data_XVP
#
_chem_comp.id XVP
_chem_comp.name
"diethyl ({4-[(2S,3R)-2-[({[(3R,3aS,6aR)-hexahydrofuro[2,3-b]furan-3-yl]oxy}carbonyl)amino]-3-hydroxy-4-({[4-(hydroxymethyl)phenyl]sulfonyl}[(2S)-2-methylbutyl]amino)butyl]phenoxy}methyl)phosphonate"
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C34 H51 N2 O12 P S"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2021-01-15
_chem_comp.pdbx_modified_date 2022-01-21
_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 742.814
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code XVP
_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 7LEC
_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
XVP C13 C1 C 0 1 N N R N N N 20.515 -0.586 15.114 1.617 1.120 1.271 C13 XVP 1
XVP C15 C2 C 0 1 N N S N N N 20.148 -0.231 16.553 0.369 1.339 0.412 C15 XVP 2
XVP C17 C3 C 0 1 N N N N N N 22.096 0.275 18.125 -0.285 -1.008 0.476 C17 XVP 3
XVP C20 C4 C 0 1 N N R N N N 23.753 1.237 19.647 -0.921 -3.296 0.713 C20 XVP 4
XVP C21 C5 C 0 1 N N N N N N 25.203 1.783 19.099 -2.444 -3.408 0.943 C21 XVP 5
XVP C24 C6 C 0 1 N N R N N N 24.037 3.507 20.174 -1.906 -5.347 -0.182 C24 XVP 6
XVP C26 C7 C 0 1 N N N N N N 21.712 3.609 19.926 -0.691 -5.554 -2.187 C26 XVP 7
XVP C28 C8 C 0 1 N N N N N N 18.804 0.512 16.553 -0.789 1.792 1.303 C28 XVP 8
XVP C01 C9 C 0 1 Y N N N N N 15.615 -6.175 13.601 7.997 1.274 -1.994 C01 XVP 9
XVP C02 C10 C 0 1 Y N N N N N 15.347 -4.690 13.801 6.839 2.020 -2.103 C02 XVP 10
XVP C03 C11 C 0 1 Y N N N N N 16.298 -3.835 14.617 5.956 2.084 -1.041 C03 XVP 11
XVP C04 C12 C 0 1 Y N N N N N 17.513 -4.529 15.216 6.232 1.401 0.129 C04 XVP 12
XVP C05 C13 C 0 1 Y N N N N N 17.782 -5.994 15.044 7.391 0.656 0.238 C05 XVP 13
XVP C06 C14 C 0 1 Y N N N N N 16.828 -6.850 14.215 8.274 0.592 -0.824 C06 XVP 14
XVP C11 C15 C 0 1 N N N N N N 20.560 -3.986 14.245 4.058 -0.989 1.813 C11 XVP 15
XVP C12 C16 C 0 1 N N N N N N 19.511 -1.594 14.587 2.776 0.667 0.380 C12 XVP 16
XVP C23 C17 C 0 1 N N S N N N 23.382 2.130 20.569 -0.549 -4.614 0.007 C23 XVP 17
XVP C25 C18 C 0 1 N N N N N N 21.903 2.454 20.548 -0.135 -4.307 -1.455 C25 XVP 18
XVP C29 C19 C 0 1 Y N N N N N 18.532 0.958 18.023 -1.982 2.125 0.444 C29 XVP 19
XVP C30 C20 C 0 1 Y N N N N N 18.188 -0.131 19.022 -2.148 3.410 -0.039 C30 XVP 20
XVP C31 C21 C 0 1 Y N N N N N 17.931 0.241 20.489 -3.240 3.718 -0.826 C31 XVP 21
XVP C32 C22 C 0 1 Y N N N N N 18.003 1.695 20.961 -4.172 2.737 -1.132 C32 XVP 22
XVP C33 C23 C 0 1 Y N N N N N 18.376 2.779 19.965 -4.004 1.448 -0.646 C33 XVP 23
XVP C34 C24 C 0 1 Y N N N N N 18.622 2.413 18.484 -2.907 1.144 0.136 C34 XVP 24
XVP C36 C25 C 0 1 N N N N N N 22.578 -6.205 13.938 4.223 -4.482 0.206 C36 XVP 25
XVP C37 C26 C 0 1 N N S N N N 22.106 -3.773 14.353 4.206 -2.033 0.705 C37 XVP 26
XVP C38 C27 C 0 1 N N N N N N 22.736 -4.776 13.378 4.201 -3.434 1.321 C38 XVP 27
XVP C39 C28 C 0 1 N N N N N N 22.600 -4.050 15.758 5.525 -1.807 -0.036 C39 XVP 28
XVP C40 C29 C 0 1 N N N N N N 14.642 -7.016 12.749 8.957 1.199 -3.154 C40 XVP 29
XVP C41 C30 C 0 1 N N N N N N 18.902 2.572 22.956 -6.167 1.977 -2.179 C41 XVP 30
XVP C45 C31 C 0 1 N N N N N N 21.120 2.933 24.998 -9.207 0.028 -0.075 C45 XVP 31
XVP C46 C32 C 0 1 N N N N N N 18.431 0.421 26.669 -6.688 0.997 1.850 C46 XVP 32
XVP C47 C33 C 0 1 N N N N N N 22.010 4.034 24.357 -10.014 -1.121 -0.683 C47 XVP 33
XVP C48 C34 C 0 1 N N N N N N 17.627 -0.925 26.543 -5.516 0.609 2.755 C48 XVP 34
XVP N10 N1 N 0 1 N N N N N N 19.839 -2.958 15.086 3.935 0.343 1.215 N10 XVP 35
XVP N16 N2 N 0 1 N N N N N N 21.125 0.676 17.106 0.010 0.085 -0.256 N16 XVP 36
XVP O08 O1 O 0 1 N N N N N N 17.823 -2.443 16.757 5.827 1.055 2.630 O08 XVP 37
XVP O09 O2 O 0 1 N N N N N N 19.216 -4.373 17.235 4.464 2.747 1.395 O09 XVP 38
XVP O14 O3 O 0 1 N N N N N N 20.291 0.505 14.259 1.967 2.343 1.922 O14 XVP 39
XVP O18 O4 O 0 1 N N N N N N 22.154 -0.811 18.581 -0.254 -0.953 1.689 O18 XVP 40
XVP O19 O5 O 0 1 N N N N N N 23.008 1.349 18.452 -0.615 -2.160 -0.138 O19 XVP 41
XVP O22 O6 O 0 1 N N N N N N 24.983 3.103 18.990 -2.905 -4.309 -0.083 O22 XVP 42
XVP O27 O7 O 0 1 N N N N N N 23.158 4.320 19.780 -1.915 -5.881 -1.512 O27 XVP 43
XVP O35 O8 O 0 1 N N N N N N 17.742 1.983 22.358 -5.248 3.037 -1.905 O35 XVP 44
XVP O43 O9 O 0 1 N N N N N N 19.825 3.418 25.366 -8.208 0.452 -1.005 O43 XVP 45
XVP O44 O10 O 0 1 N N N N N N 18.825 0.857 25.348 -6.210 1.221 0.522 O44 XVP 46
XVP O49 O11 O 0 1 N N N N N N 17.232 2.948 25.101 -7.925 2.867 -0.327 O49 XVP 47
XVP O50 O12 O 0 1 N N N N N N 15.121 -6.946 11.397 9.912 2.257 -3.051 O50 XVP 48
XVP P42 P1 P 0 1 N N N N N N 18.595 2.455 24.820 -7.173 1.646 -0.696 P42 XVP 49
XVP S07 S1 S 0 1 N N N N N N 18.642 -3.538 16.208 5.107 1.482 1.483 S07 XVP 50
XVP H131 H1 H 0 0 N N N N N N 21.541 -0.977 15.053 1.413 0.355 2.020 H131 XVP 51
XVP H151 H2 H 0 0 N N N N N N 20.069 -1.147 17.157 0.573 2.104 -0.336 H151 XVP 52
XVP H201 H3 H 0 0 N N N N N N 23.850 0.204 20.011 -0.396 -3.211 1.664 H201 XVP 53
XVP H211 H4 H 0 0 N N N N N N 25.455 1.338 18.125 -2.648 -3.821 1.931 H211 XVP 54
XVP H212 H5 H 0 0 N N N N N N 26.008 1.570 19.818 -2.917 -2.432 0.835 H212 XVP 55
XVP H241 H6 H 0 0 N N N N N N 24.645 3.872 21.015 -2.055 -6.125 0.567 H241 XVP 56
XVP H262 H7 H 0 0 N N N N N N 21.036 4.247 20.515 -0.876 -5.325 -3.236 H262 XVP 57
XVP H261 H8 H 0 0 N N N N N N 21.276 3.434 18.931 0.008 -6.386 -2.100 H261 XVP 58
XVP H282 H9 H 0 0 N N N N N N 18.858 1.392 15.895 -1.052 0.991 1.994 H282 XVP 59
XVP H281 H10 H 0 0 N N N N N N 18.002 -0.157 16.206 -0.490 2.675 1.867 H281 XVP 60
XVP H021 H11 H 0 0 N N N N N N 14.471 -4.241 13.357 6.623 2.553 -3.017 H021 XVP 61
XVP H031 H12 H 0 0 N N N N N N 16.121 -2.780 14.766 5.051 2.667 -1.125 H031 XVP 62
XVP H051 H13 H 0 0 N N N N N N 18.649 -6.443 15.506 7.607 0.123 1.152 H051 XVP 63
XVP H061 H14 H 0 0 N N N N N N 17.011 -7.904 14.070 9.179 0.009 -0.739 H061 XVP 64
XVP H112 H15 H 0 0 N N N N N N 20.250 -3.881 13.195 3.167 -1.207 2.401 H112 XVP 65
XVP H111 H16 H 0 0 N N N N N N 20.305 -4.994 14.603 4.936 -1.017 2.459 H111 XVP 66
XVP H1 H17 H 0 1 N N N N N N 19.539 -1.593 13.487 2.476 -0.216 -0.184 H1 XVP 67
XVP H2 H18 H 0 1 N N N N N N 18.503 -1.315 14.928 3.038 1.468 -0.311 H2 XVP 68
XVP H231 H19 H 0 0 N N N N N N 23.696 1.854 21.586 0.186 -5.201 0.558 H231 XVP 69
XVP H251 H20 H 0 0 N N N N N N 21.529 2.527 21.580 0.949 -4.245 -1.551 H251 XVP 70
XVP H252 H21 H 0 0 N N N N N N 21.361 1.658 20.017 -0.613 -3.395 -1.814 H252 XVP 71
XVP H301 H22 H 0 0 N N N N N N 18.124 -1.161 18.703 -1.422 4.174 0.199 H301 XVP 72
XVP H311 H23 H 0 0 N N N N N N 17.695 -0.537 21.200 -3.369 4.722 -1.203 H311 XVP 73
XVP H331 H24 H 0 0 N N N N N N 18.469 3.804 20.291 -4.728 0.682 -0.883 H331 XVP 74
XVP H341 H25 H 0 0 N N N N N N 18.859 3.189 17.771 -2.773 0.140 0.511 H341 XVP 75
XVP H361 H26 H 0 0 N N N N N N 23.029 -6.925 13.240 3.343 -4.359 -0.426 H361 XVP 76
XVP H363 H27 H 0 0 N N N N N N 23.082 -6.274 14.913 5.123 -4.353 -0.396 H363 XVP 77
XVP H362 H28 H 0 0 N N N N N N 21.509 -6.434 14.061 4.219 -5.479 0.644 H362 XVP 78
XVP H371 H29 H 0 0 N N N N N N 22.360 -2.745 14.054 3.375 -1.941 0.005 H371 XVP 79
XVP H382 H30 H 0 0 N N N N N N 23.805 -4.546 13.255 3.301 -3.563 1.922 H382 XVP 80
XVP H381 H31 H 0 0 N N N N N N 22.231 -4.706 12.403 5.081 -3.557 1.952 H381 XVP 81
XVP H393 H32 H 0 0 N N N N N N 22.147 -3.330 16.455 5.493 -0.847 -0.552 H393 XVP 82
XVP H391 H33 H 0 0 N N N N N N 22.317 -5.072 16.051 6.348 -1.809 0.678 H391 XVP 83
XVP H392 H34 H 0 0 N N N N N N 23.695 -3.950 15.788 5.674 -2.605 -0.764 H392 XVP 84
XVP H402 H35 H 0 0 N N N N N N 13.625 -6.602 12.814 9.474 0.240 -3.137 H402 XVP 85
XVP H401 H36 H 0 0 N N N N N N 14.636 -8.060 13.097 8.405 1.298 -4.089 H401 XVP 86
XVP H411 H37 H 0 0 N N N N N N 19.808 2.014 22.676 -6.819 2.265 -3.004 H411 XVP 87
XVP H412 H38 H 0 0 N N N N N N 19.008 3.622 22.646 -5.613 1.078 -2.451 H412 XVP 88
XVP H452 H39 H 0 0 N N N N N N 20.997 2.114 24.274 -9.873 0.861 0.148 H452 XVP 89
XVP H451 H40 H 0 0 N N N N N N 21.623 2.553 25.899 -8.728 -0.310 0.844 H451 XVP 90
XVP H462 H41 H 0 0 N N N N N N 19.327 0.260 27.287 -7.422 0.192 1.842 H462 XVP 91
XVP H461 H42 H 0 0 N N N N N N 17.796 1.188 27.137 -7.152 1.908 2.228 H461 XVP 92
XVP H473 H43 H 0 0 N N N N N N 22.990 3.608 24.095 -10.493 -0.783 -1.601 H473 XVP 93
XVP H472 H44 H 0 0 N N N N N N 21.522 4.417 23.449 -9.348 -1.955 -0.906 H472 XVP 94
XVP H471 H45 H 0 0 N N N N N N 22.148 4.857 25.074 -10.776 -1.445 0.027 H471 XVP 95
XVP H483 H46 H 0 0 N N N N N N 17.322 -1.266 27.544 -5.052 -0.302 2.377 H483 XVP 96
XVP H481 H47 H 0 0 N N N N N N 16.733 -0.761 25.923 -4.782 1.414 2.764 H481 XVP 97
XVP H482 H48 H 0 0 N N N N N N 18.263 -1.690 26.074 -5.881 0.438 3.768 H482 XVP 98
XVP H161 H49 H 0 0 N N N N N N 21.139 1.621 16.778 -0.015 0.042 -1.224 H161 XVP 99
XVP H141 H50 H 0 0 N N N N N N 20.874 1.217 14.494 2.162 3.070 1.315 H141 XVP 100
XVP H501 H51 H 0 0 N N N N N N 14.550 -7.452 10.832 10.563 2.270 -3.766 H501 XVP 101
#
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
XVP O50 C40 SING N N 1
XVP C40 C01 SING N N 2
XVP C38 C36 SING N N 3
XVP C38 C37 SING N N 4
XVP C01 C02 DOUB Y N 5
XVP C01 C06 SING Y N 6
XVP C02 C03 SING Y N 7
XVP C06 C05 DOUB Y N 8
XVP C11 C37 SING N N 9
XVP C11 N10 SING N N 10
XVP O14 C13 SING N N 11
XVP C37 C39 SING N N 12
XVP C12 N10 SING N N 13
XVP C12 C13 SING N N 14
XVP C03 C04 DOUB Y N 15
XVP C05 C04 SING Y N 16
XVP N10 S07 SING N N 17
XVP C13 C15 SING N N 18
XVP C04 S07 SING N N 19
XVP S07 O08 DOUB N N 20
XVP S07 O09 DOUB N N 21
XVP C15 C28 SING N N 22
XVP C15 N16 SING N N 23
XVP C28 C29 SING N N 24
XVP N16 C17 SING N N 25
XVP C29 C34 DOUB Y N 26
XVP C29 C30 SING Y N 27
XVP C17 O19 SING N N 28
XVP C17 O18 DOUB N N 29
XVP O19 C20 SING N N 30
XVP C34 C33 SING Y N 31
XVP O22 C21 SING N N 32
XVP O22 C24 SING N N 33
XVP C30 C31 DOUB Y N 34
XVP C21 C20 SING N N 35
XVP C20 C23 SING N N 36
XVP O27 C26 SING N N 37
XVP O27 C24 SING N N 38
XVP C26 C25 SING N N 39
XVP C33 C32 DOUB Y N 40
XVP C24 C23 SING N N 41
XVP C31 C32 SING Y N 42
XVP C25 C23 SING N N 43
XVP C32 O35 SING N N 44
XVP O35 C41 SING N N 45
XVP C41 P42 SING N N 46
XVP C47 C45 SING N N 47
XVP P42 O49 DOUB N N 48
XVP P42 O44 SING N N 49
XVP P42 O43 SING N N 50
XVP C45 O43 SING N N 51
XVP O44 C46 SING N N 52
XVP C48 C46 SING N N 53
XVP C13 H131 SING N N 54
XVP C15 H151 SING N N 55
XVP C20 H201 SING N N 56
XVP C21 H211 SING N N 57
XVP C21 H212 SING N N 58
XVP C24 H241 SING N N 59
XVP C26 H262 SING N N 60
XVP C26 H261 SING N N 61
XVP C28 H282 SING N N 62
XVP C28 H281 SING N N 63
XVP C02 H021 SING N N 64
XVP C03 H031 SING N N 65
XVP C05 H051 SING N N 66
XVP C06 H061 SING N N 67
XVP C11 H112 SING N N 68
XVP C11 H111 SING N N 69
XVP C12 H1 SING N N 70
XVP C12 H2 SING N N 71
XVP C23 H231 SING N N 72
XVP C25 H251 SING N N 73
XVP C25 H252 SING N N 74
XVP C30 H301 SING N N 75
XVP C31 H311 SING N N 76
XVP C33 H331 SING N N 77
XVP C34 H341 SING N N 78
XVP C36 H361 SING N N 79
XVP C36 H363 SING N N 80
XVP C36 H362 SING N N 81
XVP C37 H371 SING N N 82
XVP C38 H382 SING N N 83
XVP C38 H381 SING N N 84
XVP C39 H393 SING N N 85
XVP C39 H391 SING N N 86
XVP C39 H392 SING N N 87
XVP C40 H402 SING N N 88
XVP C40 H401 SING N N 89
XVP C41 H411 SING N N 90
XVP C41 H412 SING N N 91
XVP C45 H452 SING N N 92
XVP C45 H451 SING N N 93
XVP C46 H462 SING N N 94
XVP C46 H461 SING N N 95
XVP C47 H473 SING N N 96
XVP C47 H472 SING N N 97
XVP C47 H471 SING N N 98
XVP C48 H483 SING N N 99
XVP C48 H481 SING N N 100
XVP C48 H482 SING N N 101
XVP N16 H161 SING N N 102
XVP O14 H141 SING N N 103
XVP O50 H501 SING N N 104
#
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
XVP SMILES ACDLabs 12.01 C(C(Cc1ccc(cc1)OCP(OCC)(OCC)=O)NC(OC2C3C(OC2)OCC3)=O)(CN(CC(C)CC)S(c4ccc(cc4)CO)(=O)=O)O
XVP InChI InChI 1.03 InChI=1S/C34H51N2O12PS/c1-5-24(4)19-36(50(41,42)28-14-10-26(21-37)11-15-28)20-31(38)30(35-34(39)48-32-22-44-33-29(32)16-17-43-33)18-25-8-12-27(13-9-25)45-23-49(40,46-6-2)47-7-3/h8-15,24,29-33,37-38H,5-7,16-23H2,1-4H3,(H,35,39)/t24-,29-,30-,31+,32-,33+/m0/s1
XVP InChIKey InChI 1.03 ZDFOHGSCDGSGKK-NRCXORKASA-N
XVP SMILES_CANONICAL CACTVS 3.385 CCO[P](=O)(COc1ccc(C[C@H](NC(=O)O[C@H]2CO[C@H]3OCC[C@@H]23)[C@H](O)CN(C[C@@H](C)CC)[S](=O)(=O)c4ccc(CO)cc4)cc1)OCC
XVP SMILES CACTVS 3.385 CCO[P](=O)(COc1ccc(C[CH](NC(=O)O[CH]2CO[CH]3OCC[CH]23)[CH](O)CN(C[CH](C)CC)[S](=O)(=O)c4ccc(CO)cc4)cc1)OCC
XVP SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 CC[C@H](C)CN(C[C@H]([C@H](Cc1ccc(cc1)OCP(=O)(OCC)OCC)NC(=O)O[C@H]2CO[C@@H]3[C@H]2CCO3)O)S(=O)(=O)c4ccc(cc4)CO
XVP SMILES "OpenEye OEToolkits" 2.0.7 CCC(C)CN(CC(C(Cc1ccc(cc1)OCP(=O)(OCC)OCC)NC(=O)OC2COC3C2CCO3)O)S(=O)(=O)c4ccc(cc4)CO
#
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
XVP "SYSTEMATIC NAME" ACDLabs 12.01 "diethyl ({4-[(2S,3R)-2-[({[(3R,3aS,6aR)-hexahydrofuro[2,3-b]furan-3-yl]oxy}carbonyl)amino]-3-hydroxy-4-({[4-(hydroxymethyl)phenyl]sulfonyl}[(2S)-2-methylbutyl]amino)butyl]phenoxy}methyl)phosphonate"
XVP "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "[(3~{a}~{S},4~{R},6~{a}~{R})-2,3,3~{a},4,5,6~{a}-hexahydrofuro[2,3-b]furan-4-yl] ~{N}-[(2~{S},3~{R})-1-[4-(diethoxyphosphorylmethoxy)phenyl]-4-[[4-(hydroxymethyl)phenyl]sulfonyl-[(2~{S})-2-methylbutyl]amino]-3-oxidanyl-butan-2-yl]carbamate"
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
XVP 'Create component' 2021-01-15 RCSB
XVP 'Initial release' 2022-01-26 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
XVP C13 C 15.818 -1.451 1
XVP C15 C 16.282 -2.878 2
XVP C17 C 18.212 -4.616 3
XVP C20 C 20.143 -6.355 4
XVP C21 C 19.262 -7.568 5
XVP C24 C 21.570 -8.318 6
XVP C26 C 23.864 -7.568 7
XVP C28 C 15.278 -3.992 8
XVP C01 C 20.373 5.549 9
XVP C02 C 20.837 4.123 10
XVP C03 C 19.833 3.008 11
XVP C04 C 18.366 3.320 12
XVP C05 C 17.902 4.746 13
XVP C06 C 18.906 5.861 14
XVP C11 C 14.891 1.402 15
XVP C12 C 16.822 -0.336 16
XVP C23 C 21.570 -6.818 17
XVP C25 C 22.989 -6.361 18
XVP C29 C 13.811 -3.680 19
XVP C30 C 13.347 -2.254 20
XVP C31 C 11.880 -1.942 21
XVP C32 C 10.876 -3.057 22
XVP C33 C 11.340 -4.483 23
XVP C34 C 12.807 -4.795 24
XVP C36 C 12.497 4.567 25
XVP C37 C 14.428 2.829 26
XVP C38 C 12.960 3.141 27
XVP C39 C 15.431 3.943 28
XVP C40 C 21.377 6.664 29
XVP C41 C 8.405 -3.860 30
XVP C45 C 7.741 -6.019 31
XVP C46 C 4.467 -4.351 32
XVP C47 C 7.429 -7.486 33
XVP C48 C 3.000 -4.039 34
XVP N10 N 16.358 1.090 35
XVP N16 N 17.749 -3.189 36
XVP O08 O 16.247 3.209 37
XVP O09 O 18.477 1.201 38
XVP O14 O 14.351 -1.139 39
XVP O18 O 17.209 -5.731 40
XVP O19 O 19.680 -4.928 41
XVP O22 O 20.143 -8.782 42
XVP O27 O 22.989 -8.775 43
XVP O35 O 9.409 -2.745 44
XVP O43 O 6.626 -5.015 45
XVP O44 O 5.471 -3.236 46
XVP O49 O 7.250 -2.080 47
XVP O50 O 20.913 8.090 48
XVP P42 P 6.938 -3.548 49
XVP S07 S 17.362 2.205 50
#
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
XVP O50 C40 SINGLE NONE 1
XVP C40 C01 SINGLE NONE 2
XVP C38 C36 SINGLE NONE 3
XVP C38 C37 SINGLE NONE 4
XVP C01 C02 DOUBLE NONE 5
XVP C01 C06 SINGLE NONE 6
XVP C02 C03 SINGLE NONE 7
XVP C06 C05 DOUBLE NONE 8
XVP C11 C37 SINGLE NONE 9
XVP C11 N10 SINGLE NONE 10
XVP C13 O14 SINGLE BEGINDASH 11
XVP C37 C39 SINGLE BEGINDASH 12
XVP C12 N10 SINGLE NONE 13
XVP C12 C13 SINGLE NONE 14
XVP C03 C04 DOUBLE NONE 15
XVP C05 C04 SINGLE NONE 16
XVP N10 S07 SINGLE NONE 17
XVP C13 C15 SINGLE NONE 18
XVP C04 S07 SINGLE NONE 19
XVP S07 O08 DOUBLE NONE 20
XVP S07 O09 DOUBLE NONE 21
XVP C15 C28 SINGLE BEGINWEDGE 22
XVP C15 N16 SINGLE NONE 23
XVP C28 C29 SINGLE NONE 24
XVP N16 C17 SINGLE NONE 25
XVP C29 C34 SINGLE NONE 26
XVP C29 C30 DOUBLE NONE 27
XVP C17 O19 SINGLE NONE 28
XVP C17 O18 DOUBLE NONE 29
XVP C20 O19 SINGLE BEGINDASH 30
XVP C34 C33 DOUBLE NONE 31
XVP O22 C21 SINGLE NONE 32
XVP O22 C24 SINGLE NONE 33
XVP C30 C31 SINGLE NONE 34
XVP C21 C20 SINGLE NONE 35
XVP C20 C23 SINGLE NONE 36
XVP O27 C26 SINGLE NONE 37
XVP O27 C24 SINGLE NONE 38
XVP C26 C25 SINGLE NONE 39
XVP C33 C32 SINGLE NONE 40
XVP C24 C23 SINGLE NONE 41
XVP C31 C32 DOUBLE NONE 42
XVP C25 C23 SINGLE NONE 43
XVP C32 O35 SINGLE NONE 44
XVP O35 C41 SINGLE NONE 45
XVP C41 P42 SINGLE NONE 46
XVP C47 C45 SINGLE NONE 47
XVP P42 O49 DOUBLE NONE 48
XVP P42 O44 SINGLE NONE 49
XVP P42 O43 SINGLE NONE 50
XVP C45 O43 SINGLE NONE 51
XVP O44 C46 SINGLE NONE 52
XVP C48 C46 SINGLE NONE 53
#
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
XVP MurckoScaffold S1 scaffold 'O=C(N[C@H](CCNS(=O)(=O)c1ccccc1)Cc1ccccc1)O[C@H]1CO[C@H]2OCC[C@H]21' InChI=1S/C23H28N2O6S/c26-23(31-21-16-30-22-20(21)12-14-29-22)25-18(15-17-7-3-1-4-8-17)11-13-24-32(27,28)19-9-5-2-6-10-19/h1-10,18,20-22,24H,11-16H2,(H,25,26)/t18-,20+,21+,22-/m1/s1 FMDUZJYOYDAUAU-RYFAJOAYSA-N
XVP furanose F1 fragment OC1CCCO1 InChI=1S/C4H8O2/c5-4-2-1-3-6-4/h4-5H,1-3H2 JNODDICFTDYODH-UHFFFAOYSA-N
XVP phenyl F2 fragment c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-UHFFFAOYSA-N
XVP Z45516134 F3 fragment CCN(CC)S(=O)(=O)c1ccc(C)cc1 InChI=1S/C11H17NO2S/c1-4-12(5-2)15(13,14)11-8-6-10(3)7-9-11/h6-9H,4-5H2,1-3H3 AOJBACHWNDMRQP-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
XVP C13 S1 1
XVP C15 S1 1
XVP C17 S1 1
XVP C20 S1 1
XVP C21 S1 1
XVP C24 S1 1
XVP C26 S1 1
XVP C28 S1 1
XVP C01 S1 1
XVP C02 S1 1
XVP C03 S1 1
XVP C04 S1 1
XVP C05 S1 1
XVP C06 S1 1
XVP C12 S1 1
XVP C23 S1 1
XVP C25 S1 1
XVP C29 S1 1
XVP C30 S1 1
XVP C31 S1 1
XVP C32 S1 1
XVP C33 S1 1
XVP C34 S1 1
XVP N10 S1 1
XVP N16 S1 1
XVP O08 S1 1
XVP O09 S1 1
XVP O18 S1 1
XVP O19 S1 1
XVP O22 S1 1
XVP O27 S1 1
XVP S07 S1 1
XVP C20 F1 1
XVP C21 F1 1
XVP O22 F1 1
XVP C24 F1 1
XVP C23 F1 1
XVP O27 F1 1
XVP C25 F1 2
XVP C26 F1 2
XVP O27 F1 2
XVP C24 F1 2
XVP C23 F1 2
XVP O22 F1 2
XVP C01 F2 1
XVP C02 F2 1
XVP C03 F2 1
XVP C04 F2 1
XVP C05 F2 1
XVP C06 F2 1
XVP C29 F2 2
XVP C34 F2 2
XVP C33 F2 2
XVP C32 F2 2
XVP C31 F2 2
XVP C30 F2 2
XVP C13 F3 1
XVP C12 F3 1
XVP N10 F3 1
XVP C11 F3 1
XVP C37 F3 1
XVP S07 F3 1
XVP O08 F3 1
XVP O09 F3 1
XVP C04 F3 1
XVP C03 F3 1
XVP C02 F3 1
XVP C01 F3 1
XVP C40 F3 1
XVP C06 F3 1
XVP C05 F3 1
#
_pdbe_chem_comp_rdkit_properties.comp_id XVP
_pdbe_chem_comp_rdkit_properties.exactmw 742.290
_pdbe_chem_comp_rdkit_properties.amw 742.825
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 14
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 3
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 26
_pdbe_chem_comp_rdkit_properties.NumHBD 3
_pdbe_chem_comp_rdkit_properties.NumHBA 12
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 50
_pdbe_chem_comp_rdkit_properties.NumAtoms 101
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 16
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 1
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.618
_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 2
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 0
_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 6
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 366.355
_pdbe_chem_comp_rdkit_properties.tpsa 179.390
_pdbe_chem_comp_rdkit_properties.CrippenClogP 3.598
_pdbe_chem_comp_rdkit_properties.CrippenMR 183.505
_pdbe_chem_comp_rdkit_properties.chi0v 25.360
_pdbe_chem_comp_rdkit_properties.chi1v 15.022
_pdbe_chem_comp_rdkit_properties.chi2v 7.137
_pdbe_chem_comp_rdkit_properties.chi3v 7.137
_pdbe_chem_comp_rdkit_properties.chi4v 4.317
_pdbe_chem_comp_rdkit_properties.chi0n 74.649
_pdbe_chem_comp_rdkit_properties.chi1n 37.303
_pdbe_chem_comp_rdkit_properties.chi2n 4.775
_pdbe_chem_comp_rdkit_properties.chi3n 4.775
_pdbe_chem_comp_rdkit_properties.chi4n 2.805
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -2.590
_pdbe_chem_comp_rdkit_properties.kappa1 9.930
_pdbe_chem_comp_rdkit_properties.kappa2 18.767
_pdbe_chem_comp_rdkit_properties.kappa3 10.957
_pdbe_chem_comp_rdkit_properties.Phi 3.727
#
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
XVP UniChem ChEMBL CHEMBL5630125
XVP UniChem PubChem 162421339
#
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
XVP C13 -0.939 1.128 1.208 ETKDGv3 1
XVP C15 0.227 2.141 0.972 ETKDGv3 2
XVP C17 -1.035 4.348 0.914 ETKDGv3 3
XVP C20 -2.185 6.562 0.963 ETKDGv3 4
XVP C21 -2.839 7.338 2.087 ETKDGv3 5
XVP C24 -1.256 8.740 1.281 ETKDGv3 6
XVP C26 0.811 7.840 0.952 ETKDGv3 7
XVP C28 1.592 1.691 1.551 ETKDGv3 8
XVP C01 -3.777 -5.931 -0.398 ETKDGv3 9
XVP C02 -2.778 -5.281 -1.018 ETKDGv3 10
XVP C03 -2.212 -4.051 -0.429 ETKDGv3 11
XVP C04 -2.703 -3.563 0.720 ETKDGv3 12
XVP C05 -3.804 -4.277 1.407 ETKDGv3 13
XVP C06 -4.317 -5.393 0.874 ETKDGv3 14
XVP C11 -3.511 -0.092 0.182 ETKDGv3 15
XVP C12 -1.043 0.083 0.062 ETKDGv3 16
XVP C23 -1.432 7.662 0.229 ETKDGv3 17
XVP C25 -0.024 7.358 -0.213 ETKDGv3 18
XVP C29 2.136 0.448 0.896 ETKDGv3 19
XVP C30 2.191 -0.717 1.564 ETKDGv3 20
XVP C31 2.684 -1.937 0.895 ETKDGv3 21
XVP C32 3.089 -1.901 -0.382 ETKDGv3 22
XVP C33 3.034 -0.610 -1.122 ETKDGv3 23
XVP C34 2.592 0.498 -0.514 ETKDGv3 24
XVP C36 -5.371 -2.559 -2.212 ETKDGv3 25
XVP C37 -4.679 -0.962 -0.333 ETKDGv3 26
XVP C38 -4.428 -1.433 -1.787 ETKDGv3 27
XVP C39 -5.994 -0.174 -0.224 ETKDGv3 28
XVP C40 -4.402 -7.147 -1.024 ETKDGv3 29
XVP C41 4.174 -3.191 -2.246 ETKDGv3 30
XVP C45 6.423 -3.899 -0.032 ETKDGv3 31
XVP C46 7.317 -0.664 -1.390 ETKDGv3 32
XVP C47 7.459 -4.660 0.779 ETKDGv3 33
XVP C48 7.394 0.669 -0.664 ETKDGv3 34
XVP N10 -2.220 -0.811 0.137 ETKDGv3 35
XVP N16 -0.133 3.439 1.555 ETKDGv3 36
XVP O08 -0.634 -2.280 1.743 ETKDGv3 37
XVP O09 -2.838 -1.665 2.603 ETKDGv3 38
XVP O14 -0.803 0.491 2.451 ETKDGv3 39
XVP O18 -1.557 4.051 -0.196 ETKDGv3 40
XVP O19 -1.320 5.572 1.528 ETKDGv3 41
XVP O22 -1.996 8.407 2.435 ETKDGv3 42
XVP O27 0.110 8.863 1.619 ETKDGv3 43
XVP O35 3.548 -3.090 -0.969 ETKDGv3 44
XVP O43 6.891 -3.752 -1.352 ETKDGv3 45
XVP O44 5.979 -1.099 -1.402 ETKDGv3 46
XVP O49 6.408 -2.491 -3.592 ETKDGv3 47
XVP O50 -5.340 -6.761 -1.991 ETKDGv3 48
XVP P42 5.907 -2.621 -2.171 ETKDGv3 49
XVP S07 -2.072 -2.054 1.368 ETKDGv3 50
XVP H131 -1.890 1.706 1.204 ETKDGv3 51
XVP H151 0.369 2.294 -0.121 ETKDGv3 52
XVP H201 -2.965 6.095 0.321 ETKDGv3 53
XVP H211 -3.012 6.690 2.973 ETKDGv3 54
XVP H212 -3.821 7.742 1.753 ETKDGv3 55
XVP H241 -1.615 9.717 0.889 ETKDGv3 56
XVP H262 1.789 8.226 0.595 ETKDGv3 57
XVP H261 0.998 7.005 1.662 ETKDGv3 58
XVP H282 1.516 1.559 2.653 ETKDGv3 59
XVP H281 2.331 2.507 1.390 ETKDGv3 60
XVP H021 -2.386 -5.640 -1.962 ETKDGv3 61
XVP H031 -1.415 -3.534 -0.949 ETKDGv3 62
XVP H051 -4.210 -3.893 2.333 ETKDGv3 63
XVP H061 -5.132 -5.900 1.376 ETKDGv3 64
XVP H112 -3.727 0.248 1.219 ETKDGv3 65
XVP H111 -3.459 0.818 -0.458 ETKDGv3 66
XVP H1 -1.089 0.625 -0.907 ETKDGv3 67
XVP H2 -0.126 -0.533 0.004 ETKDGv3 68
XVP H231 -2.044 8.036 -0.623 ETKDGv3 69
XVP H251 0.158 6.292 -0.456 ETKDGv3 70
XVP H252 0.218 7.969 -1.111 ETKDGv3 71
XVP H301 1.858 -0.783 2.592 ETKDGv3 72
XVP H311 2.715 -2.868 1.448 ETKDGv3 73
XVP H331 3.354 -0.544 -2.152 ETKDGv3 74
XVP H341 2.562 1.432 -1.060 ETKDGv3 75
XVP H361 -5.326 -3.399 -1.488 ETKDGv3 76
XVP H363 -5.065 -2.940 -3.209 ETKDGv3 77
XVP H362 -6.415 -2.192 -2.290 ETKDGv3 78
XVP H371 -4.776 -1.847 0.328 ETKDGv3 79
XVP H382 -3.391 -1.819 -1.888 ETKDGv3 80
XVP H381 -4.530 -0.579 -2.491 ETKDGv3 81
XVP H393 -6.138 0.189 0.816 ETKDGv3 82
XVP H391 -5.986 0.702 -0.908 ETKDGv3 83
XVP H392 -6.861 -0.820 -0.472 ETKDGv3 84
XVP H402 -4.886 -7.782 -0.247 ETKDGv3 85
XVP H401 -3.620 -7.768 -1.510 ETKDGv3 86
XVP H411 3.607 -2.623 -3.012 ETKDGv3 87
XVP H412 4.176 -4.256 -2.556 ETKDGv3 88
XVP H452 6.257 -2.917 0.467 ETKDGv3 89
XVP H451 5.481 -4.489 -0.025 ETKDGv3 90
XVP H462 7.693 -0.516 -2.427 ETKDGv3 91
XVP H461 7.970 -1.387 -0.852 ETKDGv3 92
XVP H473 8.414 -4.093 0.801 ETKDGv3 93
XVP H472 7.637 -5.659 0.328 ETKDGv3 94
XVP H471 7.097 -4.794 1.820 ETKDGv3 95
XVP H483 8.445 1.028 -0.647 ETKDGv3 96
XVP H481 6.764 1.422 -1.183 ETKDGv3 97
XVP H482 7.036 0.553 0.382 ETKDGv3 98
XVP H161 0.287 3.734 2.466 ETKDGv3 99
XVP H141 -1.039 1.160 3.145 ETKDGv3 100
XVP H501 -6.136 -6.430 -1.499 ETKDGv3 101
#