data_MCD
#
_chem_comp.id MCD
_chem_comp.name "METHYLMALONYL(CARBADETHIA)-COENZYME A"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAC
_chem_comp.formula "C26 H42 N7 O19 P3"
_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 849.568
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code MCD
_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 5REQ
_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.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
MCD C8 C8 C 0 1 Y N N N N N 55.178 -10.962 28.271 -2.382 1.392 -8.070 C8 MCD 1
MCD N9 N9 N 0 1 Y N N N N N 55.857 -11.523 27.230 -2.282 0.128 -8.571 N9 MCD 2
MCD C4 C4 C 0 1 Y N N N N N 54.900 -12.193 26.488 -3.216 0.006 -9.569 C4 MCD 3
MCD C5 C5 C 0 1 Y N N N N N 53.703 -11.989 27.145 -3.879 1.243 -9.632 C5 MCD 4
MCD N7 N7 N 0 1 Y N N N N N 53.885 -11.211 28.257 -3.319 2.044 -8.694 N7 MCD 5
MCD N3 N3 N 0 1 Y N N N N N 55.102 -12.912 25.358 -3.586 -0.968 -10.393 N3 MCD 6
MCD C2 C2 C 0 1 Y N N N N N 53.973 -13.419 24.924 -4.553 -0.777 -11.266 C2 MCD 7
MCD N1 N1 N 0 1 Y N N N N N 52.724 -13.290 25.467 -5.201 0.368 -11.366 N1 MCD 8
MCD C6 C6 C 0 1 Y N N N N N 52.540 -12.570 26.600 -4.904 1.398 -10.580 C6 MCD 9
MCD N6 N6 N 0 1 N N N N N N 51.314 -12.462 27.120 -5.588 2.596 -10.694 N6 MCD 10
MCD "C1'" "C1'" C 0 1 N N R N N N 57.298 -11.430 26.967 -1.344 -0.906 -8.130 "C1'" MCD 11
MCD "C2'" "C2'" C 0 1 N N R N N N 57.735 -10.107 26.362 0.015 -0.763 -8.859 "C2'" MCD 12
MCD "O2'" "O2'" O 0 1 N N N N N N 57.513 -10.110 24.944 -0.001 -1.450 -10.112 "O2'" MCD 13
MCD "C3'" "C3'" C 0 1 N N S N N N 59.215 -10.042 26.749 0.991 -1.448 -7.866 "C3'" MCD 14
MCD "O3'" "O3'" O 0 1 N N N N N N 60.130 -10.844 26.004 1.245 -2.796 -8.265 "O3'" MCD 15
MCD "C4'" "C4'" C 0 1 N N R N N N 59.119 -10.575 28.177 0.242 -1.408 -6.520 "C4'" MCD 16
MCD "O4'" "O4'" O 0 1 N N N N N N 58.007 -11.518 28.175 -1.002 -0.723 -6.739 "O4'" MCD 17
MCD "C5'" "C5'" C 0 1 N N N N N N 58.867 -9.524 29.240 1.076 -0.652 -5.483 "C5'" MCD 18
MCD "O5'" "O5'" O 0 1 N N N N N N 57.589 -8.919 28.969 0.371 -0.614 -4.241 "O5'" MCD 19
MCD P1 P1 P 0 1 N N S N N N 57.543 -7.320 28.859 1.301 0.191 -3.203 P1 MCD 20
MCD O11 O11 O 0 1 N N N N N N 56.187 -6.840 28.547 1.540 1.559 -3.713 O11 MCD 21
MCD O12 O12 O 0 1 N N N N N N 58.489 -6.879 27.813 2.709 -0.573 -3.038 O12 MCD 22
MCD O6 O6 O 0 1 N N N N N N 58.039 -6.922 30.323 0.565 0.272 -1.773 O6 MCD 23
MCD P2 P2 P 0 1 N N R N N N 59.250 -6.019 30.899 1.546 1.086 -0.790 P2 MCD 24
MCD O21 O21 O 0 1 N N N N N N 60.543 -6.680 30.653 1.781 2.441 -1.338 O21 MCD 25
MCD O22 O22 O 0 1 N N N N N N 59.025 -5.828 32.339 2.949 0.307 -0.666 O22 MCD 26
MCD O7 O7 O 0 1 N N N N N N 59.282 -4.745 30.160 0.868 1.206 0.665 O7 MCD 27
MCD CPB CPB C 0 1 N N N N N N 58.419 -3.770 30.742 1.782 1.934 1.487 CPB MCD 28
MCD CPA CPA C 0 1 N N N N N N 58.518 -2.543 29.805 1.195 2.085 2.892 CPA MCD 29
MCD CP7 CP7 C 0 1 N N R N N N 59.954 -2.002 29.976 2.173 2.864 3.773 CP7 MCD 30
MCD CP9 CP9 C 0 1 N N N N N N 57.612 -1.420 30.296 0.958 0.699 3.497 CP9 MCD 31
MCD CP8 CP8 C 0 1 N N N N N N 58.232 -2.849 28.343 -0.132 2.840 2.812 CP8 MCD 32
MCD OP3 OP3 O 0 1 N N N N N N 60.255 -0.933 29.092 2.485 4.112 3.150 OP3 MCD 33
MCD CP6 CP6 C 0 1 N N N N N N 60.040 -1.480 31.437 1.545 3.118 5.119 CP6 MCD 34
MCD OP2 OP2 O 0 1 N N N N N N 60.315 -2.352 32.282 1.144 4.227 5.402 OP2 MCD 35
MCD NP2 NP2 N 0 1 N N N N N N 59.812 -0.198 31.672 1.429 2.112 6.009 NP2 MCD 36
MCD CP5 CP5 C 0 1 N N N N N N 59.949 0.205 33.148 0.800 2.354 7.310 CP5 MCD 37
MCD CP4 CP4 C 0 1 N N N N N N 60.326 1.692 33.286 0.795 1.058 8.122 CP4 MCD 38
MCD CP3 CP3 C 0 1 N N N N N N 60.451 2.123 34.740 0.148 1.307 9.461 CP3 MCD 39
MCD OP1 OP1 O 0 1 N N N N N N 60.455 1.304 35.673 -0.266 2.412 9.737 OP1 MCD 40
MCD NP1 NP1 N 0 1 N N N N N N 60.520 3.427 34.937 0.032 0.301 10.350 NP1 MCD 41
MCD CP2 CP2 C 0 1 N N N N N N 60.644 3.944 36.382 -0.596 0.543 11.651 CP2 MCD 42
MCD CP1 CP1 C 0 1 N N N N N N 60.344 5.457 36.266 -0.601 -0.752 12.464 CP1 MCD 43
MCD P3 P3 P 0 1 N N N N N N 60.943 -10.305 24.731 2.834 -2.925 -8.484 P3 MCD 44
MCD O31 O31 O 0 1 N N N N N N 60.021 -9.958 23.634 3.534 -2.611 -7.218 O31 MCD 45
MCD O32 O32 O 0 1 N N N N N N 61.869 -11.368 24.299 3.194 -4.428 -8.937 O32 MCD 46
MCD O33 O33 O 0 1 N N N N N N 61.692 -9.037 25.340 3.304 -1.893 -9.627 O33 MCD 47
MCD CPS CPS C 0 1 N N N N N N 60.461 6.278 37.499 -1.258 -0.499 13.823 CPS MCD 48
MCD CS1 CS1 C 0 1 N N N N N N 60.291 7.774 37.325 -1.263 -1.776 14.624 CS1 MCD 49
MCD OS1 OS1 O 0 1 N N N N N N 60.179 8.334 36.270 -0.790 -2.784 14.156 OS1 MCD 50
MCD CS2 CS2 C 0 1 N N S N N N 60.298 8.579 38.589 -1.858 -1.795 16.008 CS2 MCD 51
MCD CS3 CS3 C 0 1 N N N N N N 58.922 8.867 39.121 -0.774 -1.457 17.034 CS3 MCD 52
MCD CS4 CS4 C 0 1 N N N N N N 61.058 9.880 38.433 -2.414 -3.165 16.297 CS4 MCD 53
MCD OS4 OS4 O 0 1 N N N N N N 60.575 10.893 37.811 -2.335 -4.037 15.465 OS4 MCD 54
MCD OS5 OS5 O 0 1 N N N N N N 62.226 9.943 38.973 -2.996 -3.417 17.480 OS5 MCD 55
MCD H8 H8 H 0 1 N N N N N N 55.640 -10.352 29.065 -1.773 1.793 -7.273 H8 MCD 56
MCD H2 H2 H 0 1 N N N N N N 54.085 -14.017 24.004 -4.827 -1.588 -11.924 H2 MCD 57
MCD HN61 1HN6 H 0 0 N N N N N N 50.472 -12.882 26.725 -6.294 2.690 -11.352 HN61 MCD 58
MCD HN62 2HN6 H 0 0 N N N N N N 51.124 -11.464 27.220 -5.362 3.340 -10.115 HN62 MCD 59
MCD "H1'" "H1'" H 0 1 N N N N N N 57.508 -12.259 26.252 -1.764 -1.899 -8.294 "H1'" MCD 60
MCD "H2'" "H2'" H 0 1 N N N N N N 57.172 -9.215 26.723 0.273 0.286 -8.998 "H2'" MCD 61
MCD "HO2'" "'HO2" H 0 0 N N N N N N 57.786 -9.282 24.565 -0.690 -1.036 -10.648 "HO2'" MCD 62
MCD "H3'" "H3'" H 0 1 N N N N N N 59.630 -9.021 26.577 1.924 -0.888 -7.800 "H3'" MCD 63
MCD "H4'" "H4'" H 0 1 N N N N N N 60.103 -11.024 28.444 0.050 -2.423 -6.172 "H4'" MCD 64
MCD "H5'1" "1H5'" H 0 0 N N N N N N 58.941 -9.930 30.275 1.253 0.365 -5.832 "H5'1" MCD 65
MCD "H5'2" "2H5'" H 0 0 N N N N N N 59.691 -8.777 29.313 2.030 -1.160 -5.344 "H5'2" MCD 66
MCD H12 H12 H 0 1 N N N N N N 58.461 -5.931 27.747 2.509 -1.458 -2.704 H12 MCD 67
MCD H22 H22 H 0 1 N N N N N N 59.736 -5.297 32.677 2.751 -0.568 -0.306 H22 MCD 68
MCD HPB1 1HPB H 0 0 N N N N N N 57.376 -4.129 30.908 1.951 2.921 1.057 HPB1 MCD 69
MCD HPB2 2HPB H 0 0 N N N N N N 58.646 -3.543 31.809 2.728 1.396 1.544 HPB2 MCD 70
MCD HP7 HP7 H 0 1 N N N N N N 60.682 -2.814 29.748 3.087 2.285 3.902 HP7 MCD 71
MCD HP91 1HP9 H 0 0 N N N N N N 57.683 -0.535 29.620 1.916 0.212 3.675 HP91 MCD 72
MCD HP92 2HP9 H 0 0 N N N N N N 56.558 -1.762 30.420 0.421 0.801 4.440 HP92 MCD 73
MCD HP93 3HP9 H 0 0 N N N N N N 57.825 -1.149 31.356 0.367 0.098 2.805 HP93 MCD 74
MCD HP81 1HP8 H 0 0 N N N N N N 58.303 -1.964 27.667 0.036 3.827 2.382 HP81 MCD 75
MCD HP82 2HP8 H 0 0 N N N N N N 58.892 -3.670 27.980 -0.829 2.285 2.185 HP82 MCD 76
MCD HP83 3HP8 H 0 0 N N N N N N 57.238 -3.342 28.235 -0.550 2.947 3.813 HP83 MCD 77
MCD HOP3 3HOP H 0 0 N N N N N N 61.138 -0.600 29.197 1.651 4.593 3.054 HOP3 MCD 78
MCD HNP2 2HNP H 0 0 N N N N N N 59.573 0.375 30.862 1.761 1.228 5.788 HNP2 MCD 79
MCD HP51 1HP5 H 0 0 N N N N N N 59.028 -0.040 33.727 -0.224 2.694 7.160 HP51 MCD 80
MCD HP52 2HP5 H 0 0 N N N N N N 60.670 -0.452 33.687 1.361 3.118 7.848 HP52 MCD 81
MCD HP41 1HP4 H 0 0 N N N N N N 61.254 1.926 32.715 1.820 0.719 8.272 HP41 MCD 82
MCD HP42 2HP4 H 0 0 N N N N N N 59.608 2.342 32.733 0.234 0.294 7.584 HP42 MCD 83
MCD HNP1 1HNP H 0 0 N N N N N N 60.482 3.970 34.074 0.364 -0.582 10.129 HNP1 MCD 84
MCD HP21 1HP2 H 0 0 N N N N N N 60.003 3.404 37.118 -1.621 0.883 11.502 HP21 MCD 85
MCD HP22 2HP2 H 0 0 N N N N N N 61.616 3.706 36.872 -0.035 1.307 12.190 HP22 MCD 86
MCD HP11 1HP1 H 0 0 N N N N N N 60.984 5.899 35.467 0.423 -1.091 12.614 HP11 MCD 87
MCD HP12 2HP1 H 0 0 N N N N N N 59.330 5.598 35.824 -1.162 -1.516 11.926 HP12 MCD 88
MCD H32 H32 H 0 1 N N N N N N 62.350 -11.048 23.544 4.153 -4.462 -9.057 H32 MCD 89
MCD H33 H33 H 0 1 N N N N N N 62.173 -8.717 24.585 2.826 -2.132 -10.433 H33 MCD 90
MCD HPS1 1HPS H 0 0 N N N N N N 59.747 5.904 38.270 -2.283 -0.160 13.674 HPS1 MCD 91
MCD HPS2 2HPS H 0 0 N N N N N N 61.432 6.064 38.003 -0.696 0.264 14.361 HPS2 MCD 92
MCD HS2 HS2 H 0 1 N N N N N N 60.823 7.934 39.332 -2.658 -1.057 16.070 HS2 MCD 93
MCD HS31 1HS3 H 0 0 N N N N N N 58.927 9.465 40.061 0.026 -2.194 16.972 HS31 MCD 94
MCD HS32 2HS3 H 0 0 N N N N N N 58.292 9.358 38.343 -0.372 -0.466 16.824 HS32 MCD 95
MCD HS33 3HS3 H 0 0 N N N N N N 58.345 7.922 39.256 -1.204 -1.470 18.035 HS33 MCD 96
MCD HOS5 5HOS H 0 0 N N N N N N 62.702 10.758 38.875 -3.353 -4.296 17.666 HOS5 MCD 97
#
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
MCD C8 N9 SING Y N 1
MCD C8 N7 DOUB Y N 2
MCD C8 H8 SING N N 3
MCD N9 C4 SING Y N 4
MCD N9 "C1'" SING N N 5
MCD C4 C5 SING Y N 6
MCD C4 N3 DOUB Y N 7
MCD C5 N7 SING Y N 8
MCD C5 C6 DOUB Y N 9
MCD N3 C2 SING Y N 10
MCD C2 N1 DOUB Y N 11
MCD C2 H2 SING N N 12
MCD N1 C6 SING Y N 13
MCD C6 N6 SING N N 14
MCD N6 HN61 SING N N 15
MCD N6 HN62 SING N N 16
MCD "C1'" "C2'" SING N N 17
MCD "C1'" "O4'" SING N N 18
MCD "C1'" "H1'" SING N N 19
MCD "C2'" "O2'" SING N N 20
MCD "C2'" "C3'" SING N N 21
MCD "C2'" "H2'" SING N N 22
MCD "O2'" "HO2'" SING N N 23
MCD "C3'" "O3'" SING N N 24
MCD "C3'" "C4'" SING N N 25
MCD "C3'" "H3'" SING N N 26
MCD "O3'" P3 SING N N 27
MCD "C4'" "O4'" SING N N 28
MCD "C4'" "C5'" SING N N 29
MCD "C4'" "H4'" SING N N 30
MCD "C5'" "O5'" SING N N 31
MCD "C5'" "H5'1" SING N N 32
MCD "C5'" "H5'2" SING N N 33
MCD "O5'" P1 SING N N 34
MCD P1 O11 DOUB N N 35
MCD P1 O12 SING N N 36
MCD P1 O6 SING N N 37
MCD O12 H12 SING N N 38
MCD O6 P2 SING N N 39
MCD P2 O21 DOUB N N 40
MCD P2 O22 SING N N 41
MCD P2 O7 SING N N 42
MCD O22 H22 SING N N 43
MCD O7 CPB SING N N 44
MCD CPB CPA SING N N 45
MCD CPB HPB1 SING N N 46
MCD CPB HPB2 SING N N 47
MCD CPA CP7 SING N N 48
MCD CPA CP9 SING N N 49
MCD CPA CP8 SING N N 50
MCD CP7 OP3 SING N N 51
MCD CP7 CP6 SING N N 52
MCD CP7 HP7 SING N N 53
MCD CP9 HP91 SING N N 54
MCD CP9 HP92 SING N N 55
MCD CP9 HP93 SING N N 56
MCD CP8 HP81 SING N N 57
MCD CP8 HP82 SING N N 58
MCD CP8 HP83 SING N N 59
MCD OP3 HOP3 SING N N 60
MCD CP6 OP2 DOUB N N 61
MCD CP6 NP2 SING N N 62
MCD NP2 CP5 SING N N 63
MCD NP2 HNP2 SING N N 64
MCD CP5 CP4 SING N N 65
MCD CP5 HP51 SING N N 66
MCD CP5 HP52 SING N N 67
MCD CP4 CP3 SING N N 68
MCD CP4 HP41 SING N N 69
MCD CP4 HP42 SING N N 70
MCD CP3 OP1 DOUB N N 71
MCD CP3 NP1 SING N N 72
MCD NP1 CP2 SING N N 73
MCD NP1 HNP1 SING N N 74
MCD CP2 CP1 SING N N 75
MCD CP2 HP21 SING N N 76
MCD CP2 HP22 SING N N 77
MCD CP1 CPS SING N N 78
MCD CP1 HP11 SING N N 79
MCD CP1 HP12 SING N N 80
MCD P3 O31 DOUB N N 81
MCD P3 O32 SING N N 82
MCD P3 O33 SING N N 83
MCD O32 H32 SING N N 84
MCD O33 H33 SING N N 85
MCD CPS CS1 SING N N 86
MCD CPS HPS1 SING N N 87
MCD CPS HPS2 SING N N 88
MCD CS1 OS1 DOUB N N 89
MCD CS1 CS2 SING N N 90
MCD CS2 CS3 SING N N 91
MCD CS2 CS4 SING N N 92
MCD CS2 HS2 SING N N 93
MCD CS3 HS31 SING N N 94
MCD CS3 HS32 SING N N 95
MCD CS3 HS33 SING N N 96
MCD CS4 OS4 DOUB N N 97
MCD CS4 OS5 SING N N 98
MCD OS5 HOS5 SING N N 99
#
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
MCD SMILES ACDLabs 10.04 O=C(O)C(C(=O)CCCNC(=O)CCNC(=O)C(O)C(C)(C)COP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3OP(=O)(O)O)C
MCD SMILES_CANONICAL CACTVS 3.341 C[C@H](C(O)=O)C(=O)CCCNC(=O)CCNC(=O)[C@H](O)C(C)(C)CO[P@](O)(=O)O[P@](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O[P](O)(O)=O)n2cnc3c(N)ncnc23
MCD SMILES CACTVS 3.341 C[CH](C(O)=O)C(=O)CCCNC(=O)CCNC(=O)[CH](O)C(C)(C)CO[P](O)(=O)O[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O[P](O)(O)=O)n2cnc3c(N)ncnc23
MCD SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 C[C@@H](C(=O)CCCNC(=O)CCNC(=O)[C@@H](C(C)(C)CO[P@@](=O)(O)O[P@@](=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)O)C(=O)O
MCD SMILES "OpenEye OEToolkits" 1.5.0 CC(C(=O)CCCNC(=O)CCNC(=O)C(C(C)(C)COP(=O)(O)OP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)O)C(=O)O
MCD InChI InChI 1.03 InChI=1S/C26H42N7O19P3/c1-13(25(39)40)14(34)5-4-7-28-16(35)6-8-29-23(38)20(37)26(2,3)10-49-55(46,47)52-54(44,45)48-9-15-19(51-53(41,42)43)18(36)24(50-15)33-12-32-17-21(27)30-11-31-22(17)33/h11-13,15,18-20,24,36-37H,4-10H2,1-3H3,(H,28,35)(H,29,38)(H,39,40)(H,44,45)(H,46,47)(H2,27,30,31)(H2,41,42,43)/t13-,15+,18+,19+,20-,24+/m0/s1
MCD InChIKey InChI 1.03 NFOFXPNZJMTBQW-XSSXAYJJSA-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
MCD "SYSTEMATIC NAME" ACDLabs 10.04 "(3S,5R,9R,20S)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-3,5,9-trihydroxy-8,8,20-trimethyl-10,14,19-trioxo-2,4,6-trioxa-11,15-diaza-3,5-diphosphahenicosan-21-oic acid 3,5-dioxide (non-preferred name)"
MCD "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "(2S)-6-[3-[[(2R)-4-[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-hydroxy-3-phosphonooxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl]oxy-hydroxy-phosphoryl]oxy-2-hydroxy-3,3-dimethyl-butanoyl]amino]propanoylamino]-2-methyl-3-oxo-hexanoic 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
MCD 'Create component' 1999-07-08 RCSB
MCD 'Modify descriptor' 2011-06-04 RCSB
#
loop_
_software.name
_software.version
_software.description
rdkit 2025.03.3 'Core functionality.'
pdbeccdutils 1.0.0 '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
MCD C8 C 25.520 -10.475 1
MCD N9 N 24.644 -9.268 2
MCD C4 C 23.225 -9.725 3
MCD C5 C 23.225 -11.225 4
MCD N7 N 24.644 -11.682 5
MCD N3 N 21.926 -8.975 6
MCD C2 C 20.627 -9.725 7
MCD N1 N 20.627 -11.225 8
MCD C6 C 21.926 -11.975 9
MCD N6 N 21.926 -13.475 10
MCD "C1'" C 25.110 -7.842 11
MCD "C2'" C 26.538 -7.381 12
MCD "O2'" O 27.750 -8.265 13
MCD "C3'" C 26.540 -5.881 14
MCD "O3'" O 27.755 -5.001 15
MCD "C4'" C 25.114 -5.415 16
MCD "O4'" O 24.231 -6.627 17
MCD "C5'" C 24.653 -3.987 18
MCD "O5'" O 23.187 -3.673 19
MCD P1 P 22.726 -2.246 20
MCD O11 O 21.298 -2.707 21
MCD O12 O 24.153 -1.785 22
MCD O6 O 22.265 -0.818 23
MCD P2 P 20.798 -0.504 24
MCD O21 O 21.112 0.963 25
MCD O22 O 20.484 -1.971 26
MCD O7 O 19.331 -0.190 27
MCD CPB C 18.870 1.238 28
MCD CPA C 17.403 1.552 29
MCD CP7 C 15.937 1.867 30
MCD CP9 C 17.718 3.019 31
MCD CP8 C 17.089 0.086 32
MCD OP3 O 14.931 0.754 33
MCD CP6 C 15.476 3.294 34
MCD OP2 O 16.481 4.407 35
MCD NP2 N 14.009 3.609 36
MCD CP5 C 13.548 5.036 37
MCD CP4 C 12.081 5.350 38
MCD CP3 C 11.620 6.778 39
MCD OP1 O 12.626 7.891 40
MCD NP1 N 10.154 7.092 41
MCD CP2 C 9.693 8.519 42
MCD CP1 C 8.226 8.834 43
MCD P3 P 27.601 -3.509 44
MCD O31 O 27.447 -2.017 45
MCD O32 O 29.093 -3.355 46
MCD O33 O 26.109 -3.663 47
MCD CPS C 7.765 10.261 48
MCD CS1 C 6.298 10.576 49
MCD OS1 O 5.293 9.463 50
MCD CS2 C 5.837 12.003 51
MCD CS3 C 6.843 13.116 52
MCD CS4 C 4.370 12.317 53
MCD OS4 O 3.909 13.745 54
MCD OS5 O 3.365 11.204 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
MCD C8 N9 SINGLE NONE 1
MCD C8 N7 DOUBLE NONE 2
MCD N9 C4 SINGLE NONE 3
MCD "C1'" N9 SINGLE BEGINDASH 4
MCD C4 C5 DOUBLE NONE 5
MCD C4 N3 SINGLE NONE 6
MCD C5 N7 SINGLE NONE 7
MCD C5 C6 SINGLE NONE 8
MCD N3 C2 DOUBLE NONE 9
MCD C2 N1 SINGLE NONE 10
MCD N1 C6 DOUBLE NONE 11
MCD C6 N6 SINGLE NONE 12
MCD "C1'" "C2'" SINGLE NONE 13
MCD "C1'" "O4'" SINGLE NONE 14
MCD "C2'" "O2'" SINGLE BEGINWEDGE 15
MCD "C2'" "C3'" SINGLE NONE 16
MCD "C3'" "O3'" SINGLE BEGINWEDGE 17
MCD "C3'" "C4'" SINGLE NONE 18
MCD "O3'" P3 SINGLE NONE 19
MCD "C4'" "O4'" SINGLE NONE 20
MCD "C4'" "C5'" SINGLE BEGINDASH 21
MCD "C5'" "O5'" SINGLE NONE 22
MCD "O5'" P1 SINGLE NONE 23
MCD P1 O11 DOUBLE NONE 24
MCD P1 O12 SINGLE BEGINDASH 25
MCD P1 O6 SINGLE NONE 26
MCD O6 P2 SINGLE NONE 27
MCD P2 O21 DOUBLE NONE 28
MCD P2 O22 SINGLE BEGINWEDGE 29
MCD P2 O7 SINGLE NONE 30
MCD O7 CPB SINGLE NONE 31
MCD CPB CPA SINGLE NONE 32
MCD CPA CP7 SINGLE NONE 33
MCD CPA CP9 SINGLE NONE 34
MCD CPA CP8 SINGLE NONE 35
MCD CP7 OP3 SINGLE BEGINWEDGE 36
MCD CP7 CP6 SINGLE NONE 37
MCD CP6 OP2 DOUBLE NONE 38
MCD CP6 NP2 SINGLE NONE 39
MCD NP2 CP5 SINGLE NONE 40
MCD CP5 CP4 SINGLE NONE 41
MCD CP4 CP3 SINGLE NONE 42
MCD CP3 OP1 DOUBLE NONE 43
MCD CP3 NP1 SINGLE NONE 44
MCD NP1 CP2 SINGLE NONE 45
MCD CP2 CP1 SINGLE NONE 46
MCD CP1 CPS SINGLE NONE 47
MCD P3 O31 DOUBLE NONE 48
MCD P3 O32 SINGLE NONE 49
MCD P3 O33 SINGLE NONE 50
MCD CPS CS1 SINGLE NONE 51
MCD CS1 OS1 DOUBLE NONE 52
MCD CS1 CS2 SINGLE NONE 53
MCD CS2 CS3 SINGLE BEGINWEDGE 54
MCD CS2 CS4 SINGLE NONE 55
MCD CS4 OS4 DOUBLE NONE 56
MCD CS4 OS5 SINGLE NONE 57
#
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
MCD MurckoScaffold S1 scaffold 'c1ncc2ncn([C@H]3CCCO3)c2n1' InChI=1S/C9H10N4O/c1-2-8(14-3-1)13-6-12-7-4-10-5-11-9(7)13/h4-6,8H,1-3H2/t8-/m1/s1 DAKONNSVCLKUJN-MRVPVSSYSA-N
MCD 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
MCD amide F2 fragment CC(N)=O InChI=1S/C2H5NO/c1-2(3)4/h1H3,(H2,3,4) DLFVBJFMPXGRIB-UHFFFAOYSA-N
MCD imidazole F3 fragment 'c1c[nH]cn1' InChI=1S/C3H4N2/c1-2-5-3-4-1/h1-3H,(H,4,5) RAXXELZNTBOGNW-UHFFFAOYSA-N
MCD 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
MCD 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
MCD pyrimidine F6 fragment c1cncnc1 InChI=1S/C4H4N2/c1-2-5-4-6-3-1/h1-4H CZPWVGJYEJSRLH-UHFFFAOYSA-N
MCD 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
MCD C8 S1 1
MCD N9 S1 1
MCD C4 S1 1
MCD C5 S1 1
MCD N7 S1 1
MCD N3 S1 1
MCD C2 S1 1
MCD N1 S1 1
MCD C6 S1 1
MCD "C1'" S1 1
MCD "C2'" S1 1
MCD "C3'" S1 1
MCD "C4'" S1 1
MCD "O4'" S1 1
MCD N1 F1 1
MCD C6 F1 1
MCD C5 F1 1
MCD C4 F1 1
MCD N3 F1 1
MCD C2 F1 1
MCD N9 F1 1
MCD C8 F1 1
MCD N7 F1 1
MCD N6 F1 1
MCD NP2 F2 1
MCD CP6 F2 1
MCD OP2 F2 1
MCD CP7 F2 1
MCD NP1 F2 2
MCD CP3 F2 2
MCD OP1 F2 2
MCD CP4 F2 2
MCD C4 F3 1
MCD C5 F3 1
MCD N7 F3 1
MCD C8 F3 1
MCD N9 F3 1
MCD "O3'" F4 1
MCD P3 F4 1
MCD O31 F4 1
MCD O32 F4 1
MCD O33 F4 1
MCD "O5'" F4 2
MCD P1 F4 2
MCD O11 F4 2
MCD O12 F4 2
MCD O6 F4 2
MCD O6 F4 3
MCD P2 F4 3
MCD O21 F4 3
MCD O22 F4 3
MCD O7 F4 3
MCD N7 F5 1
MCD C8 F5 1
MCD N9 F5 1
MCD C4 F5 1
MCD C5 F5 1
MCD C6 F5 1
MCD N1 F5 1
MCD C2 F5 1
MCD N3 F5 1
MCD C5 F6 1
MCD C4 F6 1
MCD N3 F6 1
MCD C2 F6 1
MCD N1 F6 1
MCD C6 F6 1
MCD "C2'" F7 1
MCD "C3'" F7 1
MCD "C4'" F7 1
MCD "O4'" F7 1
MCD "C1'" F7 1
MCD "C5'" F7 1
MCD "O5'" F7 1
MCD "O3'" F7 1
MCD "O2'" F7 1
#
_pdbe_chem_comp_rdkit_properties.comp_id MCD
_pdbe_chem_comp_rdkit_properties.exactmw 849.175
_pdbe_chem_comp_rdkit_properties.amw 849.574
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 26
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 11
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 32
_pdbe_chem_comp_rdkit_properties.NumHBD 10
_pdbe_chem_comp_rdkit_properties.NumHBA 24
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 55
_pdbe_chem_comp_rdkit_properties.NumAtoms 97
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 29
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 2
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.654
_pdbe_chem_comp_rdkit_properties.NumRings 3
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 2
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 1
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 1
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 3
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 2
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumSpiroAtoms 0
_pdbe_chem_comp_rdkit_properties.NumBridgeheadAtoms 0
_pdbe_chem_comp_rdkit_properties.NumAtomStereoCenters 8
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 370.559
_pdbe_chem_comp_rdkit_properties.tpsa 400.930
_pdbe_chem_comp_rdkit_properties.CrippenClogP -2.334
_pdbe_chem_comp_rdkit_properties.CrippenMR 177.644
_pdbe_chem_comp_rdkit_properties.chi0v 27.912
_pdbe_chem_comp_rdkit_properties.chi1v 16.903
_pdbe_chem_comp_rdkit_properties.chi2v 7.493
_pdbe_chem_comp_rdkit_properties.chi3v 7.493
_pdbe_chem_comp_rdkit_properties.chi4v 4.857
_pdbe_chem_comp_rdkit_properties.chi0n 67.229
_pdbe_chem_comp_rdkit_properties.chi1n 32.667
_pdbe_chem_comp_rdkit_properties.chi2n 4.857
_pdbe_chem_comp_rdkit_properties.chi3n 4.857
_pdbe_chem_comp_rdkit_properties.chi4n 2.777
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -3.320
_pdbe_chem_comp_rdkit_properties.kappa1 14.500
_pdbe_chem_comp_rdkit_properties.kappa2 18.749
_pdbe_chem_comp_rdkit_properties.kappa3 13.397
_pdbe_chem_comp_rdkit_properties.Phi 4.943
#
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
MCD UniChem ZINC ZINC000195757938
MCD UniChem PubChem 449561
#
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
MCD C8 -7.422 0.704 -1.219 ETKDGv3 1
MCD N9 -8.319 -0.231 -0.600 ETKDGv3 2
MCD C4 -9.566 0.211 -1.101 ETKDGv3 3
MCD C5 -9.397 1.258 -1.861 ETKDGv3 4
MCD N7 -8.018 1.595 -1.959 ETKDGv3 5
MCD N3 -10.837 -0.435 -0.965 ETKDGv3 6
MCD C2 -11.861 0.060 -1.611 ETKDGv3 7
MCD N1 -11.701 1.225 -2.459 ETKDGv3 8
MCD C6 -10.540 1.810 -2.599 ETKDGv3 9
MCD N6 -10.398 2.946 -3.450 ETKDGv3 10
MCD "C1'" -7.993 -1.575 -0.130 ETKDGv3 11
MCD "C2'" -7.750 -2.523 -1.297 ETKDGv3 12
MCD "O2'" -8.926 -3.185 -1.685 ETKDGv3 13
MCD "C3'" -6.732 -3.482 -0.737 ETKDGv3 14
MCD "O3'" -7.391 -4.548 -0.075 ETKDGv3 15
MCD "C4'" -5.998 -2.607 0.288 ETKDGv3 16
MCD "O4'" -6.832 -1.530 0.668 ETKDGv3 17
MCD "C5'" -4.685 -2.055 -0.279 ETKDGv3 18
MCD "O5'" -4.066 -1.244 0.692 ETKDGv3 19
MCD P1 -2.667 -0.560 -0.000 ETKDGv3 20
MCD O11 -1.953 0.244 1.063 ETKDGv3 21
MCD O12 -3.119 0.469 -1.269 ETKDGv3 22
MCD O6 -1.642 -1.807 -0.547 ETKDGv3 23
MCD P2 -0.493 -1.110 -1.590 ETKDGv3 24
MCD O21 -1.139 -0.828 -2.929 ETKDGv3 25
MCD O22 0.766 -2.219 -1.812 ETKDGv3 26
MCD O7 0.129 0.331 -0.916 ETKDGv3 27
MCD CPB 1.078 0.875 -1.805 ETKDGv3 28
MCD CPA 1.665 2.187 -1.221 ETKDGv3 29
MCD CP7 2.287 1.913 0.198 ETKDGv3 30
MCD CP9 0.523 3.224 -1.094 ETKDGv3 31
MCD CP8 2.706 2.744 -2.222 ETKDGv3 32
MCD OP3 3.127 0.782 0.225 ETKDGv3 33
MCD CP6 2.982 3.111 0.810 ETKDGv3 34
MCD OP2 2.339 3.850 1.605 ETKDGv3 35
MCD NP2 4.345 3.429 0.490 ETKDGv3 36
MCD CP5 5.034 4.551 1.129 ETKDGv3 37
MCD CP4 6.502 4.635 0.694 ETKDGv3 38
MCD CP3 7.269 3.428 1.150 ETKDGv3 39
MCD OP1 7.636 3.346 2.354 ETKDGv3 40
MCD NP1 7.539 2.356 0.236 ETKDGv3 41
MCD CP2 8.040 1.058 0.680 ETKDGv3 42
MCD CP1 6.922 0.268 1.374 ETKDGv3 43
MCD P3 -6.424 -5.954 -0.145 ETKDGv3 44
MCD O31 -5.050 -5.679 0.425 ETKDGv3 45
MCD O32 -6.278 -6.468 -1.752 ETKDGv3 46
MCD O33 -7.163 -7.175 0.763 ETKDGv3 47
MCD CPS 7.372 -1.143 1.776 ETKDGv3 48
MCD CS1 8.412 -1.111 2.869 ETKDGv3 49
MCD OS1 8.105 -0.676 3.970 ETKDGv3 50
MCD CS2 9.814 -1.627 2.629 ETKDGv3 51
MCD CS3 10.123 -2.807 3.554 ETKDGv3 52
MCD CS4 10.815 -0.523 2.825 ETKDGv3 53
MCD OS4 11.480 -0.094 1.843 ETKDGv3 54
MCD OS5 11.002 0.040 4.085 ETKDGv3 55
MCD H8 -6.346 0.663 -1.109 ETKDGv3 56
MCD H2 -12.831 -0.409 -1.521 ETKDGv3 57
MCD HN61 -11.221 3.323 -3.970 ETKDGv3 58
MCD HN62 -9.471 3.414 -3.563 ETKDGv3 59
MCD "H1'" -8.829 -1.954 0.500 ETKDGv3 60
MCD "H2'" -7.300 -1.981 -2.164 ETKDGv3 61
MCD "HO2'" -9.428 -2.554 -2.263 ETKDGv3 62
MCD "H3'" -6.073 -3.822 -1.573 ETKDGv3 63
MCD "H4'" -5.757 -3.201 1.196 ETKDGv3 64
MCD "H5'1" -4.026 -2.915 -0.539 ETKDGv3 65
MCD "H5'2" -4.915 -1.472 -1.200 ETKDGv3 66
MCD H12 -3.728 1.130 -0.853 ETKDGv3 67
MCD H22 1.162 -2.331 -0.911 ETKDGv3 68
MCD HPB1 0.604 1.100 -2.788 ETKDGv3 69
MCD HPB2 1.908 0.152 -1.979 ETKDGv3 70
MCD HP7 1.443 1.666 0.880 ETKDGv3 71
MCD HP91 0.914 4.203 -0.745 ETKDGv3 72
MCD HP92 -0.248 2.881 -0.370 ETKDGv3 73
MCD HP93 0.026 3.386 -2.075 ETKDGv3 74
MCD HP81 3.550 2.040 -2.372 ETKDGv3 75
MCD HP82 3.111 3.719 -1.881 ETKDGv3 76
MCD HP83 2.237 2.913 -3.215 ETKDGv3 77
MCD HOP3 3.814 0.880 -0.480 ETKDGv3 78
MCD HNP2 4.850 2.853 -0.220 ETKDGv3 79
MCD HP51 4.981 4.441 2.234 ETKDGv3 80
MCD HP52 4.522 5.497 0.849 ETKDGv3 81
MCD HP41 6.960 5.544 1.138 ETKDGv3 82
MCD HP42 6.561 4.737 -0.411 ETKDGv3 83
MCD HNP1 7.360 2.496 -0.784 ETKDGv3 84
MCD HP21 8.902 1.206 1.365 ETKDGv3 85
MCD HP22 8.399 0.486 -0.203 ETKDGv3 86
MCD HP11 6.065 0.175 0.672 ETKDGv3 87
MCD HP12 6.564 0.818 2.270 ETKDGv3 88
MCD H32 -5.770 -7.317 -1.700 ETKDGv3 89
MCD H33 -8.050 -7.298 0.342 ETKDGv3 90
MCD HPS1 6.490 -1.708 2.148 ETKDGv3 91
MCD HPS2 7.748 -1.681 0.880 ETKDGv3 92
MCD HS2 9.900 -1.996 1.583 ETKDGv3 93
MCD HS31 9.396 -3.629 3.375 ETKDGv3 94
MCD HS32 11.144 -3.194 3.349 ETKDGv3 95
MCD HS33 10.063 -2.503 4.622 ETKDGv3 96
MCD HOS5 11.669 0.789 4.225 ETKDGv3 97
#