data_KMQ
# 
_chem_comp.id                                    KMQ 
_chem_comp.name                                  "[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{R},4~{R},5~{S})-4-[(~{E})-but-2-enoxy]-3,5-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate" 
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C19 H29 N5 O14 P2" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2019-06-08 
_chem_comp.pdbx_modified_date                    2024-09-27 
_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                        613.406 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     KMQ 
_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        6RXR 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  EBI 
_chem_comp.pdbx_pcm                              Y 
# 
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.pdbx_backbone_atom_flag 
_chem_comp_atom.pdbx_n_terminal_atom_flag 
_chem_comp_atom.pdbx_c_terminal_atom_flag 
_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 
KMQ C3    C1  C 0 1 N N N N N N 71.964 78.554 23.236 -9.532  1.414  -0.924 C3    KMQ 1  
KMQ C21   C2  C 0 1 N N N N N N 73.125 77.657 23.456 -10.628 2.377  -0.544 C21   KMQ 2  
KMQ C1    C3  C 0 1 N N N N N N 73.663 76.823 22.579 -11.151 3.163  -1.452 C1    KMQ 3  
KMQ C7    C4  C 0 1 N N N N N N 74.840 75.995 23.004 -12.247 4.126  -1.073 C7    KMQ 4  
KMQ O2D   O1  O 0 1 N N N N N N 71.544 79.376 24.350 -8.493  1.465  0.056  O2D   KMQ 5  
KMQ C2D   C5  C 0 1 N N R N N N 71.523 78.738 25.623 -7.399  0.585  -0.210 C2D   KMQ 6  
KMQ C3D   C6  C 0 1 N N R N N N 70.489 77.631 25.705 -6.735  0.115  1.107  C3D   KMQ 7  
KMQ O3D   O2  O 0 1 N N N N N N 70.643 76.565 24.757 -7.055  1.009  2.175  O3D   KMQ 8  
KMQ C1D   C7  C 0 1 N N S N N N 70.844 79.775 26.482 -6.239  1.339  -0.908 C1D   KMQ 9  
KMQ O1D   O3  O 0 1 N N N N N N 71.338 81.076 26.158 -6.121  2.668  -0.394 O1D   KMQ 10 
KMQ O4D   O4  O 0 1 N N N N N N 69.459 79.678 26.122 -5.075  0.555  -0.569 O4D   KMQ 11 
KMQ C4D   C8  C 0 1 N N R N N N 69.212 78.416 25.488 -5.225  0.153  0.803  C4D   KMQ 12 
KMQ C5D   C9  C 0 1 N N N N N N 68.005 77.744 26.118 -4.619  -1.237 1.007  C5D   KMQ 13 
KMQ O5D   O5  O 0 1 N N N N N N 67.760 78.405 27.350 -3.201  -1.168 0.836  O5D   KMQ 14 
KMQ PB    P1  P 0 1 N N N N N N 67.324 77.584 28.657 -2.238  -2.450 0.979  PB    KMQ 15 
KMQ O2B   O6  O 0 1 N N N N N N 65.859 77.834 28.903 -2.277  -2.984 2.497  O2B   KMQ 16 
KMQ O1B   O7  O 0 1 N N N N N N 67.618 76.118 28.466 -2.701  -3.520 0.068  O1B   KMQ 17 
KMQ O3A   O8  O 0 1 N N N N N N 68.193 78.141 29.888 -0.730  -2.034 0.595  O3A   KMQ 18 
KMQ PA    P2  P 0 1 N N N N N N 67.788 79.483 30.675 0.577   -2.858 0.145  PA    KMQ 19 
KMQ O1A   O9  O 0 1 N N N N N N 68.972 79.911 31.504 1.206   -3.607 1.423  O1A   KMQ 20 
KMQ O2A   O10 O 0 1 N N N N N N 67.369 80.556 29.697 0.201   -3.859 -0.878 O2A   KMQ 21 
KMQ "O5'" O11 O 0 1 N N N N N N 66.555 79.142 31.639 1.665   -1.844 -0.472 "O5'" KMQ 22 
KMQ "C5'" C10 C 0 1 N N N N N N 66.722 78.129 32.627 2.893   -2.281 -1.057 "C5'" KMQ 23 
KMQ "C4'" C11 C 0 1 N N R N N N 65.392 77.897 33.322 3.688   -1.067 -1.541 "C4'" KMQ 24 
KMQ "O4'" O12 O 0 1 N N N N N N 65.546 76.846 34.277 4.174   -0.303 -0.416 "O4'" KMQ 25 
KMQ "C1'" C12 C 0 1 N N R N N N 64.944 77.225 35.510 5.274   0.477  -0.932 "C1'" KMQ 26 
KMQ "C2'" C13 C 0 1 N N R N N N 64.985 78.739 35.545 6.028   -0.482 -1.880 "C2'" KMQ 27 
KMQ "O2'" O13 O 0 1 N N N N N N 63.838 79.230 36.242 6.508   0.222  -3.027 "O2'" KMQ 28 
KMQ "C3'" C14 C 0 1 N N S N N N 64.943 79.134 34.082 4.961   -1.521 -2.290 "C3'" KMQ 29 
KMQ "O3'" O14 O 0 1 N N N N N N 63.602 79.438 33.699 4.749   -1.490 -3.703 "O3'" KMQ 30 
KMQ N9    N1  N 0 1 Y N N N N N 65.701 76.635 36.637 6.150   0.909  0.160  N9    KMQ 31 
KMQ C8    C15 C 0 1 Y N N N N N 66.815 77.122 37.218 6.277   0.309  1.378  C8    KMQ 32 
KMQ N7    N2  N 0 1 Y N N N N N 67.234 76.303 38.220 7.142   0.955  2.103  N7    KMQ 33 
KMQ C5    C16 C 0 1 Y N N N N N 66.376 75.266 38.276 7.626   2.007  1.400  C5    KMQ 34 
KMQ C4    C17 C 0 1 Y N N N N N 65.373 75.489 37.228 6.999   1.987  0.142  C4    KMQ 35 
KMQ C6    C18 C 0 1 Y N N N N N 66.224 74.041 39.094 8.557   3.026  1.660  C6    KMQ 36 
KMQ N6    N3  N 0 1 N N N N N N 67.100 73.747 40.084 9.210   3.094  2.878  N6    KMQ 37 
KMQ N1    N4  N 0 1 Y N N N N N 65.181 73.227 38.816 8.797   3.923  0.709  N1    KMQ 38 
KMQ C2    C19 C 0 1 Y N N N N N 64.298 73.501 37.837 8.179   3.866  -0.456 C2    KMQ 39 
KMQ N3    N5  N 0 1 Y N N N N N 64.375 74.591 37.057 7.308   2.923  -0.749 N3    KMQ 40 
KMQ H1    H1  H 0 1 N N N N N N 72.219 79.228 22.405 -9.937  0.403  -0.971 H1    KMQ 41 
KMQ H2    H2  H 0 1 N N N N N N 71.109 77.924 22.948 -9.127  1.689  -1.898 H2    KMQ 42 
KMQ H3    H3  H 0 1 N N N N N N 73.580 77.687 24.435 -10.981 2.419  0.475  H3    KMQ 43 
KMQ H4    H4  H 0 1 N N N N N N 73.263 76.741 21.579 -10.798 3.121  -2.472 H4    KMQ 44 
KMQ H5    H5  H 0 1 N N N N N N 75.164 75.361 22.166 -13.099 3.571  -0.682 H5    KMQ 45 
KMQ H6    H6  H 0 1 N N N N N N 75.665 76.658 23.303 -11.880 4.813  -0.310 H6    KMQ 46 
KMQ H7    H7  H 0 1 N N N N N N 74.553 75.360 23.855 -12.554 4.691  -1.953 H7    KMQ 47 
KMQ H8    H8  H 0 1 N N N N N N 72.510 78.437 26.003 -7.725  -0.267 -0.807 H8    KMQ 48 
KMQ H9    H9  H 0 1 N N N N N N 70.486 77.225 26.727 -7.050  -0.899 1.352  H9    KMQ 49 
KMQ H10   H10 H 0 1 N N N N N N 71.454 76.102 24.930 -6.665  0.762  3.025  H10   KMQ 50 
KMQ H11   H11 H 0 1 N N N N N N 70.996 79.543 27.547 -6.388  1.359  -1.987 H11   KMQ 51 
KMQ H12   H12 H 0 1 N N N N N N 70.906 81.724 26.702 -5.410  3.184  -0.797 H12   KMQ 52 
KMQ H13   H13 H 0 1 N N N N N N 69.039 78.548 24.410 -4.733  0.871  1.458  H13   KMQ 53 
KMQ H14   H14 H 0 1 N N N N N N 67.131 77.840 25.457 -4.847  -1.589 2.013  H14   KMQ 54 
KMQ H15   H15 H 0 1 N N N N N N 68.215 76.679 26.296 -5.039  -1.928 0.276  H15   KMQ 55 
KMQ H16   H16 H 0 1 N N N N N N 65.390 77.008 28.891 -1.985  -2.333 3.151  H16   KMQ 56 
KMQ H17   H17 H 0 1 N N N N N N 69.236 80.788 31.251 1.476   -3.011 2.135  H17   KMQ 57 
KMQ H18   H18 H 0 1 N N N N N N 67.056 77.197 32.148 3.476   -2.825 -0.315 H18   KMQ 58 
KMQ H19   H19 H 0 1 N N N N N N 67.472 78.452 33.364 2.679   -2.936 -1.902 H19   KMQ 59 
KMQ H20   H20 H 0 1 N N N N N N 64.630 77.633 32.574 3.071   -0.442 -2.187 H20   KMQ 60 
KMQ H21   H21 H 0 1 N N N N N N 63.897 76.889 35.549 4.901   1.340  -1.484 H21   KMQ 61 
KMQ H22   H22 H 0 1 N N N N N N 65.920 79.086 36.008 6.854   -0.965 -1.357 H22   KMQ 62 
KMQ H23   H23 H 0 1 N N N N N N 63.886 78.971 37.155 6.990   -0.332 -3.656 H23   KMQ 63 
KMQ H24   H24 H 0 1 N N N N N N 65.626 79.974 33.889 5.257   -2.520 -1.969 H24   KMQ 64 
KMQ H25   H25 H 0 1 N N N N N N 63.306 80.210 34.166 5.516   -1.766 -4.222 H25   KMQ 65 
KMQ H26   H26 H 0 1 N N N N N N 67.308 78.038 36.928 5.738   -0.572 1.693  H26   KMQ 66 
KMQ H27   H27 H 0 1 N N N N N N 66.835 72.887 40.519 9.027   2.433  3.565  H27   KMQ 67 
KMQ H28   H28 H 0 1 N N N N N N 68.019 73.657 39.700 9.852   3.802  3.046  H28   KMQ 68 
KMQ H29   H29 H 0 1 N N N N N N 63.486 72.808 37.671 8.404   4.615  -1.201 H29   KMQ 69 
# 
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 
KMQ C1    C7    SING N N 1  
KMQ C1    C21   DOUB N E 2  
KMQ C3    C21   SING N N 3  
KMQ C3    O2D   SING N N 4  
KMQ O2D   C2D   SING N N 5  
KMQ O3D   C3D   SING N N 6  
KMQ C4D   C3D   SING N N 7  
KMQ C4D   C5D   SING N N 8  
KMQ C4D   O4D   SING N N 9  
KMQ C2D   C3D   SING N N 10 
KMQ C2D   C1D   SING N N 11 
KMQ C5D   O5D   SING N N 12 
KMQ O4D   C1D   SING N N 13 
KMQ O1D   C1D   SING N N 14 
KMQ O5D   PB    SING N N 15 
KMQ O1B   PB    DOUB N N 16 
KMQ PB    O2B   SING N N 17 
KMQ PB    O3A   SING N N 18 
KMQ O2A   PA    DOUB N N 19 
KMQ O3A   PA    SING N N 20 
KMQ PA    O1A   SING N N 21 
KMQ PA    "O5'" SING N N 22 
KMQ "O5'" "C5'" SING N N 23 
KMQ "C5'" "C4'" SING N N 24 
KMQ "C4'" "C3'" SING N N 25 
KMQ "C4'" "O4'" SING N N 26 
KMQ "O3'" "C3'" SING N N 27 
KMQ "C3'" "C2'" SING N N 28 
KMQ "O4'" "C1'" SING N N 29 
KMQ "C1'" "C2'" SING N N 30 
KMQ "C1'" N9    SING N N 31 
KMQ "C2'" "O2'" SING N N 32 
KMQ N9    C8    SING Y N 33 
KMQ N9    C4    SING Y N 34 
KMQ N3    C4    DOUB Y N 35 
KMQ N3    C2    SING Y N 36 
KMQ C8    N7    DOUB Y N 37 
KMQ C4    C5    SING Y N 38 
KMQ C2    N1    DOUB Y N 39 
KMQ N7    C5    SING Y N 40 
KMQ C5    C6    DOUB Y N 41 
KMQ N1    C6    SING Y N 42 
KMQ C6    N6    SING N N 43 
KMQ C3    H1    SING N N 44 
KMQ C3    H2    SING N N 45 
KMQ C21   H3    SING N N 46 
KMQ C1    H4    SING N N 47 
KMQ C7    H5    SING N N 48 
KMQ C7    H6    SING N N 49 
KMQ C7    H7    SING N N 50 
KMQ C2D   H8    SING N N 51 
KMQ C3D   H9    SING N N 52 
KMQ O3D   H10   SING N N 53 
KMQ C1D   H11   SING N N 54 
KMQ O1D   H12   SING N N 55 
KMQ C4D   H13   SING N N 56 
KMQ C5D   H14   SING N N 57 
KMQ C5D   H15   SING N N 58 
KMQ O2B   H16   SING N N 59 
KMQ O1A   H17   SING N N 60 
KMQ "C5'" H18   SING N N 61 
KMQ "C5'" H19   SING N N 62 
KMQ "C4'" H20   SING N N 63 
KMQ "C1'" H21   SING N N 64 
KMQ "C2'" H22   SING N N 65 
KMQ "O2'" H23   SING N N 66 
KMQ "C3'" H24   SING N N 67 
KMQ "O3'" H25   SING N N 68 
KMQ C8    H26   SING N N 69 
KMQ N6    H27   SING N N 70 
KMQ N6    H28   SING N N 71 
KMQ C2    H29   SING N N 72 
# 
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 
KMQ InChI            InChI                1.03  "InChI=1S/C19H29N5O14P2/c1-2-3-4-33-15-13(26)10(37-19(15)28)6-35-40(31,32)38-39(29,30)34-5-9-12(25)14(27)18(36-9)24-8-23-11-16(20)21-7-22-17(11)24/h2-3,7-10,12-15,18-19,25-28H,4-6H2,1H3,(H,29,30)(H,31,32)(H2,20,21,22)/b3-2+/t9-,10-,12-,13-,14-,15-,18-,19+/m1/s1" 
KMQ InChIKey         InChI                1.03  JOKNWQJJLFYBKK-YVAUJSGTSA-N                                                                                                                                                                                                                                            
KMQ SMILES_CANONICAL CACTVS               3.385 "C\C=C\CO[C@H]1[C@@H](O)O[C@H](CO[P](O)(=O)O[P](O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)n3cnc4c(N)ncnc34)[C@H]1O"                                                                                                                                                        
KMQ SMILES           CACTVS               3.385 "CC=CCO[CH]1[CH](O)O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]2O[CH]([CH](O)[CH]2O)n3cnc4c(N)ncnc34)[CH]1O"                                                                                                                                                                    
KMQ SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C/C=C/CO[C@@H]1[C@@H]([C@H](O[C@@H]1O)COP(=O)(O)OP(=O)(O)OC[C@@H]2[C@H]([C@H]([C@@H](O2)n3cnc4c3ncnc4N)O)O)O"                                                                                                                                                         
KMQ SMILES           "OpenEye OEToolkits" 2.0.7 "CC=CCOC1C(C(OC1O)COP(=O)(O)OP(=O)(O)OCC2C(C(C(O2)n3cnc4c3ncnc4N)O)O)O"                                                                                                                                                                                                
# 
_pdbx_chem_comp_identifier.comp_id           KMQ 
_pdbx_chem_comp_identifier.type              "SYSTEMATIC NAME" 
_pdbx_chem_comp_identifier.program           "OpenEye OEToolkits" 
_pdbx_chem_comp_identifier.program_version   2.0.7 
_pdbx_chem_comp_identifier.identifier        "[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{R},4~{R},5~{S})-4-[(~{E})-but-2-enoxy]-3,5-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
KMQ "Create component" 2019-06-08 EBI  
KMQ "Initial release"  2020-04-15 RCSB 
KMQ "Modify PCM"       2024-09-27 PDBE 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            KMQ 
_pdbx_chem_comp_pcm.modified_residue_id                LYS 
_pdbx_chem_comp_pcm.type                               None 
_pdbx_chem_comp_pcm.category                           "Covalent chemical modification" 
_pdbx_chem_comp_pcm.position                           "Amino-acid side chain" 
_pdbx_chem_comp_pcm.polypeptide_position               "Any position" 
_pdbx_chem_comp_pcm.comp_id_linking_atom               C3 
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom   NZ 
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession     ? 
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession      ? 
# 
