data_T5A
#
_chem_comp.id T5A
_chem_comp.name "P1-(5'-ADENOSYL)P5-(5'-THYMIDYL)PENTAPHOSPHATE"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C20 H30 N7 O23 P5"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 1999-07-08
_chem_comp.pdbx_modified_date 2011-06-04
_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 891.354
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code T5A
_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 3TMK
_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.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
T5A N1B BN1 N 0 1 N N N N N N 29.434 39.375 18.854 -0.041 1.135 -11.695 N1B T5A 1
T5A C6B BC6 C 0 1 N N N N N N 29.812 40.546 18.322 0.166 2.281 -12.412 C6B T5A 2
T5A C2B BC2 C 0 1 N N N N N N 28.604 39.290 20.004 0.917 0.194 -11.613 C2B T5A 3
T5A O2B BO2 O 0 1 N N N N N N 28.273 38.178 20.460 0.711 -0.816 -10.970 O2B T5A 4
T5A N3B BN3 N 0 1 N N N N N N 28.188 40.501 20.510 2.101 0.357 -12.233 N3B T5A 5
T5A C4B BC4 C 0 1 N N N N N N 28.578 41.730 20.088 2.343 1.471 -12.953 C4B T5A 6
T5A O4B BO4 O 0 1 N N N N N N 28.357 42.768 20.716 3.414 1.619 -13.515 O4B T5A 7
T5A C5B BC5 C 0 1 N N N N N N 29.382 41.695 18.816 1.345 2.471 -13.043 C5B T5A 8
T5A C7B BC7 C 0 1 N N N N N N 29.706 42.963 18.037 1.592 3.727 -13.839 C7B T5A 9
T5A C5E BC5* C 0 1 N N N N N N 32.993 37.351 16.405 -1.646 -0.860 -7.835 C5E T5A 10
T5A C4E BC4* C 0 1 N N R N N N 31.761 37.052 17.311 -2.092 -0.193 -9.138 C4E T5A 11
T5A O4E BO4* O 0 1 N N N N N N 31.484 38.302 18.018 -1.095 0.744 -9.602 O4E T5A 12
T5A C1E BC1* C 0 1 N N R N N N 30.100 38.109 18.345 -1.319 0.929 -11.009 C1E T5A 13
T5A C2E BC2* C 0 1 N N N N N N 29.539 37.567 16.945 -1.999 -0.347 -11.540 C2E T5A 14
T5A C3E BC3* C 0 1 N N S N N N 30.600 36.608 16.458 -2.175 -1.233 -10.284 C3E T5A 15
T5A O3E BO3* O 0 1 N N N N N N 30.153 35.271 16.617 -3.447 -1.884 -10.292 O3E T5A 16
T5A PA PA P 0 1 N N R N N N 33.654 38.995 14.289 -1.106 -0.648 -5.463 PA T5A 17
T5A O1A O1A O 0 1 N N N N N N 34.837 39.685 14.877 0.336 -1.317 -5.712 O1A T5A 18
T5A O2A O2A O 0 1 N N N N N N 32.809 39.796 13.336 -2.087 -1.703 -5.127 O2A T5A 19
T5A O5E BO5* O 0 1 N N N N N N 32.658 38.377 15.441 -1.579 0.119 -6.797 O5E T5A 20
T5A O3A O3A O 0 1 N N N N N N 34.021 37.667 13.626 -1.008 0.401 -4.246 O3A T5A 21
T5A PB PB P 0 1 N N S N N N 35.009 37.194 12.416 -0.533 -0.429 -2.952 PB T5A 22
T5A O1B O1B O 0 1 N N N N N N 35.398 35.818 12.633 0.784 -1.047 -3.219 O1B T5A 23
T5A O2X O2B O 0 1 N N N N N N 35.924 38.311 12.131 -1.610 -1.581 -2.628 O2X T5A 24
T5A O3B O3B O 0 1 N N N N N N 33.992 37.199 11.130 -0.413 0.564 -1.690 O3B T5A 25
T5A PC PC P 0 1 N N N N N N 32.745 36.422 10.623 0.063 -0.328 -0.439 PC T5A 26
T5A O1C O1C O 0 1 N N N N N N 32.709 34.989 10.900 -0.936 -1.389 -0.179 O1C T5A 27
T5A O2C O2C O 0 1 N N N N N N 31.670 37.389 10.941 1.486 -1.003 -0.772 O2C T5A 28
T5A O3C O3C O 0 1 N N N N N N 33.041 36.640 9.037 0.204 0.605 0.864 O3C T5A 29
T5A PD PD P 0 1 N N S N N N 32.623 37.678 7.972 0.681 -0.347 2.071 PD T5A 30
T5A O1D O1D O 0 1 N N N N N N 33.152 39.033 8.209 2.094 -1.021 1.695 O1D T5A 31
T5A O2D O2D O 0 1 N N N N N N 31.167 37.423 7.821 -0.327 -1.407 2.291 O2D T5A 32
T5A O3D O3D O 0 1 N N N N N N 33.409 37.152 6.658 0.843 0.527 3.413 O3D T5A 33
T5A PE PE P 0 1 N N R N N N 34.669 37.611 5.781 1.320 -0.483 4.572 PE T5A 34
T5A O1E O1E O 0 1 N N N N N N 34.302 38.907 5.123 0.211 -1.634 4.770 O1E T5A 35
T5A O2E O2E O 0 1 N N N N N N 35.863 37.589 6.683 2.609 -1.100 4.188 O2E T5A 36
T5A O5F AO5* O 0 1 N N N N N N 34.618 36.309 4.920 1.502 0.328 5.950 O5F T5A 37
T5A C5F AC5* C 0 1 N N N N N N 35.195 35.129 5.369 1.924 -0.618 6.934 C5F T5A 38
T5A C4F AC4* C 0 1 N N R N N N 35.595 34.240 4.186 2.117 0.092 8.275 C4F T5A 39
T5A O4F AO4* O 0 1 N N N N N N 34.497 34.164 3.223 0.870 0.657 8.713 O4F T5A 40
T5A C1F AC1* C 0 1 N N R N N N 34.994 34.705 1.940 0.849 0.568 10.154 C1F T5A 41
T5A C2F AC2* C 0 1 N N R N N N 36.172 35.534 2.341 1.468 -0.823 10.439 C2F T5A 42
T5A O2F AO2* O 0 1 N N N N N N 36.915 36.024 1.219 2.046 -0.866 11.745 O2F T5A 43
T5A C3F AC3* C 0 1 N N S N N N 36.886 34.699 3.446 2.564 -0.921 9.346 C3F T5A 44
T5A O3F AO3* O 0 1 N N N N N N 37.583 33.477 3.048 3.839 -0.562 9.883 O3F T5A 45
T5A N9A AN9 N 0 1 Y N N N N N 33.957 35.495 1.178 -0.525 0.637 10.655 N9A T5A 46
T5A C4A AC4 C 0 1 Y N N N N N 33.094 34.924 0.273 -0.920 1.116 11.879 C4A T5A 47
T5A N3A AN3 N 0 1 Y N N N N N 33.233 33.704 -0.323 -0.294 1.639 12.928 N3A T5A 48
T5A C2A AC2 C 0 1 Y N N N N N 32.258 33.477 -1.245 -0.971 2.024 13.990 C2A T5A 49
T5A N1A AN1 N 0 1 Y N N N N N 31.244 34.280 -1.578 -2.285 1.918 14.070 N1A T5A 50
T5A C6A AC6 C 0 1 Y N N N N N 31.187 35.541 -1.037 -2.996 1.411 13.068 C6A T5A 51
T5A N6A AN6 N 0 1 N N N N N N 30.275 36.442 -1.463 -4.373 1.304 13.161 N6A T5A 52
T5A C5A AC5 C 0 1 Y N N N N N 32.166 35.887 -0.038 -2.319 0.987 11.913 C5A T5A 53
T5A N7A AN7 N 0 1 Y N N N N N 32.437 37.093 0.668 -2.697 0.439 10.733 N7A T5A 54
T5A C8A AC8 C 0 1 Y N N N N N 33.539 36.812 1.326 -1.646 0.233 9.993 C8A T5A 55
T5A HB6 HB6 H 0 1 N N N N N N 30.494 40.564 17.455 -0.607 3.032 -12.472 HB6 T5A 56
T5A HN3 HN3 H 0 1 N N N N N N 27.519 40.486 21.280 2.781 -0.330 -12.164 HN3 T5A 57
T5A HB71 1HB7 H 0 0 N N N N N N 29.343 43.931 18.453 2.593 3.693 -14.269 HB71 T5A 58
T5A HB72 2HB7 H 0 0 N N N N N N 30.807 43.022 17.871 0.855 3.801 -14.638 HB72 T5A 59
T5A HB73 3HB7 H 0 0 N N N N N N 29.342 42.854 16.988 1.507 4.594 -13.184 HB73 T5A 60
T5A HB51 1HB5 H 0 0 N N N N N N 33.896 37.616 17.001 -2.363 -1.633 -7.559 HB51 T5A 61
T5A HB52 2HB5 H 0 0 N N N N N N 33.386 36.429 15.915 -0.663 -1.309 -7.975 HB52 T5A 62
T5A HB4 HB4 H 0 1 N N N N N N 31.946 36.227 18.038 -3.052 0.305 -9.003 HB4 T5A 63
T5A HB1 HB1 H 0 1 N N N N N N 29.905 37.411 19.193 -1.968 1.790 -11.171 HB1 T5A 64
T5A HB21 1HB2 H 0 0 N N N N N N 28.517 37.123 17.005 -2.968 -0.109 -11.978 HB21 T5A 65
T5A HB22 2HB2 H 0 0 N N N N N N 29.282 38.370 16.215 -1.360 -0.843 -12.271 HB22 T5A 66
T5A HB3 HB3 H 0 1 N N N N N N 30.867 36.622 15.375 -1.368 -1.962 -10.206 HB3 T5A 67
T5A "HB'3" 3HB* H 0 0 N N N N N N 29.421 34.991 16.079 -3.468 -2.447 -11.079 "HB'3" T5A 68
T5A HO1A AHO1 H 0 0 N N N N N N 35.370 39.179 15.478 0.945 -0.597 -5.928 HO1A T5A 69
T5A HO2B BHO2 H 0 0 N N N N N N 36.499 38.035 11.426 -2.452 -1.136 -2.460 HO2B T5A 70
T5A HO2C CHO2 H 0 0 N N N N N N 30.907 36.914 10.631 2.107 -0.279 -0.934 HO2C T5A 71
T5A HO1D DHO1 H 0 0 N N N N N N 32.894 39.671 7.554 2.722 -0.297 1.560 HO1D T5A 72
T5A HO1E EHO1 H 0 0 N N N N N N 35.049 39.179 4.603 -0.610 -1.190 5.018 HO1E T5A 73
T5A HA51 1HA5 H 0 0 N N N N N N 36.055 35.322 6.051 1.166 -1.394 7.040 HA51 T5A 74
T5A HA52 2HA5 H 0 0 N N N N N N 34.532 34.590 6.085 2.866 -1.070 6.624 HA52 T5A 75
T5A HA4 HA4 H 0 1 N N N N N N 35.817 33.239 4.626 2.865 0.878 8.174 HA4 T5A 76
T5A HA1 HA1 H 0 1 N N N N N N 35.261 33.895 1.221 1.458 1.357 10.596 HA1 T5A 77
T5A HC2 HC2 H 0 1 N N N N N N 35.922 36.522 2.793 0.725 -1.611 10.318 HC2 T5A 78
T5A HO2 HO2 H 0 1 N N N N N N 37.663 36.550 1.473 2.412 -1.754 11.860 HO2 T5A 79
T5A HC3 HC3 H 0 1 N N N N N N 37.688 35.288 3.947 2.597 -1.927 8.928 HC3 T5A 80
T5A HA3 HA3 H 0 1 N N N N N N 38.370 33.757 2.596 4.035 -1.197 10.586 HA3 T5A 81
T5A HA2 HA2 H 0 1 N N N N N N 32.294 32.520 -1.792 -0.431 2.441 14.827 HA2 T5A 82
T5A HA61 1HA6 H 0 0 N N N N N N 30.232 37.378 -1.061 -4.829 1.600 13.964 HA61 T5A 83
T5A HA62 2HA6 H 0 0 N N N N N N 29.350 36.019 -1.379 -4.881 0.932 12.423 HA62 T5A 84
T5A HA8 HA8 H 0 1 N N N N N N 34.048 37.584 1.926 -1.660 -0.193 9.002 HA8 T5A 85
#
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
T5A N1B C6B SING N N 1
T5A N1B C2B SING N N 2
T5A N1B C1E SING N N 3
T5A C6B C5B DOUB N N 4
T5A C6B HB6 SING N N 5
T5A C2B O2B DOUB N N 6
T5A C2B N3B SING N N 7
T5A N3B C4B SING N N 8
T5A N3B HN3 SING N N 9
T5A C4B O4B DOUB N N 10
T5A C4B C5B SING N N 11
T5A C5B C7B SING N N 12
T5A C7B HB71 SING N N 13
T5A C7B HB72 SING N N 14
T5A C7B HB73 SING N N 15
T5A C5E C4E SING N N 16
T5A C5E O5E SING N N 17
T5A C5E HB51 SING N N 18
T5A C5E HB52 SING N N 19
T5A C4E O4E SING N N 20
T5A C4E C3E SING N N 21
T5A C4E HB4 SING N N 22
T5A O4E C1E SING N N 23
T5A C1E C2E SING N N 24
T5A C1E HB1 SING N N 25
T5A C2E C3E SING N N 26
T5A C2E HB21 SING N N 27
T5A C2E HB22 SING N N 28
T5A C3E O3E SING N N 29
T5A C3E HB3 SING N N 30
T5A O3E "HB'3" SING N N 31
T5A PA O1A SING N N 32
T5A PA O2A DOUB N N 33
T5A PA O5E SING N N 34
T5A PA O3A SING N N 35
T5A O1A HO1A SING N N 36
T5A O3A PB SING N N 37
T5A PB O1B DOUB N N 38
T5A PB O2X SING N N 39
T5A PB O3B SING N N 40
T5A O2X HO2B SING N N 41
T5A O3B PC SING N N 42
T5A PC O1C DOUB N N 43
T5A PC O2C SING N N 44
T5A PC O3C SING N N 45
T5A O2C HO2C SING N N 46
T5A O3C PD SING N N 47
T5A PD O1D SING N N 48
T5A PD O2D DOUB N N 49
T5A PD O3D SING N N 50
T5A O1D HO1D SING N N 51
T5A O3D PE SING N N 52
T5A PE O1E SING N N 53
T5A PE O2E DOUB N N 54
T5A PE O5F SING N N 55
T5A O1E HO1E SING N N 56
T5A O5F C5F SING N N 57
T5A C5F C4F SING N N 58
T5A C5F HA51 SING N N 59
T5A C5F HA52 SING N N 60
T5A C4F O4F SING N N 61
T5A C4F C3F SING N N 62
T5A C4F HA4 SING N N 63
T5A O4F C1F SING N N 64
T5A C1F C2F SING N N 65
T5A C1F N9A SING N N 66
T5A C1F HA1 SING N N 67
T5A C2F O2F SING N N 68
T5A C2F C3F SING N N 69
T5A C2F HC2 SING N N 70
T5A O2F HO2 SING N N 71
T5A C3F O3F SING N N 72
T5A C3F HC3 SING N N 73
T5A O3F HA3 SING N N 74
T5A N9A C4A SING Y N 75
T5A N9A C8A SING Y N 76
T5A C4A N3A SING Y N 77
T5A C4A C5A DOUB Y N 78
T5A N3A C2A DOUB Y N 79
T5A C2A N1A SING Y N 80
T5A C2A HA2 SING N N 81
T5A N1A C6A DOUB Y N 82
T5A C6A N6A SING N N 83
T5A C6A C5A SING Y N 84
T5A N6A HA61 SING N N 85
T5A N6A HA62 SING N N 86
T5A C5A N7A SING Y N 87
T5A N7A C8A DOUB Y N 88
T5A C8A HA8 SING N N 89
#
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
T5A SMILES_CANONICAL CACTVS 3.341 CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P@](O)(=O)O[P@@](O)(=O)O[P@](O)(=O)O[P@](O)(=O)O[P@@](O)(=O)OC[C@H]3O[C@H]([C@H](O)[C@@H]3O)n4cnc5c(N)ncnc45)O2)C(=O)NC1=O
T5A SMILES CACTVS 3.341 CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(=O)O[P](O)(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O)[CH]3O)n4cnc5c(N)ncnc45)O2)C(=O)NC1=O
T5A SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)CO[P@@](=O)(O)O[P@](=O)(O)O[P@@](=O)(O)O[P@@](=O)(O)O[P@](=O)(O)OC[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4ncnc5N)O)O)O
T5A SMILES "OpenEye OEToolkits" 1.5.0 CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(O)OP(=O)(O)OP(=O)(O)OP(=O)(O)OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)O)O)O
T5A InChI InChI 1.03 InChI=1S/C20H30N7O23P5/c1-8-3-26(20(32)25-18(8)31)12-2-9(28)10(45-12)4-43-51(33,34)47-53(37,38)49-55(41,42)50-54(39,40)48-52(35,36)44-5-11-14(29)15(30)19(46-11)27-7-24-13-16(21)22-6-23-17(13)27/h3,6-7,9-12,14-15,19,28-30H,2,4-5H2,1H3,(H,33,34)(H,35,36)(H,37,38)(H,39,40)(H,41,42)(H2,21,22,23)(H,25,31,32)/t9-,10+,11+,12+,14+,15+,19+/m0/s1
T5A InChIKey InChI 1.03 JCFDSPQTEMXXLO-SLFMBYJQSA-N
#
_pdbx_chem_comp_identifier.comp_id T5A
_pdbx_chem_comp_identifier.type "SYSTEMATIC NAME"
_pdbx_chem_comp_identifier.program "OpenEye OEToolkits"
_pdbx_chem_comp_identifier.program_version 1.5.0
_pdbx_chem_comp_identifier.identifier
"[[[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl]oxy-hydroxy-phosphoryl]oxy-hydroxy-phosphoryl]oxy-hydroxy-phosphoryl] [(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-pyrimidin-1-yl)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
T5A 'Create component' 1999-07-08 PDBJ
T5A 'Modify descriptor' 2011-06-04 RCSB
#
_pdbe_chem_comp_drugbank_details.comp_id T5A
_pdbe_chem_comp_drugbank_details.drugbank_id DB03280
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name "p1-(5'-adenosyl)p5-(5'-thymidyl)pentaphosphate"
_pdbe_chem_comp_drugbank_details.description ?
_pdbe_chem_comp_drugbank_details.cas_number ?
_pdbe_chem_comp_drugbank_details.mechanism_of_action ?
#
_pdbe_chem_comp_drugbank_classification.comp_id T5A
_pdbe_chem_comp_drugbank_classification.drugbank_id DB03280
_pdbe_chem_comp_drugbank_classification.parent "(5'->5')-dinucleotides"
_pdbe_chem_comp_drugbank_classification.kingdom 'Organic compounds'
_pdbe_chem_comp_drugbank_classification.class "(5'->5')-dinucleotides"
_pdbe_chem_comp_drugbank_classification.superclass 'Nucleosides, nucleotides, and analogues'
_pdbe_chem_comp_drugbank_classification.description
"This compound belongs to the class of organic compounds known as (5'->5')-dinucleotides. These are dinucleotides where the two bases are connected via a (5'->5')-phosphodiester linkage."
#
loop_
_pdbe_chem_comp_drugbank_targets.comp_id
_pdbe_chem_comp_drugbank_targets.drugbank_id
_pdbe_chem_comp_drugbank_targets.name
_pdbe_chem_comp_drugbank_targets.organism
_pdbe_chem_comp_drugbank_targets.uniprot_id
_pdbe_chem_comp_drugbank_targets.pharmacologically_active
_pdbe_chem_comp_drugbank_targets.ordinal
T5A DB03280 'Thymidylate kinase' 'Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)' P9WKE1 unknown 1
T5A DB03280 'Thymidylate kinase' Humans P23919 unknown 2
T5A DB03280 'Thymidylate kinase' 'Shigella flexneri' P0A721 unknown 3
T5A DB03280 'Thymidine kinase' EHV-4 P24425 unknown 4
T5A DB03280 'Thymidine kinase' 'Escherichia coli (strain K12)' P23331 unknown 5
#
loop_
_software.name
_software.version
_software.description
rdkit 2023.03.3 'Core functionality.'
pdbeccdutils 0.8.4 'Wrapper to provide 2D templates and molecular fragments.'
#
loop_
_pdbe_chem_comp_atom_depiction.comp_id
_pdbe_chem_comp_atom_depiction.atom_id
_pdbe_chem_comp_atom_depiction.element
_pdbe_chem_comp_atom_depiction.model_Cartn_x
_pdbe_chem_comp_atom_depiction.model_Cartn_y
_pdbe_chem_comp_atom_depiction.pdbx_ordinal
T5A N1B N 10.303 13.099 1
T5A C6B C 9.301 14.215 2
T5A C2B C 11.771 13.408 3
T5A O2B O 12.773 12.292 4
T5A N3B N 12.237 14.834 5
T5A C4B C 11.235 15.950 6
T5A O4B O 11.701 17.376 7
T5A C5B C 9.767 15.641 8
T5A C7B C 8.766 16.757 9
T5A C5E C 10.294 7.819 10
T5A C4E C 9.833 9.246 11
T5A O4E O 10.717 10.458 12
T5A C1E C 9.837 11.673 13
T5A C2E C 8.410 11.212 14
T5A C3E C 8.407 9.712 15
T5A O3E O 7.192 8.832 16
T5A PA P 9.749 5.278 17
T5A O1A O 11.177 5.739 18
T5A O2A O 8.322 4.817 19
T5A O5E O 9.288 6.705 20
T5A O3A O 10.210 3.851 21
T5A PB P 9.205 2.738 22
T5A O1B O 8.092 3.743 23
T5A O2X O 10.318 1.732 24
T5A O3B O 8.199 1.625 25
T5A PC P 8.660 0.197 26
T5A O1C O 10.088 0.658 27
T5A O2C O 7.233 -0.264 28
T5A O3C O 9.121 -1.230 29
T5A PD P 8.116 -2.343 30
T5A O1D O 7.003 -1.337 31
T5A O2D O 9.229 -3.349 32
T5A O3D O 7.110 -3.456 33
T5A PE P 7.571 -4.883 34
T5A O1E O 8.998 -4.422 35
T5A O2E O 6.144 -5.344 36
T5A O5F O 8.032 -6.311 37
T5A C5F C 7.027 -7.424 38
T5A C4F C 7.487 -8.851 39
T5A O4F O 6.604 -10.063 40
T5A C1F C 7.483 -11.278 41
T5A C2F C 8.911 -10.817 42
T5A O2F O 10.123 -11.701 43
T5A C3F C 8.913 -9.317 44
T5A O3F O 10.129 -8.438 45
T5A N9A N 7.018 -12.704 46
T5A C4A C 5.598 -13.161 47
T5A N3A N 4.299 -12.411 48
T5A C2A C 3.000 -13.161 49
T5A N1A N 3.000 -14.661 50
T5A C6A C 4.299 -15.411 51
T5A N6A N 4.299 -16.911 52
T5A C5A C 5.598 -14.661 53
T5A N7A N 7.018 -15.118 54
T5A C8A C 7.893 -13.911 55
#
loop_
_pdbe_chem_comp_bond_depiction.comp_id
_pdbe_chem_comp_bond_depiction.atom_id_1
_pdbe_chem_comp_bond_depiction.atom_id_2
_pdbe_chem_comp_bond_depiction.value_order
_pdbe_chem_comp_bond_depiction.bond_dir
_pdbe_chem_comp_bond_depiction.pdbx_ordinal
T5A N1B C6B SINGLE NONE 1
T5A N1B C2B SINGLE NONE 2
T5A C1E N1B SINGLE BEGINDASH 3
T5A C6B C5B DOUBLE NONE 4
T5A C2B O2B DOUBLE NONE 5
T5A C2B N3B SINGLE NONE 6
T5A N3B C4B SINGLE NONE 7
T5A C4B O4B DOUBLE NONE 8
T5A C4B C5B SINGLE NONE 9
T5A C5B C7B SINGLE NONE 10
T5A C4E C5E SINGLE BEGINDASH 11
T5A C5E O5E SINGLE NONE 12
T5A C4E O4E SINGLE NONE 13
T5A C4E C3E SINGLE NONE 14
T5A O4E C1E SINGLE NONE 15
T5A C1E C2E SINGLE NONE 16
T5A C2E C3E SINGLE NONE 17
T5A C3E O3E SINGLE BEGINWEDGE 18
T5A PA O1A SINGLE BEGINDASH 19
T5A PA O2A DOUBLE NONE 20
T5A PA O5E SINGLE NONE 21
T5A PA O3A SINGLE NONE 22
T5A O3A PB SINGLE NONE 23
T5A PB O1B DOUBLE NONE 24
T5A PB O2X SINGLE BEGINWEDGE 25
T5A PB O3B SINGLE NONE 26
T5A O3B PC SINGLE NONE 27
T5A PC O1C DOUBLE NONE 28
T5A PC O2C SINGLE BEGINWEDGE 29
T5A PC O3C SINGLE NONE 30
T5A O3C PD SINGLE NONE 31
T5A PD O1D SINGLE BEGINWEDGE 32
T5A PD O2D DOUBLE NONE 33
T5A PD O3D SINGLE NONE 34
T5A O3D PE SINGLE NONE 35
T5A PE O1E SINGLE BEGINWEDGE 36
T5A PE O2E DOUBLE NONE 37
T5A PE O5F SINGLE NONE 38
T5A O5F C5F SINGLE NONE 39
T5A C4F C5F SINGLE BEGINDASH 40
T5A C4F O4F SINGLE NONE 41
T5A C4F C3F SINGLE NONE 42
T5A O4F C1F SINGLE NONE 43
T5A C1F C2F SINGLE NONE 44
T5A C1F N9A SINGLE BEGINDASH 45
T5A C2F O2F SINGLE BEGINWEDGE 46
T5A C2F C3F SINGLE NONE 47
T5A C3F O3F SINGLE BEGINWEDGE 48
T5A N9A C4A SINGLE NONE 49
T5A N9A C8A SINGLE NONE 50
T5A C4A N3A DOUBLE NONE 51
T5A C4A C5A SINGLE NONE 52
T5A N3A C2A SINGLE NONE 53
T5A C2A N1A DOUBLE NONE 54
T5A N1A C6A SINGLE NONE 55
T5A C6A N6A SINGLE NONE 56
T5A C6A C5A DOUBLE NONE 57
T5A C5A N7A SINGLE NONE 58
T5A N7A C8A DOUBLE NONE 59
#
loop_
_pdbe_chem_comp_substructure.comp_id
_pdbe_chem_comp_substructure.substructure_name
_pdbe_chem_comp_substructure.id
_pdbe_chem_comp_substructure.substructure_type
_pdbe_chem_comp_substructure.substructure_smiles
_pdbe_chem_comp_substructure.substructure_inchis
_pdbe_chem_comp_substructure.substructure_inchikeys
T5A MurckoScaffold S1 scaffold 'O=c1ccn([C@H]2CC[C@@H](CO[PH](=O)O[PH](=O)O[PH](=O)O[PH](=O)O[PH](=O)OC[C@@H]3CC[C@H](n4cnc5cncnc54)O3)O2)c(=O)[nH]1' InChI=1S/C19H27N6O15P5/c26-15-5-6-24(19(27)23-15)16-3-1-12(35-16)8-33-41(28)37-43(30)39-45(32)40-44(31)38-42(29)34-9-13-2-4-17(36-13)25-11-22-14-7-20-10-21-18(14)25/h5-7,10-13,16-17,41-45H,1-4,8-9H2,(H,23,26,27)/t12-,13-,16+,17+/m0/s1 UUEUPNGKWXTGHN-WRFANHODSA-N
T5A adenine F1 fragment 'Nc1ncnc2nc[nH]c12' InChI=1S/C5H5N5/c6-4-3-5(9-1-7-3)10-2-8-4/h1-2H,(H3,6,7,8,9,10) GFFGJBXGBJISGV-UHFFFAOYSA-N
T5A deoxyribose F2 fragment 'OCC1OC[CH2]C1O' InChI=1S/C5H10O3/c6-3-5-4(7)1-2-8-5/h4-7H,1-3H2 NSMOSDAEGJTOIQ-UHFFFAOYSA-N
T5A imidazole F3 fragment 'c1c[nH]cn1' InChI=1S/C3H4N2/c1-2-5-3-4-1/h1-3H,(H,4,5) RAXXELZNTBOGNW-UHFFFAOYSA-N
T5A phosphate F4 fragment O=P(O)(O)O InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4) NBIIXXVUZAFLBC-UHFFFAOYSA-N
T5A purine F5 fragment 'c1ncc2[nH]cnc2n1' InChI=1S/C5H4N4/c1-4-5(8-2-6-1)9-3-7-4/h1-3H,(H,6,7,8,9) KDCGOANMDULRCW-UHFFFAOYSA-N
T5A pyrimidine F6 fragment c1cncnc1 InChI=1S/C4H4N2/c1-2-5-4-6-3-1/h1-4H CZPWVGJYEJSRLH-UHFFFAOYSA-N
T5A ribose F7 fragment OCC1OCC(O)C1O InChI=1S/C5H10O4/c6-1-4-5(8)3(7)2-9-4/h3-8H,1-2H2 KZVAAIRBJJYZOW-UHFFFAOYSA-N
#
loop_
_pdbe_chem_comp_substructure_mapping.comp_id
_pdbe_chem_comp_substructure_mapping.atom_id
_pdbe_chem_comp_substructure_mapping.substructure_id
_pdbe_chem_comp_substructure_mapping.substructure_ordinal
T5A N1B S1 1
T5A C6B S1 1
T5A C2B S1 1
T5A O2B S1 1
T5A N3B S1 1
T5A C4B S1 1
T5A O4B S1 1
T5A C5B S1 1
T5A C5E S1 1
T5A C4E S1 1
T5A O4E S1 1
T5A C1E S1 1
T5A C2E S1 1
T5A C3E S1 1
T5A PA S1 1
T5A O2A S1 1
T5A O5E S1 1
T5A O3A S1 1
T5A PB S1 1
T5A O1B S1 1
T5A O3B S1 1
T5A PC S1 1
T5A O1C S1 1
T5A O3C S1 1
T5A PD S1 1
T5A O2D S1 1
T5A O3D S1 1
T5A PE S1 1
T5A O2E S1 1
T5A O5F S1 1
T5A C5F S1 1
T5A C4F S1 1
T5A O4F S1 1
T5A C1F S1 1
T5A C2F S1 1
T5A C3F S1 1
T5A N9A S1 1
T5A C4A S1 1
T5A N3A S1 1
T5A C2A S1 1
T5A N1A S1 1
T5A C6A S1 1
T5A C5A S1 1
T5A N7A S1 1
T5A C8A S1 1
T5A N1A F1 1
T5A C6A F1 1
T5A C5A F1 1
T5A C4A F1 1
T5A N3A F1 1
T5A C2A F1 1
T5A N9A F1 1
T5A C8A F1 1
T5A N7A F1 1
T5A N6A F1 1
T5A C1E F2 1
T5A C2E F2 1
T5A C3E F2 1
T5A O3E F2 1
T5A C4E F2 1
T5A O4E F2 1
T5A C5E F2 1
T5A O5E F2 1
T5A C4A F3 1
T5A C5A F3 1
T5A N7A F3 1
T5A C8A F3 1
T5A N9A F3 1
T5A O1A F4 1
T5A PA F4 1
T5A O2A F4 1
T5A O5E F4 1
T5A O3A F4 1
T5A O3A F4 2
T5A PB F4 2
T5A O1B F4 2
T5A O2X F4 2
T5A O3B F4 2
T5A O3B F4 3
T5A PC F4 3
T5A O1C F4 3
T5A O2C F4 3
T5A O3C F4 3
T5A O3C F4 4
T5A PD F4 4
T5A O2D F4 4
T5A O1D F4 4
T5A O3D F4 4
T5A O3D F4 5
T5A PE F4 5
T5A O2E F4 5
T5A O1E F4 5
T5A O5F F4 5
T5A N7A F5 1
T5A C8A F5 1
T5A N9A F5 1
T5A C4A F5 1
T5A C5A F5 1
T5A C6A F5 1
T5A N1A F5 1
T5A C2A F5 1
T5A N3A F5 1
T5A C5B F6 1
T5A C6B F6 1
T5A N1B F6 1
T5A C2B F6 1
T5A N3B F6 1
T5A C4B F6 1
T5A C5A F6 2
T5A C4A F6 2
T5A N3A F6 2
T5A C2A F6 2
T5A N1A F6 2
T5A C6A F6 2
T5A C2F F7 1
T5A C3F F7 1
T5A C4F F7 1
T5A O4F F7 1
T5A C1F F7 1
T5A C5F F7 1
T5A O5F F7 1
T5A O3F F7 1
T5A O2F F7 1
#
_pdbe_chem_comp_rdkit_properties.comp_id T5A
_pdbe_chem_comp_rdkit_properties.exactmw 891.008
_pdbe_chem_comp_rdkit_properties.amw 891.356
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 30
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 11
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 26
_pdbe_chem_comp_rdkit_properties.NumHBD 10
_pdbe_chem_comp_rdkit_properties.NumHBA 29
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 55
_pdbe_chem_comp_rdkit_properties.NumAtoms 85
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 35
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.550
_pdbe_chem_comp_rdkit_properties.NumRings 5
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 3
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 2
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 2
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 5
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 3
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 2
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 2
_pdbe_chem_comp_rdkit_properties.NumSpiroAtoms 0
_pdbe_chem_comp_rdkit_properties.NumBridgeheadAtoms 0
_pdbe_chem_comp_rdkit_properties.NumAtomStereoCenters 12
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 346.590
_pdbe_chem_comp_rdkit_properties.tpsa 445.510
_pdbe_chem_comp_rdkit_properties.CrippenClogP -0.928
_pdbe_chem_comp_rdkit_properties.CrippenMR 168.543
_pdbe_chem_comp_rdkit_properties.chi0v 29.228
_pdbe_chem_comp_rdkit_properties.chi1v 19.804
_pdbe_chem_comp_rdkit_properties.chi2v 12.202
_pdbe_chem_comp_rdkit_properties.chi3v 12.202
_pdbe_chem_comp_rdkit_properties.chi4v 9.004
_pdbe_chem_comp_rdkit_properties.chi0n 54.756
_pdbe_chem_comp_rdkit_properties.chi1n 26.609
_pdbe_chem_comp_rdkit_properties.chi2n 5.172
_pdbe_chem_comp_rdkit_properties.chi3n 5.172
_pdbe_chem_comp_rdkit_properties.chi4n 3.266
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -2.460
_pdbe_chem_comp_rdkit_properties.kappa1 18.636
_pdbe_chem_comp_rdkit_properties.kappa2 16.060
_pdbe_chem_comp_rdkit_properties.kappa3 10.737
_pdbe_chem_comp_rdkit_properties.Phi 5.441
#
loop_
_pdbe_chem_comp_external_mappings.comp_id
_pdbe_chem_comp_external_mappings.source
_pdbe_chem_comp_external_mappings.resource
_pdbe_chem_comp_external_mappings.resource_id
T5A UniChem ChEMBL CHEMBL1236157
T5A UniChem DrugBank DB03280
T5A UniChem PDBe T5A
T5A UniChem ZINC ZINC000169331553
T5A UniChem BindingDb 50366828
T5A UniChem BRENDA 172198
T5A UniChem BRENDA 215184
T5A UniChem BRENDA 33274
T5A UniChem BRENDA 94647
T5A UniChem 'Probes And Drugs' PD059819
T5A UniChem Nikkaji J952.328F
T5A UniChem PubChem 447202
#
loop_
_pdbe_chem_comp_rdkit_conformer.comp_id
_pdbe_chem_comp_rdkit_conformer.atom_id
_pdbe_chem_comp_rdkit_conformer.Cartn_x_rdkit
_pdbe_chem_comp_rdkit_conformer.Cartn_y_rdkit
_pdbe_chem_comp_rdkit_conformer.Cartn_z_rdkit
_pdbe_chem_comp_rdkit_conformer.rdkit_method
_pdbe_chem_comp_rdkit_conformer.rdkit_ordinal
T5A N1B 0.539 1.249 2.984 ETKDGv3 1
T5A C6B -0.154 2.301 3.688 ETKDGv3 2
T5A C2B -0.223 0.225 2.313 ETKDGv3 3
T5A O2B 0.354 -0.705 1.691 ETKDGv3 4
T5A N3B -1.649 0.264 2.357 ETKDGv3 5
T5A C4B -2.301 1.325 3.056 ETKDGv3 6
T5A O4B -3.560 1.357 3.105 ETKDGv3 7
T5A C5B -1.495 2.374 3.715 ETKDGv3 8
T5A C7B -2.177 3.486 4.462 ETKDGv3 9
T5A C5E 3.774 -0.448 0.364 ETKDGv3 10
T5A C4E 3.609 0.249 1.718 ETKDGv3 11
T5A O4E 2.498 1.110 1.673 ETKDGv3 12
T5A C1E 2.011 1.222 2.993 ETKDGv3 13
T5A C2E 2.535 0.055 3.835 ETKDGv3 14
T5A C3E 3.377 -0.737 2.862 ETKDGv3 15
T5A O3E 4.578 -1.195 3.436 ETKDGv3 16
T5A PA 5.063 -2.076 -1.098 ETKDGv3 17
T5A O1A 6.319 -3.208 -1.006 ETKDGv3 18
T5A O2A 5.465 -0.998 -2.079 ETKDGv3 19
T5A O5E 4.824 -1.384 0.445 ETKDGv3 20
T5A O3A 3.657 -2.845 -1.674 ETKDGv3 21
T5A PB 3.104 -3.967 -0.506 ETKDGv3 22
T5A O1B 4.144 -4.269 0.553 ETKDGv3 23
T5A O2X 2.730 -5.419 -1.292 ETKDGv3 24
T5A O3B 1.718 -3.353 0.268 ETKDGv3 25
T5A PC 0.495 -3.205 -0.907 ETKDGv3 26
T5A O1C -0.691 -2.520 -0.268 ETKDGv3 27
T5A O2C 1.037 -2.249 -2.200 ETKDGv3 28
T5A O3C 0.010 -4.759 -1.417 ETKDGv3 29
T5A PD -0.665 -4.617 -2.974 ETKDGv3 30
T5A O1D -1.546 -6.020 -3.326 ETKDGv3 31
T5A O2D 0.455 -4.492 -3.983 ETKDGv3 32
T5A O3D -1.663 -3.241 -3.092 ETKDGv3 33
T5A PE -3.132 -3.554 -2.275 ETKDGv3 34
T5A O1E -4.246 -4.214 -3.364 ETKDGv3 35
T5A O2E -2.942 -4.520 -1.125 ETKDGv3 36
T5A O5F -3.767 -2.104 -1.634 ETKDGv3 37
T5A C5F -3.493 -1.053 -2.529 ETKDGv3 38
T5A C4F -3.996 0.263 -1.929 ETKDGv3 39
T5A O4F -3.378 0.482 -0.679 ETKDGv3 40
T5A C1F -3.054 1.854 -0.580 ETKDGv3 41
T5A C2F -3.499 2.580 -1.854 ETKDGv3 42
T5A O2F -4.683 3.313 -1.637 ETKDGv3 43
T5A C3F -3.697 1.453 -2.838 ETKDGv3 44
T5A O3F -4.758 1.714 -3.721 ETKDGv3 45
T5A N9A -1.614 1.999 -0.377 ETKDGv3 46
T5A C4A -0.937 3.098 0.195 ETKDGv3 47
T5A N3A -1.431 4.077 0.888 ETKDGv3 48
T5A C2A -0.505 5.075 1.380 ETKDGv3 49
T5A N1A 0.780 4.976 1.123 ETKDGv3 50
T5A C6A 1.308 3.881 0.340 ETKDGv3 51
T5A N6A 2.705 3.790 0.059 ETKDGv3 52
T5A C5A 0.440 2.973 -0.102 ETKDGv3 53
T5A N7A 0.641 1.812 -0.898 ETKDGv3 54
T5A C8A -0.549 1.289 -1.046 ETKDGv3 55
T5A HB6 0.426 3.061 4.200 ETKDGv3 56
T5A HN3 -2.210 -0.473 1.875 ETKDGv3 57
T5A HB71 -2.491 3.121 5.462 ETKDGv3 58
T5A HB72 -3.073 3.830 3.903 ETKDGv3 59
T5A HB73 -1.506 4.362 4.591 ETKDGv3 60
T5A HB51 2.818 -0.948 0.100 ETKDGv3 61
T5A HB52 3.995 0.336 -0.395 ETKDGv3 62
T5A HB4 4.518 0.863 1.911 ETKDGv3 63
T5A HB1 2.408 2.173 3.415 ETKDGv3 64
T5A HB21 1.719 -0.575 4.251 ETKDGv3 65
T5A HB22 3.144 0.445 4.681 ETKDGv3 66
T5A HB3 2.791 -1.613 2.506 ETKDGv3 67
T5A "HB'3" 5.096 -0.406 3.745 ETKDGv3 68
T5A HO1A 7.060 -2.728 -0.558 ETKDGv3 69
T5A HO2B 3.535 -5.631 -1.828 ETKDGv3 70
T5A HO2C 1.203 -1.357 -1.804 ETKDGv3 71
T5A HO1D -1.901 -5.874 -4.240 ETKDGv3 72
T5A HO1E -4.144 -3.676 -4.189 ETKDGv3 73
T5A HA51 -2.398 -0.952 -2.698 ETKDGv3 74
T5A HA52 -4.008 -1.227 -3.501 ETKDGv3 75
T5A HA4 -5.094 0.183 -1.764 ETKDGv3 76
T5A HA1 -3.578 2.275 0.306 ETKDGv3 77
T5A HC2 -2.717 3.281 -2.222 ETKDGv3 78
T5A HO2 -5.375 2.691 -1.288 ETKDGv3 79
T5A HC3 -2.746 1.304 -3.404 ETKDGv3 80
T5A HA3 -4.702 1.030 -4.437 ETKDGv3 81
T5A HA2 -0.873 5.903 1.970 ETKDGv3 82
T5A HA61 3.093 3.002 -0.505 ETKDGv3 83
T5A HA62 3.358 4.516 0.428 ETKDGv3 84
T5A HA8 -0.714 0.394 -1.628 ETKDGv3 85
#