 2015-11-20 PDBJ 
TD5 "Initial release"  2016-11-02 RCSB 
# 
