data_P3E
#
_chem_comp.id P3E
_chem_comp.name
"[[(2~{R},3~{S},4~{R},5~{R})-5-[2-azanyl-7-[(3-methylphenyl)methyl]-6-oxidanylidene-1~{H}-purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-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 "C28 H36 N10 O18 P3"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 1
_chem_comp.pdbx_initial_date 2020-04-14
_chem_comp.pdbx_modified_date 2020-04-24
_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 893.563
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code P3E
_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 6YLT
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site PDBE
#
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
P3E C1 C2 C 0 1 N N N N N N 82.833 -67.562 -11.585 8.219 5.234 -0.766 C1 P3E 1
P3E C2 C4 C 0 1 Y N N N N N 81.306 -66.227 -12.744 7.764 3.065 -0.116 C2 P3E 2
P3E C3 C5 C 0 1 Y N N N N N 80.292 -67.012 -12.382 8.107 3.375 1.205 C3 P3E 3
P3E C4 C6 C 0 1 N N N N N N 80.499 -68.074 -11.605 8.526 4.692 1.505 C4 P3E 4
P3E O1 O6 O 0 1 N N N N N N 79.560 -68.783 -11.256 8.835 5.006 2.641 O1 P3E 5
P3E C5 C1* C 0 1 N N R N N N 81.646 -64.209 -14.096 6.964 0.966 -1.276 C5 P3E 6
P3E C6 C2* C 0 1 N N R N N N 81.195 -63.723 -15.447 8.181 0.354 -2.004 C6 P3E 7
P3E C7 C3* C 0 1 N N S N N N 81.767 -62.331 -15.383 7.685 -1.036 -2.462 C7 P3E 8
P3E C8 C4* C 0 1 N N R N N N 81.382 -61.894 -13.971 6.227 -1.099 -1.955 C8 P3E 9
P3E C9 C5* C 0 1 N N N N N N 80.063 -61.105 -14.054 5.890 -2.513 -1.476 C9 P3E 10
P3E C10 C8 C 0 1 Y N N N N N 79.503 -65.429 -13.618 7.538 1.284 1.162 C10 P3E 11
P3E C11 CAZ C 0 1 Y N N N N N 75.005 -69.156 -16.786 -6.472 0.227 0.504 C11 P3E 12
P3E C12 CBE C 0 1 N N N N N N 76.003 -73.390 -17.715 -7.123 4.570 -0.082 C12 P3E 13
P3E C13 CBG C 0 1 N N N N N N 73.846 -72.363 -17.587 -8.407 2.836 -1.024 C13 P3E 14
P3E C14 CBH C 0 1 Y N N N N N 74.437 -71.196 -17.281 -7.573 1.915 -0.368 C14 P3E 15
P3E C15 CBI C 0 1 Y N N N N N 75.767 -71.122 -17.218 -6.522 2.393 0.423 C15 P3E 16
P3E C16 CBK C 0 1 N N R N N N 77.588 -69.691 -16.782 -4.727 1.364 1.813 C16 P3E 17
P3E C17 CBM C 0 1 N N R N N N 78.185 -69.484 -18.165 -5.175 1.453 3.289 C17 P3E 18
P3E C18 CBO C 0 1 N N S N N N 78.043 -68.018 -18.326 -4.145 0.586 4.047 C18 P3E 19
P3E C19 CBP C 0 1 N N R N N N 78.625 -67.582 -16.971 -3.197 0.075 2.939 C19 P3E 20
P3E C20 CBQ C 0 1 N N N N N N 78.347 -66.078 -16.830 -2.766 -1.364 3.230 C20 P3E 21
P3E C21 CBZ C 0 1 N N N N N N 72.534 -69.512 -16.998 -8.416 -0.409 -0.956 C21 P3E 22
P3E C22 CCA C 0 1 Y N N N N N 71.954 -69.391 -18.275 -7.932 -0.664 -2.360 C22 P3E 23
P3E C23 CCB C 0 1 Y N N N N N 70.156 -68.558 -19.661 -6.600 -1.927 -3.898 C23 P3E 24
P3E C24 CCC C 0 1 Y N N N N N 70.758 -68.694 -18.413 -7.043 -1.693 -2.609 C24 P3E 25
P3E C25 CCD C 0 1 Y N N N N N 70.745 -69.120 -20.787 -7.046 -1.132 -4.937 C25 P3E 26
P3E C26 CCE C 0 1 Y N N N N N 72.535 -69.948 -19.410 -8.382 0.127 -3.400 C26 P3E 27
P3E C27 CCF C 0 1 Y N N N N N 71.938 -69.819 -20.658 -7.939 -0.106 -4.689 C27 P3E 28
P3E C28 CCG C 0 1 N N N N N N 72.540 -70.386 -21.773 -8.425 0.760 -5.822 C28 P3E 29
P3E N1 N1 N 0 1 N N N N N N 81.790 -68.388 -11.176 8.571 5.595 0.500 N1 P3E 30
P3E N2 N2 N 0 1 N N N N N N 84.079 -67.826 -11.204 8.275 6.173 -1.766 N2 P3E 31
P3E N3 N3 N 0 1 N N N N N N 82.566 -66.507 -12.367 7.833 4.013 -1.059 N3 P3E 32
P3E N4 N7 N 0 1 Y N N N N N 79.178 -66.510 -12.914 7.948 2.245 1.937 N4 P3E 33
P3E N5 N9 N 0 1 Y N N N N N 80.823 -65.291 -13.558 7.403 1.745 -0.115 N5 P3E 34
P3E N6 NBA N 0 1 Y N N N N N 73.966 -69.965 -17.032 -7.515 0.537 -0.293 N6 P3E 35
P3E N7 NBC N 0 1 N N N N N N 76.538 -72.205 -17.411 -6.336 3.722 0.536 N7 P3E 36
P3E N8 NBD N 0 1 N N N N N N 76.782 -74.448 -17.920 -6.895 5.917 0.062 N8 P3E 37
P3E N9 NBF N 0 1 N N N N N N 74.622 -73.501 -17.812 -8.160 4.155 -0.864 N9 P3E 38
P3E N10 NBJ N 1 1 Y N N N N N 76.114 -69.888 -16.866 -5.892 1.318 0.926 N10 P3E 39
P3E O2 O2* O 0 1 N N N N N N 81.861 -64.463 -16.472 8.543 1.153 -3.133 O2 P3E 40
P3E O3 O3* O 0 1 N N N N N N 83.191 -62.386 -15.491 7.725 -1.138 -3.886 O3 P3E 41
P3E O4 O4* O 0 1 N N N N N N 81.154 -63.149 -13.295 6.179 -0.169 -0.851 O4 P3E 42
P3E O5 O5* O 0 1 N N N N N N 79.049 -61.650 -14.933 4.508 -2.579 -1.122 O5 P3E 43
P3E O6 OAU O 0 1 N N N N N N 77.237 -60.378 -16.105 4.548 -4.419 0.605 O6 P3E 44
P3E O7 OAV O 0 1 N N N N N N 77.268 -60.288 -13.584 3.818 -5.042 -1.729 O7 P3E 45
P3E O8 OAX O 0 1 N N N N N N 76.565 -62.484 -14.872 2.285 -3.598 -0.155 O8 P3E 46
P3E O9 OAY O 0 1 N N N N N N 77.895 -68.446 -16.079 -3.981 0.130 1.728 O9 P3E 47
P3E O10 OBB O 0 1 N N N N N N 72.623 -72.478 -17.678 -9.332 2.454 -1.721 O10 P3E 48
P3E O11 OBL O 0 1 N N N N N N 79.577 -69.823 -18.136 -5.123 2.806 3.747 O11 P3E 49
P3E O12 OBN O 0 1 N N N N N N 78.885 -67.570 -19.394 -3.427 1.376 4.996 O12 P3E 50
P3E O13 OBR O 0 1 N N N N N N 76.946 -65.836 -16.773 -1.801 -1.777 2.260 O13 P3E 51
P3E O14 OBS O 0 1 N N N N N N 74.790 -65.060 -17.996 -2.257 -4.350 1.972 O14 P3E 52
P3E O15 OBT O 0 1 N N N N N N 77.065 -64.903 -19.075 -0.508 -3.497 3.579 O15 P3E 53
P3E O16 OBV O 0 1 N N N N N N 76.578 -63.298 -17.186 0.001 -3.311 1.114 O16 P3E 54
P3E O17 OBW O 0 1 N N N N N N 74.787 -63.764 -15.607 0.632 -5.632 0.052 O17 P3E 55
P3E O18 OBY O 0 1 N N N N N N 74.960 -61.508 -16.390 1.862 -4.728 2.062 O18 P3E 56
P3E P1 PAW P 0 1 N N N N N N 77.512 -61.131 -14.820 3.806 -3.921 -0.574 P1 P3E 57
P3E P2 PBU P 0 1 N N N N N N 76.268 -64.802 -17.791 -1.128 -3.239 2.260 P2 P3E 58
P3E P3 PBX P 0 1 N N N N N N 75.659 -62.694 -15.991 1.209 -4.326 0.796 P3 P3E 59
P3E H1 H1 H 0 1 N N N N N N 82.730 -64.385 -14.028 6.388 1.593 -1.957 H1 P3E 60
P3E H2 H2 H 0 1 N N N N N N 80.100 -63.721 -15.546 9.024 0.253 -1.321 H2 P3E 61
P3E H3 H3 H 0 1 N N N N N N 81.311 -61.675 -16.139 8.283 -1.824 -2.004 H3 P3E 62
P3E H4 H4 H 0 1 N N N N N N 82.178 -61.296 -13.503 5.538 -0.790 -2.742 H4 P3E 63
P3E H5 H5 H 0 1 N N N N N N 80.300 -60.089 -14.404 6.095 -3.226 -2.275 H5 P3E 64
P3E H6 H6 H 0 1 N N N N N N 79.638 -61.054 -13.041 6.500 -2.756 -0.606 H6 P3E 65
P3E H7 H7 H 0 1 N N N N N N 78.818 -64.781 -14.143 7.335 0.272 1.482 H7 P3E 66
P3E H8 H8 H 0 1 N N N N N N 74.952 -68.101 -16.563 -6.164 -0.777 0.759 H8 P3E 67
P3E H9 H9 H 0 1 N N N N N N 78.065 -70.550 -16.288 -4.090 2.211 1.558 H9 P3E 68
P3E H10 H10 H 0 1 N N N N N N 77.626 -70.040 -18.932 -6.180 1.049 3.408 H10 P3E 69
P3E H11 H11 H 0 1 N N N N N N 76.994 -67.706 -18.437 -4.640 -0.250 4.541 H11 P3E 70
P3E H12 H12 H 0 1 N N N N N N 79.707 -67.778 -16.937 -2.324 0.723 2.858 H12 P3E 71
P3E H13 H13 H 0 1 N N N N N N 78.817 -65.708 -15.907 -2.326 -1.418 4.225 H13 P3E 72
P3E H14 H14 H 0 1 N N N N N N 78.771 -65.548 -17.696 -3.634 -2.021 3.180 H14 P3E 73
P3E H15 H15 H 0 1 N N N N N N 72.490 -68.532 -16.501 -9.422 0.009 -0.988 H15 P3E 74
P3E H16 H16 H 0 1 N N N N N N 71.951 -70.243 -16.418 -8.430 -1.347 -0.401 H16 P3E 75
P3E H17 H17 H 0 1 N N N N N N 69.228 -68.014 -19.754 -5.905 -2.730 -4.092 H17 P3E 76
P3E H18 H18 H 0 1 N N N N N N 70.292 -68.254 -17.544 -6.695 -2.314 -1.798 H18 P3E 77
P3E H19 H19 H 0 1 N N N N N N 70.279 -69.014 -21.755 -6.700 -1.314 -5.944 H19 P3E 78
P3E H20 H20 H 0 1 N N N N N N 73.465 -70.489 -19.319 -9.080 0.928 -3.206 H20 P3E 79
P3E H21 H21 H 0 1 N N N N N N 73.228 -69.659 -22.228 -9.327 0.324 -6.252 H21 P3E 80
P3E H22 H22 H 0 1 N N N N N N 73.101 -71.282 -21.470 -8.649 1.758 -5.446 H22 P3E 81
P3E H23 H23 H 0 1 N N N N N N 71.767 -70.667 -22.504 -7.652 0.825 -6.587 H23 P3E 82
P3E H24 H24 H 0 1 N N N N N N 81.960 -69.182 -10.593 8.856 6.504 0.682 H24 P3E 83
P3E H25 H25 H 0 1 N N N N N N 84.829 -67.235 -11.501 8.561 7.078 -1.566 H25 P3E 84
P3E H26 H26 H 0 1 N N N N N N 84.267 -68.616 -10.620 8.027 5.931 -2.672 H26 P3E 85
P3E H27 H27 H 0 1 N N N N N N 77.775 -74.359 -17.847 -6.161 6.228 0.615 H27 P3E 86
P3E H28 H28 H 0 1 N N N N N N 76.374 -75.332 -18.147 -7.468 6.557 -0.388 H28 P3E 87
P3E H29 H29 H 0 1 N N N N N N 74.194 -74.376 -18.038 -8.722 4.809 -1.307 H29 P3E 88
P3E H30 H30 H 0 1 N N N N N N 81.501 -65.341 -16.514 9.264 0.783 -3.661 H30 P3E 89
P3E H31 H31 H 0 1 N N N N N N 83.546 -61.506 -15.450 8.611 -1.044 -4.263 H31 P3E 90
P3E H32 H32 H 0 1 N N N N N N 76.980 -59.421 -13.843 3.349 -4.783 -2.534 H32 P3E 91
P3E H33 H33 H 0 1 N N N N N N 79.673 -70.763 -18.033 -5.395 2.920 4.668 H33 P3E 92
P3E H34 H34 H 0 1 N N N N N N 78.794 -66.630 -19.497 -3.983 1.772 5.680 H34 P3E 93
P3E H35 H35 H 0 1 N N N N N N 74.624 -65.243 -18.913 -2.706 -4.243 1.122 H35 P3E 94
P3E H36 H36 H 0 1 N N N N N N 73.884 -63.482 -15.690 0.190 -5.443 -0.787 H36 P3E 95
#
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
P3E C28 C27 SING N N 1
P3E C25 C27 DOUB Y N 2
P3E C25 C23 SING Y N 3
P3E C27 C26 SING Y N 4
P3E C23 C24 DOUB Y N 5
P3E C26 C22 DOUB Y N 6
P3E O12 C18 SING N N 7
P3E O15 P2 DOUB N N 8
P3E C24 C22 SING Y N 9
P3E C18 C17 SING N N 10
P3E C18 C19 SING N N 11
P3E C22 C21 SING N N 12
P3E C17 O11 SING N N 13
P3E C17 C16 SING N N 14
P3E O14 P2 SING N N 15
P3E N8 C12 SING N N 16
P3E N9 C12 SING N N 17
P3E N9 C13 SING N N 18
P3E P2 O16 SING N N 19
P3E P2 O13 SING N N 20
P3E C12 N7 DOUB N N 21
P3E O10 C13 DOUB N N 22
P3E C13 C14 SING N N 23
P3E N7 C15 SING N N 24
P3E C14 C15 DOUB Y N 25
P3E C14 N6 SING Y N 26
P3E C15 N10 SING Y N 27
P3E O16 P3 SING N N 28
P3E N6 C21 SING N N 29
P3E N6 C11 SING Y N 30
P3E C19 C20 SING N N 31
P3E C19 O9 SING N N 32
P3E N10 C11 DOUB Y N 33
P3E N10 C16 SING N N 34
P3E C20 O13 SING N N 35
P3E C16 O9 SING N N 36
P3E O2 C6 SING N N 37
P3E O18 P3 DOUB N N 38
P3E O6 P1 DOUB N N 39
P3E P3 O17 SING N N 40
P3E P3 O8 SING N N 41
P3E O3 C7 SING N N 42
P3E C6 C7 SING N N 43
P3E C6 C5 SING N N 44
P3E C7 C8 SING N N 45
P3E O5 P1 SING N N 46
P3E O5 C9 SING N N 47
P3E O8 P1 SING N N 48
P3E P1 O7 SING N N 49
P3E C5 N5 SING N N 50
P3E C5 O4 SING N N 51
P3E C9 C8 SING N N 52
P3E C8 O4 SING N N 53
P3E C10 N5 SING Y N 54
P3E C10 N4 DOUB Y N 55
P3E N5 C2 SING Y N 56
P3E N4 C3 SING Y N 57
P3E C2 C3 DOUB Y N 58
P3E C2 N3 SING N N 59
P3E C3 C4 SING N N 60
P3E N3 C1 DOUB N N 61
P3E C4 O1 DOUB N N 62
P3E C4 N1 SING N N 63
P3E C1 N2 SING N N 64
P3E C1 N1 SING N N 65
P3E C5 H1 SING N N 66
P3E C6 H2 SING N N 67
P3E C7 H3 SING N N 68
P3E C8 H4 SING N N 69
P3E C9 H5 SING N N 70
P3E C9 H6 SING N N 71
P3E C10 H7 SING N N 72
P3E C11 H8 SING N N 73
P3E C16 H9 SING N N 74
P3E C17 H10 SING N N 75
P3E C18 H11 SING N N 76
P3E C19 H12 SING N N 77
P3E C20 H13 SING N N 78
P3E C20 H14 SING N N 79
P3E C21 H15 SING N N 80
P3E C21 H16 SING N N 81
P3E C23 H17 SING N N 82
P3E C24 H18 SING N N 83
P3E C25 H19 SING N N 84
P3E C26 H20 SING N N 85
P3E C28 H21 SING N N 86
P3E C28 H22 SING N N 87
P3E C28 H23 SING N N 88
P3E N1 H24 SING N N 89
P3E N2 H25 SING N N 90
P3E N2 H26 SING N N 91
P3E N8 H27 SING N N 92
P3E N8 H28 SING N N 93
P3E N9 H29 SING N N 94
P3E O2 H30 SING N N 95
P3E O3 H31 SING N N 96
P3E O7 H32 SING N N 97
P3E O11 H33 SING N N 98
P3E O12 H34 SING N N 99
P3E O14 H35 SING N N 100
P3E O17 H36 SING N N 101
#
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
P3E InChI InChI 1.03 InChI=1S/C28H35N10O18P3/c1-11-3-2-4-12(5-11)6-36-10-38(22-16(36)24(44)35-28(30)33-22)26-20(42)18(40)14(54-26)8-52-58(47,48)56-59(49,50)55-57(45,46)51-7-13-17(39)19(41)25(53-13)37-9-31-15-21(37)32-27(29)34-23(15)43/h2-5,9-10,13-14,17-20,25-26,39-42H,6-8H2,1H3,(H8-,29,30,32,33,34,35,43,44,45,46,47,48,49,50)/p+1/t13-,14-,17-,18-,19-,20-,25-,26-/m1/s1
P3E InChIKey InChI 1.03 PSRZFZZOIWOJQD-RTZOWOBBSA-O
P3E SMILES_CANONICAL CACTVS 3.385 Cc1cccc(Cn2c[n+]([C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(=O)OC[C@H]4O[C@H]([C@H](O)[C@@H]4O)n5cnc6C(=O)NC(=Nc56)N)[C@@H](O)[C@H]3O)c7N=C(N)NC(=O)c27)c1
P3E SMILES CACTVS 3.385 Cc1cccc(Cn2c[n+]([CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(=O)OC[CH]4O[CH]([CH](O)[CH]4O)n5cnc6C(=O)NC(=Nc56)N)[CH](O)[CH]3O)c7N=C(N)NC(=O)c27)c1
P3E SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 Cc1cccc(c1)Cn2c[n+](c3c2C(=O)NC(=N3)N)[C@H]4[C@@H]([C@@H]([C@H](O4)COP(=O)(O)OP(=O)(O)OP(=O)(O)OC[C@@H]5[C@H]([C@H]([C@@H](O5)n6cnc7c6N=C(NC7=O)N)O)O)O)O
P3E SMILES "OpenEye OEToolkits" 2.0.7 Cc1cccc(c1)Cn2c[n+](c3c2C(=O)NC(=N3)N)C4C(C(C(O4)COP(=O)(O)OP(=O)(O)OP(=O)(O)OCC5C(C(C(O5)n6cnc7c6N=C(NC7=O)N)O)O)O)O
#
_pdbx_chem_comp_identifier.comp_id P3E
_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-[2-azanyl-7-[(3-methylphenyl)methyl]-6-oxidanylidene-1~{H}-purin-9-ium-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-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
P3E 'Create component' 2020-04-14 PDBE
P3E 'Initial release' 2020-04-29 RCSB
#
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
P3E C1 C 29.698 -6.096 1
P3E C2 C 27.101 -6.096 2
P3E C3 C 27.101 -7.596 3
P3E C4 C 28.399 -8.346 4
P3E O1 O 28.399 -9.846 5
P3E C5 C 25.215 -4.213 6
P3E C6 C 26.095 -2.998 7
P3E C7 C 25.211 -1.786 8
P3E C8 C 23.785 -2.252 9
P3E C9 C 22.570 -1.373 10
P3E C10 C 24.806 -6.846 11
P3E C11 C 9.997 5.169 12
P3E C12 C 5.104 4.419 13
P3E C13 C 6.404 6.669 14
P3E C14 C 7.702 5.919 15
P3E C15 C 7.702 4.419 16
P3E C16 C 9.588 2.536 17
P3E C17 C 8.708 1.321 18
P3E C18 C 9.592 0.109 19
P3E C19 C 11.018 0.575 20
P3E C20 C 12.233 -0.304 21
P3E C21 C 9.588 7.802 22
P3E C22 C 11.056 8.111 23
P3E C23 C 12.989 9.846 24
P3E C24 C 11.522 9.537 25
P3E C25 C 13.991 8.730 26
P3E C26 C 12.057 6.995 27
P3E C27 C 13.525 7.304 28
P3E C28 C 14.527 6.188 29
P3E N1 N 29.698 -7.596 30
P3E N2 N 30.998 -5.346 31
P3E N3 N 28.399 -5.346 32
P3E N4 N 25.681 -8.053 33
P3E N5 N 25.681 -5.639 34
P3E N6 N 9.122 6.376 35
P3E N7 N 6.404 3.669 36
P3E N8 N 3.805 3.669 37
P3E N9 N 5.104 5.919 38
P3E N10 N 9.122 3.962 39
P3E O2 O 27.595 -2.996 40
P3E O3 O 25.672 -0.359 41
P3E O4 O 23.788 -3.752 42
P3E O5 O 21.201 -1.985 43
P3E O6 O 20.865 0.109 44
P3E O7 O 19.106 -2.321 45
P3E O8 O 18.771 -0.226 46
P3E O9 O 11.015 2.075 47
P3E O10 O 6.404 8.169 48
P3E O11 O 7.208 1.319 49
P3E O12 O 9.131 -1.318 50
P3E O13 O 13.602 0.308 51
P3E O14 O 13.938 -1.787 52
P3E O15 O 15.697 0.643 53
P3E O16 O 16.032 -1.451 54
P3E O17 O 16.789 0.531 55
P3E O18 O 18.014 -2.208 56
P3E P1 P 19.986 -1.106 57
P3E P2 P 14.817 -0.572 58
P3E P3 P 17.401 -0.839 59
#
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
P3E C28 C27 SINGLE NONE 1
P3E C25 C27 SINGLE NONE 2
P3E C25 C23 DOUBLE NONE 3
P3E C27 C26 DOUBLE NONE 4
P3E C23 C24 SINGLE NONE 5
P3E C26 C22 SINGLE NONE 6
P3E C18 O12 SINGLE BEGINWEDGE 7
P3E O15 P2 DOUBLE NONE 8
P3E C24 C22 DOUBLE NONE 9
P3E C18 C17 SINGLE NONE 10
P3E C18 C19 SINGLE NONE 11
P3E C22 C21 SINGLE NONE 12
P3E C17 O11 SINGLE BEGINWEDGE 13
P3E C17 C16 SINGLE NONE 14
P3E P2 O14 SINGLE BEGINWEDGE 15
P3E N8 C12 SINGLE NONE 16
P3E N9 C12 SINGLE NONE 17
P3E N9 C13 SINGLE NONE 18
P3E P2 O16 SINGLE NONE 19
P3E P2 O13 SINGLE NONE 20
P3E C12 N7 DOUBLE NONE 21
P3E O10 C13 DOUBLE NONE 22
P3E C13 C14 SINGLE NONE 23
P3E N7 C15 SINGLE NONE 24
P3E C14 C15 DOUBLE NONE 25
P3E C14 N6 SINGLE NONE 26
P3E C15 N10 SINGLE NONE 27
P3E O16 P3 SINGLE NONE 28
P3E N6 C21 SINGLE NONE 29
P3E N6 C11 SINGLE NONE 30
P3E C19 C20 SINGLE BEGINDASH 31
P3E C19 O9 SINGLE NONE 32
P3E N10 C11 DOUBLE NONE 33
P3E C16 N10 SINGLE BEGINDASH 34
P3E C20 O13 SINGLE NONE 35
P3E C16 O9 SINGLE NONE 36
P3E C6 O2 SINGLE BEGINWEDGE 37
P3E O18 P3 DOUBLE NONE 38
P3E O6 P1 DOUBLE NONE 39
P3E P3 O17 SINGLE BEGINDASH 40
P3E P3 O8 SINGLE NONE 41
P3E C7 O3 SINGLE BEGINWEDGE 42
P3E C6 C7 SINGLE NONE 43
P3E C6 C5 SINGLE NONE 44
P3E C7 C8 SINGLE NONE 45
P3E O5 P1 SINGLE NONE 46
P3E O5 C9 SINGLE NONE 47
P3E O8 P1 SINGLE NONE 48
P3E P1 O7 SINGLE BEGINWEDGE 49
P3E C5 N5 SINGLE BEGINDASH 50
P3E C5 O4 SINGLE NONE 51
P3E C8 C9 SINGLE BEGINDASH 52
P3E C8 O4 SINGLE NONE 53
P3E C10 N5 SINGLE NONE 54
P3E C10 N4 DOUBLE NONE 55
P3E N5 C2 SINGLE NONE 56
P3E N4 C3 SINGLE NONE 57
P3E C2 C3 DOUBLE NONE 58
P3E C2 N3 SINGLE NONE 59
P3E C3 C4 SINGLE NONE 60
P3E N3 C1 DOUBLE NONE 61
P3E C4 O1 DOUBLE NONE 62
P3E C4 N1 SINGLE NONE 63
P3E C1 N2 SINGLE NONE 64
P3E C1 N1 SINGLE NONE 65
#
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
P3E MurckoScaffold S1 scaffold 'O=c1[nH]cnc2c1ncn2[C@H]1CC[C@@H](CO[PH](=O)O[PH](=O)O[PH](=O)OC[C@@H]2CC[C@H]([n+]3cn(Cc4ccccc4)c4c(=O)[nH]cnc43)O2)O1' InChI=1S/C27H31N8O11P3/c36-26-22-24(28-13-30-26)34(15-32-22)20-8-6-18(43-20)11-41-47(38)45-49(40)46-48(39)42-12-19-7-9-21(44-19)35-16-33(10-17-4-2-1-3-5-17)23-25(35)29-14-31-27(23)37/h1-5,13-16,18-21,47-49H,6-12H2,(H-,28,29,30,31,36,37)/p+1/t18-,19-,20+,21+/m0/s1 XJXMVQAYSHNOAN-UWHLTILDSA-O
P3E imidazole F1 fragment 'c1c[nH]cn1' InChI=1S/C3H4N2/c1-2-5-3-4-1/h1-3H,(H,4,5) RAXXELZNTBOGNW-UHFFFAOYSA-N
P3E phenyl F2 fragment c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-UHFFFAOYSA-N
P3E phosphate F3 fragment O=P(O)(O)O InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4) NBIIXXVUZAFLBC-UHFFFAOYSA-N
P3E purine F4 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
P3E pyrimidine F5 fragment c1cncnc1 InChI=1S/C4H4N2/c1-2-5-4-6-3-1/h1-4H CZPWVGJYEJSRLH-UHFFFAOYSA-N
P3E 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
P3E C1 S1 1
P3E C2 S1 1
P3E C3 S1 1
P3E C4 S1 1
P3E O1 S1 1
P3E C5 S1 1
P3E C6 S1 1
P3E C7 S1 1
P3E C8 S1 1
P3E C9 S1 1
P3E C10 S1 1
P3E C11 S1 1
P3E C12 S1 1
P3E C13 S1 1
P3E C14 S1 1
P3E C15 S1 1
P3E C16 S1 1
P3E C17 S1 1
P3E C18 S1 1
P3E C19 S1 1
P3E C20 S1 1
P3E C21 S1 1
P3E C22 S1 1
P3E C23 S1 1
P3E C24 S1 1
P3E C25 S1 1
P3E C26 S1 1
P3E C27 S1 1
P3E N1 S1 1
P3E N3 S1 1
P3E N4 S1 1
P3E N5 S1 1
P3E N6 S1 1
P3E N7 S1 1
P3E N9 S1 1
P3E N10 S1 1
P3E O4 S1 1
P3E O5 S1 1
P3E O6 S1 1
P3E O8 S1 1
P3E O9 S1 1
P3E O10 S1 1
P3E O13 S1 1
P3E O15 S1 1
P3E O16 S1 1
P3E O18 S1 1
P3E P1 S1 1
P3E P2 S1 1
P3E P3 S1 1
P3E C2 F1 1
P3E C3 F1 1
P3E N4 F1 1
P3E C10 F1 1
P3E N5 F1 1
P3E C14 F1 2
P3E C15 F1 2
P3E N10 F1 2
P3E C11 F1 2
P3E N6 F1 2
P3E C22 F2 1
P3E C26 F2 1
P3E C27 F2 1
P3E C25 F2 1
P3E C23 F2 1
P3E C24 F2 1
P3E O5 F3 1
P3E P1 F3 1
P3E O6 F3 1
P3E O8 F3 1
P3E O7 F3 1
P3E O8 F3 2
P3E P3 F3 2
P3E O18 F3 2
P3E O16 F3 2
P3E O17 F3 2
P3E O13 F3 3
P3E P2 F3 3
P3E O15 F3 3
P3E O14 F3 3
P3E O16 F3 3
P3E N4 F4 1
P3E C10 F4 1
P3E N5 F4 1
P3E C2 F4 1
P3E C3 F4 1
P3E C4 F4 1
P3E N1 F4 1
P3E C1 F4 1
P3E N3 F4 1
P3E N6 F4 2
P3E C11 F4 2
P3E N10 F4 2
P3E C15 F4 2
P3E C14 F4 2
P3E C13 F4 2
P3E N9 F4 2
P3E C12 F4 2
P3E N7 F4 2
P3E C3 F5 1
P3E C2 F5 1
P3E N3 F5 1
P3E C1 F5 1
P3E N1 F5 1
P3E C4 F5 1
P3E C14 F5 2
P3E C13 F5 2
P3E N9 F5 2
P3E C12 F5 2
P3E N7 F5 2
P3E C15 F5 2
P3E C6 F6 1
P3E C7 F6 1
P3E C8 F6 1
P3E O4 F6 1
P3E C5 F6 1
P3E C9 F6 1
P3E O5 F6 1
P3E O3 F6 1
P3E O2 F6 1
P3E C17 F6 2
P3E C18 F6 2
P3E C19 F6 2
P3E O9 F6 2
P3E C16 F6 2
P3E C20 F6 2
P3E O13 F6 2
P3E O12 F6 2
P3E O11 F6 2
#
_pdbe_chem_comp_rdkit_properties.comp_id P3E
_pdbe_chem_comp_rdkit_properties.exactmw 893.142
_pdbe_chem_comp_rdkit_properties.amw 893.570
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 28
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 13
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 24
_pdbe_chem_comp_rdkit_properties.NumHBD 11
_pdbe_chem_comp_rdkit_properties.NumHBA 25
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 59
_pdbe_chem_comp_rdkit_properties.NumAtoms 95
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 31
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.429
_pdbe_chem_comp_rdkit_properties.NumRings 7
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 5
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 2
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 2
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 6
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 4
_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 379.069
_pdbe_chem_comp_rdkit_properties.tpsa 418.370
_pdbe_chem_comp_rdkit_properties.CrippenClogP -2.655
_pdbe_chem_comp_rdkit_properties.CrippenMR 186.824
_pdbe_chem_comp_rdkit_properties.chi0v 29.846
_pdbe_chem_comp_rdkit_properties.chi1v 18.718
_pdbe_chem_comp_rdkit_properties.chi2v 10.348
_pdbe_chem_comp_rdkit_properties.chi3v 10.348
_pdbe_chem_comp_rdkit_properties.chi4v 7.349
_pdbe_chem_comp_rdkit_properties.chi0n 63.162
_pdbe_chem_comp_rdkit_properties.chi1n 31.377
_pdbe_chem_comp_rdkit_properties.chi2n 6.519
_pdbe_chem_comp_rdkit_properties.chi3n 6.519
_pdbe_chem_comp_rdkit_properties.chi4n 4.346
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -4.310
_pdbe_chem_comp_rdkit_properties.kappa1 16.863
_pdbe_chem_comp_rdkit_properties.kappa2 15.944
_pdbe_chem_comp_rdkit_properties.kappa3 8.938
_pdbe_chem_comp_rdkit_properties.Phi 4.557
#
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
P3E UniChem PDBe P3E
P3E UniChem PubChem 146026051
#
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
P3E C1 -10.607 -0.952 0.624 ETKDGv3 1
P3E C2 -8.308 -0.490 0.223 ETKDGv3 2
P3E C3 -8.346 0.708 0.741 ETKDGv3 3
P3E C4 -9.597 1.227 1.281 ETKDGv3 4
P3E O1 -9.678 2.384 1.772 ETKDGv3 5
P3E C5 -6.681 -1.718 -1.346 ETKDGv3 6
P3E C6 -7.106 -1.241 -2.733 ETKDGv3 7
P3E C7 -6.008 -1.779 -3.618 ETKDGv3 8
P3E C8 -4.811 -1.846 -2.664 ETKDGv3 9
P3E C9 -3.916 -0.606 -2.792 ETKDGv3 10
P3E C10 -6.363 0.513 -0.063 ETKDGv3 11
P3E C11 7.026 -0.874 1.025 ETKDGv3 12
P3E C12 3.698 -0.116 -1.935 ETKDGv3 13
P3E C13 6.114 0.359 -2.298 ETKDGv3 14
P3E C14 6.342 -0.265 -0.995 ETKDGv3 15
P3E C15 5.330 -0.750 -0.318 ETKDGv3 16
P3E C16 4.920 -1.492 2.130 ETKDGv3 17
P3E C17 4.329 -0.222 2.755 ETKDGv3 18
P3E C18 2.853 -0.344 2.446 ETKDGv3 19
P3E C19 2.678 -1.844 2.256 ETKDGv3 20
P3E C20 1.517 -2.186 1.316 ETKDGv3 21
P3E C21 8.629 0.653 -0.251 ETKDGv3 22
P3E C22 8.164 2.020 0.187 ETKDGv3 23
P3E C23 7.479 4.325 -0.269 ETKDGv3 24
P3E C24 7.998 3.013 -0.704 ETKDGv3 25
P3E C25 7.155 4.529 1.013 ETKDGv3 26
P3E C26 7.825 2.260 1.613 ETKDGv3 27
P3E C27 7.320 3.442 2.006 ETKDGv3 28
P3E C28 6.984 3.679 3.447 ETKDGv3 29
P3E N1 -10.739 0.359 1.223 ETKDGv3 30
P3E N2 -11.740 -1.816 0.544 ETKDGv3 31
P3E N3 -9.455 -1.349 0.147 ETKDGv3 32
P3E N4 -7.104 1.379 0.565 ETKDGv3 33
P3E N5 -7.024 -0.735 -0.320 ETKDGv3 34
P3E N6 7.524 -0.303 -0.195 ETKDGv3 35
P3E N7 3.974 -0.664 -0.781 ETKDGv3 36
P3E N8 2.342 -0.036 -2.373 ETKDGv3 37
P3E N9 4.756 0.421 -2.760 ETKDGv3 38
P3E N10 5.757 -1.152 0.977 ETKDGv3 39
P3E O2 -8.362 -1.751 -3.098 ETKDGv3 40
P3E O3 -6.319 -3.053 -4.135 ETKDGv3 41
P3E O4 -5.287 -1.947 -1.337 ETKDGv3 42
P3E O5 -2.937 -0.643 -1.782 ETKDGv3 43
P3E O6 -2.763 1.997 -1.955 ETKDGv3 44
P3E O7 -1.069 0.625 -3.389 ETKDGv3 45
P3E O8 -0.821 0.796 -0.652 ETKDGv3 46
P3E O9 3.878 -2.355 1.725 ETKDGv3 47
P3E O10 7.059 0.803 -3.001 ETKDGv3 48
P3E O11 4.563 -0.226 4.142 ETKDGv3 49
P3E O12 2.045 0.128 3.494 ETKDGv3 50
P3E O13 0.331 -1.597 1.791 ETKDGv3 51
P3E O14 -1.462 -3.614 1.204 ETKDGv3 52
P3E O15 -0.535 -2.076 -0.681 ETKDGv3 53
P3E O16 -2.279 -0.997 0.965 ETKDGv3 54
P3E O17 -0.669 0.954 2.102 ETKDGv3 55
P3E O18 -2.860 1.552 0.854 ETKDGv3 56
P3E P1 -1.935 0.730 -1.939 ETKDGv3 57
P3E P2 -0.961 -2.058 0.772 ETKDGv3 58
P3E P3 -1.691 0.594 0.802 ETKDGv3 59
P3E H1 -7.185 -2.680 -1.106 ETKDGv3 60
P3E H2 -7.102 -0.126 -2.791 ETKDGv3 61
P3E H3 -5.826 -1.092 -4.474 ETKDGv3 62
P3E H4 -4.192 -2.742 -2.891 ETKDGv3 63
P3E H5 -3.442 -0.617 -3.800 ETKDGv3 64
P3E H6 -4.549 0.304 -2.689 ETKDGv3 65
P3E H7 -5.350 0.729 -0.374 ETKDGv3 66
P3E H8 7.615 -0.951 1.931 ETKDGv3 67
P3E H9 5.541 -2.036 2.879 ETKDGv3 68
P3E H10 4.752 0.702 2.291 ETKDGv3 69
P3E H11 2.622 0.198 1.498 ETKDGv3 70
P3E H12 2.494 -2.330 3.242 ETKDGv3 71
P3E H13 1.418 -3.296 1.278 ETKDGv3 72
P3E H14 1.764 -1.805 0.302 ETKDGv3 73
P3E H15 9.445 0.312 0.421 ETKDGv3 74
P3E H16 9.048 0.676 -1.280 ETKDGv3 75
P3E H17 7.356 5.120 -0.993 ETKDGv3 76
P3E H18 8.234 2.867 -1.750 ETKDGv3 77
P3E H19 6.773 5.495 1.321 ETKDGv3 78
P3E H20 7.981 1.472 2.339 ETKDGv3 79
P3E H21 6.319 4.562 3.556 ETKDGv3 80
P3E H22 6.458 2.797 3.871 ETKDGv3 81
P3E H23 7.917 3.859 4.021 ETKDGv3 82
P3E H24 -11.659 0.677 1.600 ETKDGv3 83
P3E H25 -11.655 -2.763 0.111 ETKDGv3 84
P3E H26 -12.665 -1.511 0.919 ETKDGv3 85
P3E H27 2.108 0.405 -3.290 ETKDGv3 86
P3E H28 1.569 -0.409 -1.779 ETKDGv3 87
P3E H29 4.537 0.856 -3.684 ETKDGv3 88
P3E H30 -9.039 -1.183 -2.647 ETKDGv3 89
P3E H31 -6.454 -3.676 -3.372 ETKDGv3 90
P3E H32 -0.625 -0.260 -3.351 ETKDGv3 91
P3E H33 4.492 0.716 4.448 ETKDGv3 92
P3E H34 2.071 1.119 3.443 ETKDGv3 93
P3E H35 -1.707 -3.541 2.161 ETKDGv3 94
P3E H36 -0.220 1.798 1.845 ETKDGv3 95
#