data_4RA
#
_chem_comp.id 4RA
_chem_comp.name
"[(2R,3R,4R,5S,6R)-3-acetamido-6-methyl-5-[(E)-[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylideneamino]-4-oxidanyl-oxan-2-yl] [[(2R,3S,4R,5R)-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] hydrogen phosphate"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C25 H36 N5 O20 P3"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2015-05-14
_chem_comp.pdbx_modified_date 2015-07-24
_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 819.496
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code 4RA
_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 4ZTC
_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
4RA O2C O1 O 0 1 N N N N N N 31.082 12.534 0.799 -6.441 -4.331 -1.743 O2C 4RA 1
4RA O3 O2 O 0 1 N N N N N N 22.643 2.467 -7.422 2.669 -2.415 -0.115 O3 4RA 2
4RA C2 C1 C 0 1 Y N N N N N 20.535 2.352 -8.311 4.189 -4.242 -0.307 C2 4RA 3
4RA C3 C2 C 0 1 Y N N N N N 21.379 2.969 -7.433 3.942 -2.883 -0.167 C3 4RA 4
4RA C4 C3 C 0 1 Y N N N N N 20.923 3.963 -6.579 5.031 -2.002 -0.081 C4 4RA 5
4RA C5 C4 C 0 1 Y N N N N N 19.592 4.353 -6.649 6.322 -2.541 -0.140 C5 4RA 6
4RA C6 C5 C 0 1 Y N N N N N 18.775 3.708 -7.586 6.472 -3.905 -0.280 C6 4RA 7
4RA C2C C6 C 0 1 N N N N N N 32.016 11.759 1.152 -6.925 -4.203 -0.636 C2C 4RA 8
4RA N3C N1 N 0 1 N N N N N N 33.216 12.271 1.408 -7.161 -5.295 0.115 N3C 4RA 9
4RA C4C C7 C 0 1 N N N N N N 34.231 11.451 1.806 -7.697 -5.171 1.346 C4C 4RA 10
4RA O4C O3 O 0 1 N N N N N N 35.342 11.949 2.033 -7.911 -6.159 2.026 O4C 4RA 11
4RA C5C C8 C 0 1 N N N N N N 34.041 10.077 1.956 -8.010 -3.882 1.841 C5C 4RA 12
4RA C6C C9 C 0 1 N N N N N N 32.771 9.565 1.694 -7.763 -2.804 1.067 C6C 4RA 13
4RA N1C N2 N 0 1 N N N N N N 31.827 10.421 1.263 -7.213 -2.972 -0.175 N1C 4RA 14
4RA C1B C10 C 0 1 N N R N N N 30.504 9.924 0.951 -6.940 -1.802 -1.013 C1B 4RA 15
4RA C2B C11 C 0 1 N N R N N N 30.522 8.927 -0.210 -8.251 -1.050 -1.330 C2B 4RA 16
4RA "O2'" O4 O 0 1 N N N N N N 30.877 9.417 -1.546 -8.736 -1.412 -2.625 "O2'" 4RA 17
4RA C3B C12 C 0 1 N N S N N N 29.120 8.367 -0.031 -7.846 0.441 -1.301 C3B 4RA 18
4RA O3B O5 O 0 1 N N N N N N 28.104 9.080 -0.757 -8.067 1.045 -2.577 O3B 4RA 19
4RA O4B O6 O 0 1 N N N N N N 29.989 9.210 2.053 -6.131 -0.846 -0.293 O4B 4RA 20
4RA C4B C13 C 0 1 N N R N N N 28.906 8.459 1.484 -6.337 0.413 -0.970 C4B 4RA 21
4RA C5B C14 C 0 1 N N N N N N 28.894 7.074 2.118 -5.972 1.579 -0.049 C5B 4RA 22
4RA O5B O7 O 0 1 N N N N N N 27.723 6.406 1.732 -4.557 1.603 0.151 O5B 4RA 23
4RA PA P1 P 0 1 N N N N N N 27.764 4.817 1.374 -3.820 2.702 1.069 PA 4RA 24
4RA O1A O8 O 0 1 N N N N N N 27.731 4.106 2.654 -4.282 2.518 2.601 O1A 4RA 25
4RA O2A O9 O 0 1 N N N N N N 28.827 4.595 0.391 -4.185 4.058 0.604 O2A 4RA 26
4RA O3A O10 O 0 1 N N N N N N 26.341 4.759 0.747 -2.226 2.508 0.962 O3A 4RA 27
4RA PB P2 P 0 1 N N N N N N 25.551 3.475 0.279 -0.959 3.419 1.358 PB 4RA 28
4RA O2B O11 O 0 1 N N N N N N 26.550 2.506 -0.175 -1.241 4.831 1.015 O2B 4RA 29
4RA O1B O12 O 0 1 N N N N N N 24.512 3.077 1.329 -0.683 3.296 2.940 O1B 4RA 30
4RA "O1'" O13 O 0 1 N N N N N N 24.737 4.102 -0.991 0.338 2.918 0.546 "O1'" 4RA 31
4RA "C1'" C15 C 0 1 N N R N N N 25.424 4.692 -2.113 1.598 3.590 0.600 "C1'" 4RA 32
4RA "C2'" C16 C 0 1 N N R N N N 24.713 5.964 -2.621 2.339 3.393 -0.724 "C2'" 4RA 33
4RA "N2'" N3 N 0 1 N N N N N N 24.378 6.710 -1.373 1.513 3.892 -1.827 "N2'" 4RA 34
4RA "C7'" C17 C 0 1 N N N N N N 25.187 7.645 -0.976 1.543 5.199 -2.153 "C7'" 4RA 35
4RA "C8'" C18 C 0 1 N N N N N N 24.811 8.275 0.331 0.694 5.713 -3.287 "C8'" 4RA 36
4RA "O7'" O14 O 0 1 N N N N N N 26.167 8.036 -1.621 2.255 5.962 -1.535 "O7'" 4RA 37
4RA "C3'" C19 C 0 1 N N S N N N 23.501 5.581 -3.454 2.617 1.900 -0.928 "C3'" 4RA 38
4RA "O3'" O15 O 0 1 N N N N N N 23.041 6.776 -4.061 3.371 1.714 -2.127 "O3'" 4RA 39
4RA "C4'" C20 C 0 1 N N S N N N 23.926 4.594 -4.561 3.414 1.373 0.269 "C4'" 4RA 40
4RA "C5'" C21 C 0 1 N N R N N N 24.556 3.338 -3.974 2.632 1.648 1.555 "C5'" 4RA 41
4RA "C6'" C22 C 0 1 N N N N N N 25.155 2.383 -4.994 3.449 1.178 2.760 "C6'" 4RA 42
4RA "O5'" O16 O 0 1 N N N N N N 25.612 3.655 -3.085 2.380 3.050 1.668 "O5'" 4RA 43
4RA "N4'" N4 N 0 1 N N N N N N 22.837 4.120 -5.370 3.622 -0.070 0.121 "N4'" 4RA 44
4RA C4A C23 C 0 1 N N N N N N 21.768 4.622 -5.616 4.822 -0.548 0.068 C4A 4RA 45
4RA C2A C24 C 0 1 N N N N N N 20.999 1.263 -9.240 3.032 -5.203 -0.401 C2A 4RA 46
4RA N1 N5 N 0 1 Y N N N N N 19.240 2.714 -8.356 5.422 -4.701 -0.363 N1 4RA 47
4RA C5A C25 C 0 1 N N N N N N 18.968 5.407 -5.734 7.530 -1.645 -0.053 C5A 4RA 48
4RA O4P O17 O 0 1 N N N N N N 19.631 6.676 -5.813 8.717 -2.436 -0.138 O4P 4RA 49
4RA P P3 P 0 1 N N N N N N 19.424 7.716 -4.665 10.197 -1.805 -0.078 P 4RA 50
4RA O3P O18 O 0 1 N N N N N N 20.540 7.419 -3.715 10.433 -0.868 -1.367 O3P 4RA 51
4RA O1P O19 O 0 1 N N N N N N 19.700 9.054 -5.411 10.340 -0.995 1.153 O1P 4RA 52
4RA O2P O20 O 0 1 N N N N N N 18.036 7.536 -4.091 11.286 -2.990 -0.070 O2P 4RA 53
4RA H1 H1 H 0 1 N N N N N N 23.168 2.944 -6.790 2.303 -2.369 0.778 H1 4RA 54
4RA H2 H2 H 0 1 N N N N N N 17.746 4.019 -7.691 7.464 -4.329 -0.327 H2 4RA 55
4RA H3 H3 H 0 1 N N N N N N 33.374 13.253 1.309 -6.944 -6.175 -0.231 H3 4RA 56
4RA H4 H4 H 0 1 N N N N N N 34.850 9.432 2.265 -8.440 -3.763 2.824 H4 4RA 57
4RA H5 H5 H 0 1 N N N N N N 32.552 8.516 1.832 -7.995 -1.812 1.427 H5 4RA 58
4RA H6 H6 H 0 1 N N N N N N 29.840 10.761 0.690 -6.441 -2.104 -1.934 H6 4RA 59
4RA H7 H7 H 0 1 N N N N N N 31.230 8.129 0.058 -9.003 -1.256 -0.568 H7 4RA 60
4RA H8 H8 H 0 1 N N N N N N 31.770 9.741 -1.538 -9.524 -0.925 -2.900 H8 4RA 61
4RA H9 H9 H 0 1 N N N N N N 29.119 7.307 -0.325 -8.397 0.972 -0.525 H9 4RA 62
4RA H10 H10 H 0 1 N N N N N N 27.416 8.477 -1.014 -8.991 1.035 -2.862 H10 4RA 63
4RA H11 H11 H 0 1 N N N N N N 27.946 8.957 1.683 -5.747 0.452 -1.885 H11 4RA 64
4RA H12 H12 H 0 1 N N N N N N 29.772 6.505 1.778 -6.291 2.516 -0.505 H12 4RA 65
4RA H13 H13 H 0 1 N N N N N N 28.920 7.170 3.214 -6.473 1.454 0.911 H13 4RA 66
4RA H14 H14 H 0 1 N N N N N N 28.477 3.521 2.711 -4.074 1.649 2.972 H14 4RA 67
4RA H15 H15 H 0 1 N N N N N N 24.649 2.172 1.584 -0.491 2.396 3.236 H15 4RA 68
4RA H16 H16 H 0 1 N N N N N N 26.418 5.009 -1.765 1.435 4.654 0.771 H16 4RA 69
4RA H17 H17 H 0 1 N N N N N N 25.412 6.551 -3.234 3.282 3.940 -0.699 H17 4RA 70
4RA H18 H18 H 0 1 N N N N N N 23.550 6.495 -0.855 0.944 3.282 -2.321 H18 4RA 71
4RA H19 H19 H 0 1 N N N N N N 25.523 9.079 0.569 -0.357 5.520 -3.070 H19 4RA 72
4RA H20 H20 H 0 1 N N N N N N 23.796 8.693 0.258 0.850 6.785 -3.402 H20 4RA 73
4RA H21 H21 H 0 1 N N N N N N 24.838 7.515 1.125 0.973 5.204 -4.210 H21 4RA 74
4RA H22 H22 H 0 1 N N N N N N 22.730 5.122 -2.817 1.673 1.361 -1.003 H22 4RA 75
4RA H23 H23 H 0 1 N N N N N N 22.776 7.392 -3.388 3.583 0.790 -2.319 H23 4RA 76
4RA H24 H24 H 0 1 N N N N N N 24.671 5.092 -5.199 4.379 1.878 0.314 H24 4RA 77
4RA H25 H25 H 0 1 N N N N N N 23.773 2.795 -3.425 1.684 1.110 1.526 H25 4RA 78
4RA H26 H26 H 0 1 N N N N N N 25.583 1.512 -4.475 4.396 1.717 2.789 H26 4RA 79
4RA H27 H27 H 0 1 N N N N N N 24.370 2.047 -5.687 2.891 1.374 3.676 H27 4RA 80
4RA H28 H28 H 0 1 N N N N N N 25.946 2.898 -5.558 3.641 0.109 2.674 H28 4RA 81
4RA H29 H29 H 0 1 N N N N N N 21.455 5.535 -5.131 5.672 0.116 0.133 H29 4RA 82
4RA H30 H30 H 0 1 N N N N N N 20.152 0.913 -9.848 2.750 -5.330 -1.446 H30 4RA 83
4RA H31 H31 H 0 1 N N N N N N 21.786 1.655 -9.900 3.325 -6.167 0.016 H31 4RA 84
4RA H32 H32 H 0 1 N N N N N N 21.399 0.424 -8.651 2.185 -4.808 0.159 H32 4RA 85
4RA H33 H33 H 0 1 N N N N N N 17.915 5.542 -6.021 7.511 -0.929 -0.874 H33 4RA 86
4RA H34 H34 H 0 1 N N N N N N 19.021 5.047 -4.696 7.517 -1.109 0.896 H34 4RA 87
4RA H35 H35 H 0 1 N N N N N N 21.190 8.111 -3.763 10.355 -1.334 -2.211 H35 4RA 88
4RA H36 H36 H 0 1 N N N N N N 17.512 8.305 -4.281 12.202 -2.683 -0.035 H36 4RA 89
#
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
4RA C2A C2 SING N N 1
4RA N1 C2 DOUB Y N 2
4RA N1 C6 SING Y N 3
4RA C2 C3 SING Y N 4
4RA C6 C5 DOUB Y N 5
4RA C3 O3 SING N N 6
4RA C3 C4 DOUB Y N 7
4RA C5 C4 SING Y N 8
4RA C5 C5A SING N N 9
4RA C4 C4A SING N N 10
4RA O4P C5A SING N N 11
4RA O4P P SING N N 12
4RA C4A "N4'" DOUB N N 13
4RA O1P P DOUB N N 14
4RA "N4'" "C4'" SING N N 15
4RA "C6'" "C5'" SING N N 16
4RA P O2P SING N N 17
4RA P O3P SING N N 18
4RA "C4'" "C5'" SING N N 19
4RA "C4'" "C3'" SING N N 20
4RA "O3'" "C3'" SING N N 21
4RA "C5'" "O5'" SING N N 22
4RA "C3'" "C2'" SING N N 23
4RA "O5'" "C1'" SING N N 24
4RA "C2'" "C1'" SING N N 25
4RA "C2'" "N2'" SING N N 26
4RA "C1'" "O1'" SING N N 27
4RA "O7'" "C7'" DOUB N N 28
4RA "O2'" C2B SING N N 29
4RA "N2'" "C7'" SING N N 30
4RA "O1'" PB SING N N 31
4RA "C7'" "C8'" SING N N 32
4RA O3B C3B SING N N 33
4RA C2B C3B SING N N 34
4RA C2B C1B SING N N 35
4RA O2B PB DOUB N N 36
4RA C3B C4B SING N N 37
4RA PB O3A SING N N 38
4RA PB O1B SING N N 39
4RA O2A PA DOUB N N 40
4RA O3A PA SING N N 41
4RA O2C C2C DOUB N N 42
4RA C1B N1C SING N N 43
4RA C1B O4B SING N N 44
4RA C2C N1C SING N N 45
4RA C2C N3C SING N N 46
4RA N1C C6C SING N N 47
4RA PA O5B SING N N 48
4RA PA O1A SING N N 49
4RA N3C C4C SING N N 50
4RA C4B O4B SING N N 51
4RA C4B C5B SING N N 52
4RA C6C C5C DOUB N N 53
4RA O5B C5B SING N N 54
4RA C4C C5C SING N N 55
4RA C4C O4C DOUB N N 56
4RA O3 H1 SING N N 57
4RA C6 H2 SING N N 58
4RA N3C H3 SING N N 59
4RA C5C H4 SING N N 60
4RA C6C H5 SING N N 61
4RA C1B H6 SING N N 62
4RA C2B H7 SING N N 63
4RA "O2'" H8 SING N N 64
4RA C3B H9 SING N N 65
4RA O3B H10 SING N N 66
4RA C4B H11 SING N N 67
4RA C5B H12 SING N N 68
4RA C5B H13 SING N N 69
4RA O1A H14 SING N N 70
4RA O1B H15 SING N N 71
4RA "C1'" H16 SING N N 72
4RA "C2'" H17 SING N N 73
4RA "N2'" H18 SING N N 74
4RA "C8'" H19 SING N N 75
4RA "C8'" H20 SING N N 76
4RA "C8'" H21 SING N N 77
4RA "C3'" H22 SING N N 78
4RA "O3'" H23 SING N N 79
4RA "C4'" H24 SING N N 80
4RA "C5'" H25 SING N N 81
4RA "C6'" H26 SING N N 82
4RA "C6'" H27 SING N N 83
4RA "C6'" H28 SING N N 84
4RA C4A H29 SING N N 85
4RA C2A H30 SING N N 86
4RA C2A H31 SING N N 87
4RA C2A H32 SING N N 88
4RA C5A H33 SING N N 89
4RA C5A H34 SING N N 90
4RA O3P H35 SING N N 91
4RA O2P H36 SING N N 92
#
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
4RA SMILES ACDLabs 12.01 O=C1N(C=CC(N1)=O)C2OC(C(C2O)O)COP(O)(=O)OP(O)(=O)OC3C(NC(C)=O)C(O)C(C(O3)C)\N=C\c4c(O)c(C)ncc4COP(O)(O)=O
4RA InChI InChI 1.03 InChI=1S/C25H36N5O20P3/c1-10-19(33)14(13(6-26-10)8-45-51(38,39)40)7-27-17-11(2)47-24(18(21(17)35)28-12(3)31)49-53(43,44)50-52(41,42)46-9-15-20(34)22(36)23(48-15)30-5-4-16(32)29-25(30)37/h4-7,11,15,17-18,20-24,33-36H,8-9H2,1-3H3,(H,28,31)(H,41,42)(H,43,44)(H,29,32,37)(H2,38,39,40)/b27-7+/t11-,15-,17-,18-,20-,21+,22-,23-,24-/m1/s1
4RA InChIKey InChI 1.03 BKHPSAUTHKIVAK-OTBUILFPSA-N
4RA SMILES_CANONICAL CACTVS 3.385 C[C@H]1O[C@H](O[P](O)(=O)O[P](O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)N3C=CC(=O)NC3=O)[C@H](NC(C)=O)[C@@H](O)[C@@H]1N=Cc4c(O)c(C)ncc4CO[P](O)(O)=O
4RA SMILES CACTVS 3.385 C[CH]1O[CH](O[P](O)(=O)O[P](O)(=O)OC[CH]2O[CH]([CH](O)[CH]2O)N3C=CC(=O)NC3=O)[CH](NC(C)=O)[CH](O)[CH]1N=Cc4c(O)c(C)ncc4CO[P](O)(O)=O
4RA SMILES_CANONICAL "OpenEye OEToolkits" 1.9.2 Cc1c(c(c(cn1)COP(=O)(O)O)/C=N/[C@@H]2[C@H](O[C@@H]([C@@H]([C@H]2O)NC(=O)C)OP(=O)(O)OP(=O)(O)OC[C@@H]3[C@H]([C@H]([C@@H](O3)N4C=CC(=O)NC4=O)O)O)C)O
4RA SMILES "OpenEye OEToolkits" 1.9.2 Cc1c(c(c(cn1)COP(=O)(O)O)C=NC2C(OC(C(C2O)NC(=O)C)OP(=O)(O)OP(=O)(O)OCC3C(C(C(O3)N4C=CC(=O)NC4=O)O)O)C)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
4RA "SYSTEMATIC NAME" ACDLabs 12.01 "(2R,3R,4R,5S,6R)-3-(acetylamino)-4-hydroxy-5-[(E)-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)amino]-6-methyltetrahydro-2H-pyran-2-yl [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate (non-preferred name)"
4RA "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.9.2 "[(2R,3R,4R,5S,6R)-3-acetamido-6-methyl-5-[(E)-[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylideneamino]-4-oxidanyl-oxan-2-yl] [[(2R,3S,4R,5R)-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] 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
4RA 'Create component' 2015-05-14 RCSB
4RA 'Modify name' 2015-06-03 RCSB
4RA 'Initial release' 2015-07-29 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
4RA O2C O -7.946 2.601 1
4RA O3 O -0.438 -6.399 2
4RA C2 C 0.866 -8.647 3
4RA C3 C 0.861 -7.146 4
4RA C4 C 2.160 -6.395 5
4RA C5 C 3.459 -7.141 6
4RA C6 C 3.465 -8.642 7
4RA C2C C -8.832 3.814 8
4RA N3C N -10.323 3.649 9
4RA C4C C -11.206 4.863 10
4RA O4C O -12.699 4.702 11
4RA C5C C -10.603 6.235 12
4RA C6C C -9.111 6.393 13
4RA N1C N -8.223 5.184 14
4RA C1B C -6.735 5.342 15
4RA C2B C -5.983 6.643 16
4RA "O2'" O -6.592 8.013 17
4RA C3B C -4.517 6.327 18
4RA O3B O -3.399 7.330 19
4RA O4B O -5.732 4.232 20
4RA C4B C -4.359 4.836 21
4RA C5B C -3.043 4.004 22
4RA O5B O -1.782 4.721 23
4RA PA P -0.348 4.141 24
4RA O1A O -0.749 2.672 25
4RA O2A O 0.027 5.570 26
4RA O3A O 1.194 3.939 27
4RA PB P 2.185 2.741 28
4RA O2B O 3.199 3.815 29
4RA O1B O 1.144 1.629 30
4RA "O1'" O 3.435 1.811 31
4RA "C1'" C 3.444 0.356 32
4RA "C2'" C 4.744 -0.391 33
4RA "N2'" N 6.043 0.362 34
4RA "C7'" C 6.040 1.862 35
4RA "C8'" C 7.337 2.615 36
4RA "O7'" O 4.739 2.609 37
4RA "C3'" C 4.749 -1.891 38
4RA "O3'" O 6.048 -2.638 39
4RA "C4'" C 3.449 -2.642 40
4RA "C5'" C 2.151 -1.896 41
4RA "C6'" C 0.852 -2.649 42
4RA "O5'" O 2.145 -0.396 43
4RA "N4'" N 3.453 -4.142 44
4RA C4A C 2.156 -4.895 45
4RA C2A C -0.433 -9.399 46
4RA N1 N 2.165 -9.393 47
4RA C5A C 4.758 -6.389 48
4RA O4P O 6.059 -7.136 49
4RA P P 7.356 -6.384 50
4RA O3P O 6.603 -5.086 51
4RA O1P O 8.653 -5.631 52
4RA O2P O 8.109 -7.681 53
#
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
4RA C2A C2 SINGLE NONE 1
4RA N1 C2 DOUBLE NONE 2
4RA N1 C6 SINGLE NONE 3
4RA C2 C3 SINGLE NONE 4
4RA C6 C5 DOUBLE NONE 5
4RA C3 O3 SINGLE NONE 6
4RA C3 C4 DOUBLE NONE 7
4RA C5 C4 SINGLE NONE 8
4RA C5 C5A SINGLE NONE 9
4RA C4 C4A SINGLE ENDUPRIGHT 10
4RA O4P C5A SINGLE NONE 11
4RA O4P P SINGLE NONE 12
4RA C4A "N4'" DOUBLE NONE 13
4RA O1P P DOUBLE NONE 14
4RA "C4'" "N4'" SINGLE BEGINDASH 15
4RA "C5'" "C6'" SINGLE BEGINWEDGE 16
4RA P O2P SINGLE NONE 17
4RA P O3P SINGLE NONE 18
4RA "C4'" "C5'" SINGLE NONE 19
4RA "C4'" "C3'" SINGLE NONE 20
4RA "C3'" "O3'" SINGLE BEGINWEDGE 21
4RA "C5'" "O5'" SINGLE NONE 22
4RA "C3'" "C2'" SINGLE NONE 23
4RA "O5'" "C1'" SINGLE NONE 24
4RA "C2'" "C1'" SINGLE NONE 25
4RA "C2'" "N2'" SINGLE BEGINDASH 26
4RA "C1'" "O1'" SINGLE BEGINDASH 27
4RA "O7'" "C7'" DOUBLE NONE 28
4RA C2B "O2'" SINGLE BEGINDASH 29
4RA "N2'" "C7'" SINGLE NONE 30
4RA "O1'" PB SINGLE NONE 31
4RA "C7'" "C8'" SINGLE NONE 32
4RA C3B O3B SINGLE BEGINDASH 33
4RA C2B C3B SINGLE NONE 34
4RA C2B C1B SINGLE NONE 35
4RA O2B PB DOUBLE NONE 36
4RA C3B C4B SINGLE NONE 37
4RA PB O3A SINGLE NONE 38
4RA PB O1B SINGLE BEGINWEDGE 39
4RA O2A PA DOUBLE NONE 40
4RA O3A PA SINGLE NONE 41
4RA O2C C2C DOUBLE NONE 42
4RA C1B N1C SINGLE BEGINWEDGE 43
4RA C1B O4B SINGLE NONE 44
4RA C2C N1C SINGLE NONE 45
4RA C2C N3C SINGLE NONE 46
4RA N1C C6C SINGLE NONE 47
4RA PA O5B SINGLE NONE 48
4RA PA O1A SINGLE BEGINWEDGE 49
4RA N3C C4C SINGLE NONE 50
4RA C4B O4B SINGLE NONE 51
4RA C4B C5B SINGLE BEGINWEDGE 52
4RA C6C C5C DOUBLE NONE 53
4RA O5B C5B SINGLE NONE 54
4RA C4C C5C SINGLE NONE 55
4RA C4C O4C DOUBLE NONE 56
#
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
4RA MurckoScaffold S1 scaffold 'O=c1ccn([C@H]2CC[C@@H](CO[PH](=O)O[PH](=O)O[C@@H]3CC[C@H](/N=C/c4ccncc4)CO3)O2)c(=O)[nH]1' InChI=1S/C20H26N4O9P2/c25-17-7-10-24(20(26)23-17)18-3-2-16(31-18)13-30-34(27)33-35(28)32-19-4-1-15(12-29-19)22-11-14-5-8-21-9-6-14/h5-11,15-16,18-19,34-35H,1-4,12-13H2,(H,23,25,26)/b22-11+/t15-,16-,18+,19+/m0/s1 XJHCTFSMUYUEKC-TUHUWRINSA-N
4RA amide F1 fragment CC(N)=O InChI=1S/C2H5NO/c1-2(3)4/h1H3,(H2,3,4) DLFVBJFMPXGRIB-UHFFFAOYSA-N
4RA phosphate F2 fragment O=P(O)(O)O InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4) NBIIXXVUZAFLBC-UHFFFAOYSA-N
4RA pyranose F3 fragment OC1CCCCO1 InChI=1S/C5H10O2/c6-5-3-1-2-4-7-5/h5-6H,1-4H2 CELWCAITJAEQNL-UHFFFAOYSA-N
4RA pyridine F4 fragment c1ccncc1 InChI=1S/C5H5N/c1-2-4-6-5-3-1/h1-5H JUJWROOIHBZHMG-UHFFFAOYSA-N
4RA pyrimidine F5 fragment c1cncnc1 InChI=1S/C4H4N2/c1-2-5-4-6-3-1/h1-4H CZPWVGJYEJSRLH-UHFFFAOYSA-N
4RA ribose F6 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
4RA O2C S1 1
4RA C2 S1 1
4RA C3 S1 1
4RA C4 S1 1
4RA C5 S1 1
4RA C6 S1 1
4RA C2C S1 1
4RA N3C S1 1
4RA C4C S1 1
4RA O4C S1 1
4RA C5C S1 1
4RA C6C S1 1
4RA N1C S1 1
4RA C1B S1 1
4RA C2B S1 1
4RA C3B S1 1
4RA O4B S1 1
4RA C4B S1 1
4RA C5B S1 1
4RA O5B S1 1
4RA PA S1 1
4RA O2A S1 1
4RA O3A S1 1
4RA PB S1 1
4RA O2B S1 1
4RA "O1'" S1 1
4RA "C1'" S1 1
4RA "C2'" S1 1
4RA "C3'" S1 1
4RA "C4'" S1 1
4RA "C5'" S1 1
4RA "O5'" S1 1
4RA "N4'" S1 1
4RA C4A S1 1
4RA N1 S1 1
4RA "N2'" F1 1
4RA "C7'" F1 1
4RA "O7'" F1 1
4RA "C8'" F1 1
4RA O5B F2 1
4RA PA F2 1
4RA O2A F2 1
4RA O3A F2 1
4RA O1A F2 1
4RA O3A F2 2
4RA PB F2 2
4RA O2B F2 2
4RA "O1'" F2 2
4RA O1B F2 2
4RA O4P F2 3
4RA P F2 3
4RA O1P F2 3
4RA O2P F2 3
4RA O3P F2 3
4RA "C4'" F3 1
4RA "C5'" F3 1
4RA "O5'" F3 1
4RA "C1'" F3 1
4RA "C2'" F3 1
4RA "C3'" F3 1
4RA "O1'" F3 1
4RA C2 F4 1
4RA C3 F4 1
4RA C4 F4 1
4RA C5 F4 1
4RA C6 F4 1
4RA N1 F4 1
4RA C5C F5 1
4RA C6C F5 1
4RA N1C F5 1
4RA C2C F5 1
4RA N3C F5 1
4RA C4C F5 1
4RA C2B F6 1
4RA C3B F6 1
4RA C4B F6 1
4RA O4B F6 1
4RA C1B F6 1
4RA C5B F6 1
4RA O5B F6 1
4RA O3B F6 1
4RA "O2'" F6 1
#
_pdbe_chem_comp_rdkit_properties.comp_id 4RA
_pdbe_chem_comp_rdkit_properties.exactmw 819.117
_pdbe_chem_comp_rdkit_properties.amw 819.500
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 25
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 10
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 25
_pdbe_chem_comp_rdkit_properties.NumHBD 10
_pdbe_chem_comp_rdkit_properties.NumHBA 23
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 53
_pdbe_chem_comp_rdkit_properties.NumAtoms 89
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 28
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 1
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.560
_pdbe_chem_comp_rdkit_properties.NumRings 4
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 2
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 2
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 2
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 4
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 2
_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 11
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 348.187
_pdbe_chem_comp_rdkit_properties.tpsa 377.640
_pdbe_chem_comp_rdkit_properties.CrippenClogP -1.304
_pdbe_chem_comp_rdkit_properties.CrippenMR 170.627
_pdbe_chem_comp_rdkit_properties.chi0v 26.926
_pdbe_chem_comp_rdkit_properties.chi1v 16.640
_pdbe_chem_comp_rdkit_properties.chi2v 7.693
_pdbe_chem_comp_rdkit_properties.chi3v 7.693
_pdbe_chem_comp_rdkit_properties.chi4v 5.087
_pdbe_chem_comp_rdkit_properties.chi0n 60.243
_pdbe_chem_comp_rdkit_properties.chi1n 29.419
_pdbe_chem_comp_rdkit_properties.chi2n 5.074
_pdbe_chem_comp_rdkit_properties.chi3n 5.074
_pdbe_chem_comp_rdkit_properties.chi4n 3.116
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -3.060
_pdbe_chem_comp_rdkit_properties.kappa1 15.121
_pdbe_chem_comp_rdkit_properties.kappa2 16.752
_pdbe_chem_comp_rdkit_properties.kappa3 11.016
_pdbe_chem_comp_rdkit_properties.Phi 4.779
#
_pdbe_chem_comp_external_mappings.comp_id 4RA
_pdbe_chem_comp_external_mappings.source UniChem
_pdbe_chem_comp_external_mappings.resource ZINC
_pdbe_chem_comp_external_mappings.resource_id ZINC000263620272
#
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
4RA O2C 6.260 0.474 1.816 ETKDGv3 1
4RA O3 -3.646 -1.759 -2.557 ETKDGv3 2
4RA C2 -4.794 -3.420 -1.075 ETKDGv3 3
4RA C3 -4.534 -2.019 -1.509 ETKDGv3 4
4RA C4 -5.172 -1.002 -0.883 ETKDGv3 5
4RA C5 -6.139 -1.316 0.218 ETKDGv3 6
4RA C6 -6.330 -2.599 0.568 ETKDGv3 7
4RA C2C 7.454 0.104 1.976 ETKDGv3 8
4RA N3C 8.418 1.034 2.472 ETKDGv3 9
4RA C4C 9.761 0.600 2.691 ETKDGv3 10
4RA O4C 10.624 1.406 3.127 ETKDGv3 11
4RA C5C 10.128 -0.794 2.412 ETKDGv3 12
4RA C6C 9.220 -1.653 1.938 ETKDGv3 13
4RA N1C 7.860 -1.249 1.673 ETKDGv3 14
4RA C1B 6.900 -2.256 1.190 ETKDGv3 15
4RA C2B 6.001 -2.751 2.336 ETKDGv3 16
4RA "O2'" 6.168 -4.133 2.560 ETKDGv3 17
4RA C3B 4.600 -2.401 1.873 ETKDGv3 18
4RA O3B 3.685 -3.435 2.137 ETKDGv3 19
4RA O4B 6.095 -1.710 0.166 ETKDGv3 20
4RA C4B 4.786 -2.184 0.375 ETKDGv3 21
4RA C5B 3.775 -1.183 -0.191 ETKDGv3 22
4RA O5B 3.981 -1.054 -1.578 ETKDGv3 23
4RA PA 2.881 0.104 -2.173 ETKDGv3 24
4RA O1A 1.298 -0.408 -1.845 ETKDGv3 25
4RA O2A 3.066 0.215 -3.669 ETKDGv3 26
4RA O3A 3.220 1.610 -1.450 ETKDGv3 27
4RA PB 1.868 2.612 -1.693 ETKDGv3 28
4RA O2B 2.225 4.014 -1.253 ETKDGv3 29
4RA O1B 1.447 2.645 -3.336 ETKDGv3 30
4RA "O1'" 0.578 2.047 -0.725 ETKDGv3 31
4RA "C1'" -0.647 2.529 -1.234 ETKDGv3 32
4RA "C2'" -1.713 2.375 -0.130 ETKDGv3 33
4RA "N2'" -1.793 0.979 0.324 ETKDGv3 34
4RA "C7'" -2.456 0.601 1.539 ETKDGv3 35
4RA "C8'" -2.639 -0.844 1.874 ETKDGv3 36
4RA "O7'" -2.844 1.480 2.354 ETKDGv3 37
4RA "C3'" -3.079 2.856 -0.655 ETKDGv3 38
4RA "O3'" -3.060 4.253 -0.797 ETKDGv3 39
4RA "C4'" -3.415 2.176 -2.005 ETKDGv3 40
4RA "C5'" -2.213 2.214 -2.983 ETKDGv3 41
4RA "C6'" -2.053 3.554 -3.721 ETKDGv3 42
4RA "O5'" -1.002 1.772 -2.383 ETKDGv3 43
4RA "N4'" -3.782 0.778 -1.773 ETKDGv3 44
4RA C4A -4.907 0.416 -1.237 ETKDGv3 45
4RA C2A -4.103 -4.577 -1.728 ETKDGv3 46
4RA N1 -5.633 -3.651 -0.109 ETKDGv3 47
4RA C5A -6.868 -0.223 0.961 ETKDGv3 48
4RA O4P -5.928 0.572 1.646 ETKDGv3 49
4RA P -6.730 1.936 2.283 ETKDGv3 50
4RA O3P -5.615 2.890 3.125 ETKDGv3 51
4RA O1P -7.819 1.499 3.237 ETKDGv3 52
4RA O2P -7.410 2.853 1.032 ETKDGv3 53
4RA H1 -3.150 -2.490 -3.049 ETKDGv3 54
4RA H2 -7.011 -2.861 1.368 ETKDGv3 55
4RA H3 8.142 2.020 2.681 ETKDGv3 56
4RA H4 11.141 -1.129 2.595 ETKDGv3 57
4RA H5 9.525 -2.675 1.751 ETKDGv3 58
4RA H6 7.456 -3.112 0.745 ETKDGv3 59
4RA H7 6.223 -2.217 3.287 ETKDGv3 60
4RA H8 5.956 -4.611 1.715 ETKDGv3 61
4RA H9 4.280 -1.459 2.378 ETKDGv3 62
4RA H10 2.779 -3.050 2.013 ETKDGv3 63
4RA H11 4.669 -3.154 -0.164 ETKDGv3 64
4RA H12 2.749 -1.565 0.015 ETKDGv3 65
4RA H13 3.919 -0.205 0.323 ETKDGv3 66
4RA H14 1.223 -1.295 -2.280 ETKDGv3 67
4RA H15 2.240 3.023 -3.793 ETKDGv3 68
4RA H16 -0.557 3.615 -1.470 ETKDGv3 69
4RA H17 -1.409 3.014 0.730 ETKDGv3 70
4RA H18 -1.363 0.222 -0.255 ETKDGv3 71
4RA H19 -1.749 -1.211 2.425 ETKDGv3 72
4RA H20 -3.543 -0.979 2.505 ETKDGv3 73
4RA H21 -2.765 -1.440 0.946 ETKDGv3 74
4RA H22 -3.858 2.597 0.099 ETKDGv3 75
4RA H23 -4.004 4.547 -0.887 ETKDGv3 76
4RA H24 -4.280 2.693 -2.479 ETKDGv3 77
4RA H25 -2.442 1.480 -3.787 ETKDGv3 78
4RA H26 -2.943 3.741 -4.358 ETKDGv3 79
4RA H27 -1.159 3.513 -4.379 ETKDGv3 80
4RA H28 -1.943 4.411 -3.030 ETKDGv3 81
4RA H29 -5.620 1.179 -0.956 ETKDGv3 82
4RA H30 -3.005 -4.474 -1.609 ETKDGv3 83
4RA H31 -4.361 -4.608 -2.807 ETKDGv3 84
4RA H32 -4.417 -5.538 -1.265 ETKDGv3 85
4RA H33 -7.447 0.366 0.214 ETKDGv3 86
4RA H34 -7.594 -0.656 1.686 ETKDGv3 87
4RA H35 -5.007 3.244 2.428 ETKDGv3 88
4RA H36 -6.647 3.086 0.446 ETKDGv3 89
#