data_UD0
#
_chem_comp.id UD0
_chem_comp.name
"(2S,3S,4R,5R,6R)-5-(acetylamino)-6-{[(S)-{[(S)-{[(2S,3R,4S,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}-3-hydroxy-4-{[(1E)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]amino}tetrahydro-2H-pyran-2-carboxylic acid"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C25 H34 N5 O22 P3"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2010-07-13
_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 849.479
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code UD0
_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 3NUB
_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
UD0 P P P 0 1 N N N N N N -20.215 -59.242 16.852 1.311 -5.851 -0.160 P UD0 1
UD0 C1 C1 C 0 1 N N R N N N -15.000 -63.403 13.558 2.901 3.455 -0.236 C1 UD0 2
UD0 N1 N1 N 0 1 Y N N N N N -19.684 -63.885 20.966 6.689 -4.341 -0.416 N1 UD0 3
UD0 O1 O1 O 0 1 N N N N N N -14.813 -61.954 13.463 3.269 4.023 1.023 O1 UD0 4
UD0 C2 C2 C 0 1 N N R N N N -15.648 -63.876 14.868 3.792 2.245 -0.528 C2 UD0 5
UD0 C3 C3 C 0 1 N N R N N N -16.992 -63.162 15.147 3.652 1.231 0.612 C3 UD0 6
UD0 C4 C4 C 0 1 N N S N N N -16.960 -61.642 14.909 4.012 1.913 1.935 C4 UD0 7
UD0 C5 C5 C 0 1 N N S N N N -15.951 -61.098 13.868 3.112 3.136 2.132 C5 UD0 8
UD0 C6 C6 C 0 1 N N N N N N -15.452 -59.761 14.464 3.500 3.846 3.403 C6 UD0 9
UD0 PA PA P 0 1 N N N N N N -15.191 -64.654 11.110 0.312 4.004 -0.603 PA UD0 10
UD0 PB PB P 0 1 N N N N N N -12.653 -65.767 10.458 -2.522 3.383 -1.212 PB UD0 11
UD0 "C1'" "C1'" C 0 1 Y N N N N N -19.309 -64.868 20.125 7.200 -3.133 -0.294 "C1'" UD0 12
UD0 "O1'" "O1'" O 0 1 N N N N N N -18.580 -65.540 17.938 6.915 -0.791 0.053 "O1'" UD0 13
UD0 "C1'A" C1* C 0 0 N N R N N N -12.404 -65.910 5.076 -6.573 -0.454 -0.416 C1* UD0 14
UD0 C1A C1A C 0 1 N N N N N N -19.287 -66.311 20.639 8.692 -2.943 -0.397 C1A UD0 15
UD0 "C2'" "C2'" C 0 1 Y N N N N N -18.952 -64.567 18.807 6.383 -2.034 -0.072 "C2'" UD0 16
UD0 "C2'A" C2* C 0 0 N N S N N N -13.230 -67.198 4.881 -7.765 0.311 0.213 C2* UD0 17
UD0 "O2'" O2* O 0 1 N N N N N N -13.050 -67.758 3.572 -7.948 -0.055 1.582 O2* UD0 18
UD0 C2A C2A C 0 1 N N N N N N -16.073 -66.200 15.677 3.856 2.094 -2.959 C2A UD0 19
UD0 N2A N2A N 0 1 N N N N N N -15.859 -65.323 14.701 3.379 1.625 -1.789 N2A UD0 20
UD0 O2A O2A O 0 1 N N N N N N -16.147 -65.936 16.873 4.627 3.030 -2.967 O2A UD0 21
UD0 C2B C2B C 0 1 N N N N N N -16.242 -67.627 15.185 3.431 1.457 -4.256 C2B UD0 22
UD0 "C3'" "C3'" C 0 1 Y N N N N N -18.977 -63.247 18.361 4.995 -2.229 0.021 "C3'" UD0 23
UD0 "C3'A" C3* C 0 0 N N R N N N -12.686 -68.131 5.975 -7.274 1.778 0.086 C3* UD0 24
UD0 "O3'" O3* O 0 1 N N N N N N -11.576 -68.914 5.492 -7.845 2.596 1.110 O3* UD0 25
UD0 N3A N3A N 0 1 N N N N N N -17.444 -63.393 16.543 4.558 0.103 0.379 N3A UD0 26
UD0 "C4'" "C4'" C 0 1 N N N N N N -18.614 -62.969 17.030 4.083 -1.093 0.255 "C4'" UD0 27
UD0 "C4'A" C4* C 0 0 N N S N N N -12.218 -67.175 7.080 -5.750 1.632 0.285 C4* UD0 28
UD0 "O4'" O4* O 0 1 N N N N N N -12.359 -65.807 6.540 -5.404 0.273 -0.007 O4* UD0 29
UD0 O4A O4A O 0 1 N N N N N N -18.277 -61.245 14.515 3.816 0.996 3.014 O4A UD0 30
UD0 "C5'" "C5'" C 0 1 Y N N N N N -19.378 -62.249 19.257 4.503 -3.533 -0.116 "C5'" UD0 31
UD0 "C5'A" C5* C 0 0 N N N N N N -13.071 -67.361 8.347 -5.009 2.573 -0.667 C5* UD0 32
UD0 "O5'" O5* O 0 1 N N N N N N -13.286 -66.100 8.996 -3.607 2.517 -0.396 O5* UD0 33
UD0 "C6'" "C6'" C 0 1 Y N N N N N -19.721 -62.621 20.568 5.391 -4.565 -0.335 "C6'" UD0 34
UD0 O6A O6A O 0 1 N N N N N N -14.260 -59.444 14.246 3.958 4.963 3.355 O6A UD0 35
UD0 O6B O6B O 0 1 N N N N N N -16.256 -59.052 15.132 3.338 3.238 4.588 O6B UD0 36
UD0 "C7'" "C7'" C 0 1 N N N N N N -19.458 -60.752 18.924 3.023 -3.804 -0.026 "C7'" UD0 37
UD0 OA1 OA1 O 0 1 N N N N N N -15.796 -64.017 12.491 1.534 3.040 -0.191 OA1 UD0 38
UD0 OA2 OA2 O 0 1 N N N N N N -16.373 -65.629 10.587 0.229 5.236 0.430 OA2 UD0 39
UD0 OA3 OA3 O 0 1 N N N N N N -14.879 -63.587 10.119 0.531 4.521 -1.972 OA3 UD0 40
UD0 OAE OAE O 0 1 N N N N N N -7.308 -65.602 2.827 -6.419 -5.539 1.394 OAE UD0 41
UD0 OAF OAF O 0 1 N N N N N N -11.834 -65.761 2.271 -6.824 -2.640 -1.944 OAF UD0 42
UD0 CAT CAT C 0 1 N N N N N N -8.589 -65.740 4.705 -6.301 -3.313 1.901 CAT UD0 43
UD0 CAU CAU C 0 1 N N N N N N -9.866 -65.814 5.260 -6.338 -2.047 1.431 CAU UD0 44
UD0 OB1 OB1 O 0 1 N N N N N N -12.002 -64.272 10.351 -2.887 4.816 -1.152 OB1 UD0 45
UD0 OB2 OB2 O 0 1 N N N N N N -11.652 -66.765 10.927 -2.495 2.900 -2.747 OB2 UD0 46
UD0 OB4 OB4 O 0 1 N N N N N N -13.925 -65.618 11.486 -1.066 3.172 -0.557 OB4 UD0 47
UD0 NBB NBB N 0 1 N N N N N N -9.568 -65.679 2.484 -6.624 -4.130 -0.318 NBB UD0 48
UD0 CBO CBO C 0 1 N N N N N N -8.435 -65.669 3.320 -6.449 -4.389 0.994 CBO UD0 49
UD0 CBP CBP C 0 1 N N N N N N -10.864 -65.755 3.032 -6.667 -2.859 -0.758 CBP UD0 50
UD0 NBZ NBZ N 0 1 N N N N N N -11.029 -65.833 4.443 -6.522 -1.827 0.093 NBZ UD0 51
UD0 OP1 OP1 O 0 1 N N N N N N -19.638 -58.010 17.655 1.405 -7.418 -0.518 OP1 UD0 52
UD0 OP2 OP2 O 0 1 N N N N N N -19.116 -59.638 15.759 0.446 -5.170 -1.149 OP2 UD0 53
UD0 OP3 OP3 O 0 1 N N N N N N -21.471 -58.949 16.113 0.684 -5.674 1.313 OP3 UD0 54
UD0 OP4 OP4 O 0 1 N N N N N N -20.350 -60.527 17.825 2.784 -5.202 -0.198 OP4 UD0 55
UD0 H1 H1 H 0 1 N N N N N N -13.953 -63.732 13.483 3.030 4.199 -1.022 H1 UD0 56
UD0 H2 H2 H 0 1 N N N N N N -15.003 -63.642 15.728 4.831 2.567 -0.602 H2 UD0 57
UD0 H3 H3 H 0 1 N N N N N N -17.692 -63.606 14.424 2.624 0.870 0.654 H3 UD0 58
UD0 H4 H4 H 0 1 N N N N N N -16.613 -61.212 15.860 5.055 2.228 1.910 H4 UD0 59
UD0 H5 H5 H 0 1 N N N N N N -16.488 -61.019 12.911 2.072 2.815 2.197 H5 UD0 60
UD0 "HO1'" "HO1'" H 0 0 N N N N N N -17.659 -65.442 17.727 6.994 -0.312 -0.783 "HO1'" UD0 61
UD0 "H1'" H1* H 0 1 N N N N N N -12.877 -65.071 4.544 -6.656 -0.457 -1.503 H1* UD0 62
UD0 H1A H1A H 0 1 N N N N N N -19.603 -66.330 21.692 8.964 -2.757 -1.436 H1A UD0 63
UD0 H1AA H1AA H 0 0 N N N N N N -19.975 -66.924 20.039 8.993 -2.093 0.215 H1AA UD0 64
UD0 H1AB H1AB H 0 0 N N N N N N -18.267 -66.715 20.555 9.198 -3.842 -0.044 H1AB UD0 65
UD0 "H2'" H2* H 0 1 N N N N N N -14.313 -67.025 4.960 -8.679 0.152 -0.360 H2* UD0 66
UD0 "HO2'" HO2* H 0 0 N N N N N N -12.618 -67.123 3.012 -8.683 0.399 2.016 HO2* UD0 67
UD0 HN2A HN2A H 0 0 N N N N N N -15.840 -65.679 13.767 2.762 0.876 -1.782 HN2A UD0 68
UD0 H2B H2B H 0 1 N N N N N N -16.424 -68.292 16.042 3.915 1.967 -5.088 H2B UD0 69
UD0 H2BA H2BA H 0 0 N N N N N N -17.096 -67.678 14.494 3.720 0.406 -4.256 H2BA UD0 70
UD0 H2BB H2BB H 0 0 N N N N N N -15.328 -67.945 14.662 2.349 1.535 -4.362 H2BB UD0 71
UD0 "H3'" H3* H 0 1 N N N N N N -13.443 -68.852 6.318 -7.499 2.179 -0.902 H3* UD0 72
UD0 "HO3'" HO3* H 0 0 N N N N N N -11.261 -69.480 6.187 -8.810 2.647 1.080 HO3* UD0 73
UD0 "H4'" "H4'" H 0 1 N N N N N N -19.286 -62.409 16.397 3.018 -1.261 0.324 "H4'" UD0 74
UD0 "H4'A" H4* H 0 0 N N N N N N -11.175 -67.374 7.367 -5.488 1.868 1.317 H4* UD0 75
UD0 HO4A HO4A H 0 0 N N N N N N -18.584 -60.551 15.087 4.025 1.362 3.884 HO4A UD0 76
UD0 "H5'" H5* H 0 1 N N N N N N -14.043 -67.793 8.067 -5.193 2.266 -1.696 H5* UD0 77
UD0 "H5'A" H5*A H 0 0 N N N N N N -12.547 -68.038 9.038 -5.367 3.592 -0.522 H5*A UD0 78
UD0 "H6'" "H6'" H 0 1 N N N N N N -20.023 -61.857 21.270 5.018 -5.573 -0.442 "H6'" UD0 79
UD0 HO6B HO6B H 0 0 N N N N N N -15.814 -58.265 15.429 3.601 3.733 5.376 HO6B UD0 80
UD0 "H7'" "H7'" H 0 1 N N N N N N -19.827 -60.207 19.805 2.655 -3.490 0.951 "H7'" UD0 81
UD0 "H7'A" "H7'A" H 0 0 N N N N N N -18.455 -60.389 18.654 2.503 -3.248 -0.806 "H7'A" UD0 82
UD0 HOA2 HOA2 H 0 0 N N N N N N -16.663 -65.344 9.728 0.086 4.971 1.348 HOA2 UD0 83
UD0 HAT HAT H 0 1 N N N N N N -7.720 -65.738 5.346 -6.156 -3.501 2.954 HAT UD0 84
UD0 HAU HAU H 0 1 N N N N N N -9.974 -65.858 6.334 -6.223 -1.214 2.107 HAU UD0 85
UD0 HOB2 HOB2 H 0 0 N N N N N N -10.819 -66.333 11.075 -2.262 1.968 -2.863 HOB2 UD0 86
UD0 HOP1 HOP1 H 0 0 N N N N N N -18.781 -57.783 17.315 0.553 -7.874 -0.514 HOP1 UD0 87
UD0 HOP3 HOP3 H 0 0 N N N N N N -21.325 -59.065 15.181 1.200 -6.096 2.013 HOP3 UD0 88
UD0 HNBB HNBB H 0 0 N N N N N N -9.452 -65.632 1.492 -6.730 -4.862 -0.945 HNBB UD0 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
UD0 OP2 P DOUB N N 1
UD0 OP3 P SING N N 2
UD0 P OP1 SING N N 3
UD0 P OP4 SING N N 4
UD0 OA1 C1 SING N N 5
UD0 O1 C1 SING N N 6
UD0 C1 C2 SING N N 7
UD0 C1 H1 SING N N 8
UD0 "C1'" N1 DOUB Y N 9
UD0 "C6'" N1 SING Y N 10
UD0 O1 C5 SING N N 11
UD0 N2A C2 SING N N 12
UD0 C2 C3 SING N N 13
UD0 C2 H2 SING N N 14
UD0 C4 C3 SING N N 15
UD0 C3 N3A SING N N 16
UD0 C3 H3 SING N N 17
UD0 C5 C4 SING N N 18
UD0 O4A C4 SING N N 19
UD0 C4 H4 SING N N 20
UD0 C5 C6 SING N N 21
UD0 C5 H5 SING N N 22
UD0 O6A C6 DOUB N N 23
UD0 C6 O6B SING N N 24
UD0 OA3 PA DOUB N N 25
UD0 OA2 PA SING N N 26
UD0 PA OB4 SING N N 27
UD0 PA OA1 SING N N 28
UD0 "O5'" PB SING N N 29
UD0 OB1 PB DOUB N N 30
UD0 PB OB2 SING N N 31
UD0 PB OB4 SING N N 32
UD0 "C2'" "C1'" SING Y N 33
UD0 "C1'" C1A SING N N 34
UD0 "O1'" "C2'" SING N N 35
UD0 "O1'" "HO1'" SING N N 36
UD0 NBZ "C1'A" SING N N 37
UD0 "C2'A" "C1'A" SING N N 38
UD0 "C1'A" "O4'" SING N N 39
UD0 "C1'A" "H1'" SING N N 40
UD0 C1A H1A SING N N 41
UD0 C1A H1AA SING N N 42
UD0 C1A H1AB SING N N 43
UD0 "C3'" "C2'" DOUB Y N 44
UD0 "O2'" "C2'A" SING N N 45
UD0 "C2'A" "C3'A" SING N N 46
UD0 "C2'A" "H2'" SING N N 47
UD0 "O2'" "HO2'" SING N N 48
UD0 N2A C2A SING N N 49
UD0 C2B C2A SING N N 50
UD0 C2A O2A DOUB N N 51
UD0 N2A HN2A SING N N 52
UD0 C2B H2B SING N N 53
UD0 C2B H2BA SING N N 54
UD0 C2B H2BB SING N N 55
UD0 "C4'" "C3'" SING N N 56
UD0 "C3'" "C5'" SING Y N 57
UD0 "O3'" "C3'A" SING N N 58
UD0 "C3'A" "C4'A" SING N N 59
UD0 "C3'A" "H3'" SING N N 60
UD0 "O3'" "HO3'" SING N N 61
UD0 N3A "C4'" DOUB N N 62
UD0 "C4'" "H4'" SING N N 63
UD0 "O4'" "C4'A" SING N N 64
UD0 "C4'A" "C5'A" SING N N 65
UD0 "C4'A" "H4'A" SING N N 66
UD0 O4A HO4A SING N N 67
UD0 "C7'" "C5'" SING N N 68
UD0 "C5'" "C6'" DOUB Y N 69
UD0 "C5'A" "O5'" SING N N 70
UD0 "C5'A" "H5'" SING N N 71
UD0 "C5'A" "H5'A" SING N N 72
UD0 "C6'" "H6'" SING N N 73
UD0 O6B HO6B SING N N 74
UD0 OP4 "C7'" SING N N 75
UD0 "C7'" "H7'" SING N N 76
UD0 "C7'" "H7'A" SING N N 77
UD0 OA2 HOA2 SING N N 78
UD0 OAE CBO DOUB N N 79
UD0 OAF CBP DOUB N N 80
UD0 CBO CAT SING N N 81
UD0 CAT CAU DOUB N N 82
UD0 CAT HAT SING N N 83
UD0 NBZ CAU SING N N 84
UD0 CAU HAU SING N N 85
UD0 OB2 HOB2 SING N N 86
UD0 NBB CBP SING N N 87
UD0 NBB CBO SING N N 88
UD0 CBP NBZ SING N N 89
UD0 OP1 HOP1 SING N N 90
UD0 OP3 HOP3 SING N N 91
UD0 NBB HNBB 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
UD0 SMILES ACDLabs 12.01 O=C1C=CN(C(=O)N1)C2OC(C(O)C2O)COP(=O)(OP(=O)(OC4OC(C(=O)O)C(O)C(/N=C/c3c(cnc(c3O)C)COP(=O)(O)O)C4NC(=O)C)O)O
UD0 SMILES_CANONICAL CACTVS 3.370 CC(=O)N[C@H]1[C@H](O[C@@H]([C@@H](O)[C@@H]1N=Cc2c(O)c(C)ncc2CO[P](O)(O)=O)C(O)=O)O[P](O)(=O)O[P](O)(=O)OC[C@@H]3O[C@H]([C@@H](O)[C@H]3O)N4C=CC(=O)NC4=O
UD0 SMILES CACTVS 3.370 CC(=O)N[CH]1[CH](O[CH]([CH](O)[CH]1N=Cc2c(O)c(C)ncc2CO[P](O)(O)=O)C(O)=O)O[P](O)(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O)[CH]3O)N4C=CC(=O)NC4=O
UD0 SMILES_CANONICAL "OpenEye OEToolkits" 1.7.0 Cc1c(c(c(cn1)COP(=O)(O)O)/C=N/[C@@H]2[C@H]([C@H](O[C@@H]([C@H]2O)C(=O)O)O[P@](=O)(O)O[P@@](=O)(O)OC[C@H]3[C@@H]([C@@H]([C@@H](O3)N4C=CC(=O)NC4=O)O)O)NC(=O)C)O
UD0 SMILES "OpenEye OEToolkits" 1.7.0 Cc1c(c(c(cn1)COP(=O)(O)O)C=NC2C(C(OC(C2O)C(=O)O)OP(=O)(O)OP(=O)(O)OCC3C(C(C(O3)N4C=CC(=O)NC4=O)O)O)NC(=O)C)O
UD0 InChI InChI 1.03 InChI=1S/C25H34N5O22P3/c1-9-17(33)12(11(5-26-9)7-47-53(40,41)42)6-27-15-16(28-10(2)31)24(50-21(19(15)35)23(37)38)51-55(45,46)52-54(43,44)48-8-13-18(34)20(36)22(49-13)30-4-3-14(32)29-25(30)39/h3-6,13,15-16,18-22,24,33-36H,7-8H2,1-2H3,(H,28,31)(H,37,38)(H,43,44)(H,45,46)(H,29,32,39)(H2,40,41,42)/b27-6+/t13-,15+,16+,18-,19-,20-,21-,22+,24+/m0/s1
UD0 InChIKey InChI 1.03 IGKBPIFLZAFLLV-VUZHIUKYSA-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
UD0 "SYSTEMATIC NAME" ACDLabs 12.01 "(2S,3S,4R,5R,6R)-5-(acetylamino)-6-{[(S)-{[(S)-{[(2S,3R,4S,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}-3-hydroxy-4-{[(E)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]amino}tetrahydro-2H-pyran-2-carboxylic acid"
UD0 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.0 "(2S,3S,4R,5R,6R)-5-acetamido-6-[[[(2S,3R,4S,5R)-5-(2,4-dioxopyrimidin-1-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl]oxy-hydroxy-phosphoryl]oxy-3-hydroxy-4-[(E)-[3-hydroxy-2-methyl-5-(phosphonooxymethyl)pyridin-4-yl]methylideneamino]oxane-2-carboxylic 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
UD0 'Create component' 2010-07-13 RCSB
UD0 'Modify aromatic_flag' 2011-06-04 RCSB
UD0 'Modify descriptor' 2011-06-04 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
UD0 P P -1.968 -8.057 1
UD0 C1 C 0.643 -2.061 2
UD0 N1 N 3.223 -11.066 3
UD0 O1 O 1.942 -1.315 4
UD0 C2 C 0.637 -3.562 5
UD0 C3 C 1.937 -4.313 6
UD0 C4 C 3.236 -3.567 7
UD0 C5 C 3.242 -2.066 8
UD0 C6 C 4.541 -1.320 9
UD0 PA P -0.499 0.289 10
UD0 PB P -0.536 3.138 11
UD0 "C1'" C 4.522 -10.320 12
UD0 "O1'" O 5.827 -8.072 13
UD0 "C1'A" C -2.681 9.254 14
UD0 C1A C 5.821 -11.072 15
UD0 "C2'" C 4.527 -8.819 16
UD0 "C2'A" C -1.185 9.247 17
UD0 "O2'" O -0.296 10.457 18
UD0 C2A C -1.959 -3.556 19
UD0 N2A N -0.662 -4.309 20
UD0 O2A O -1.957 -2.056 21
UD0 C2B C -3.260 -4.304 22
UD0 "C3'" C 3.228 -8.068 23
UD0 "C3'A" C -0.724 7.816 24
UD0 "O3'" O 0.699 7.346 25
UD0 N3A N 1.933 -5.815 26
UD0 "C4'" C 3.231 -6.567 27
UD0 "C4'A" C -1.944 6.945 28
UD0 "O4'" O -3.154 7.831 29
UD0 O4A O 4.535 -4.320 30
UD0 "C5'" C 1.929 -8.814 31
UD0 "C5'A" C -2.008 5.390 32
UD0 "O5'" O -0.755 4.662 33
UD0 "C6'" C 1.923 -10.315 34
UD0 O6A O 5.839 -2.072 35
UD0 O6B O 4.544 0.180 36
UD0 "C7'" C 0.630 -8.062 37
UD0 OA1 O -0.713 -1.212 38
UD0 OA2 O -1.975 0.656 39
UD0 OA3 O 0.932 -0.086 40
UD0 OAE O -6.200 14.113 41
UD0 OAF O -1.457 11.990 42
UD0 CAT C -5.936 11.531 43
UD0 CAU C -5.054 10.312 44
UD0 OB1 O 0.888 3.527 45
UD0 OB2 O -2.009 2.745 46
UD0 OB4 O 0.055 1.716 47
UD0 NBB N -3.830 13.054 48
UD0 CBO C -5.320 12.896 49
UD0 CBP C -2.948 11.836 50
UD0 NBZ N -3.563 10.469 51
UD0 OP1 O -1.215 -6.760 52
UD0 OP2 O -3.266 -7.304 53
UD0 OP3 O -2.721 -9.355 54
UD0 OP4 O -0.671 -8.810 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
UD0 OP2 P DOUBLE NONE 1
UD0 OP3 P SINGLE NONE 2
UD0 P OP1 SINGLE NONE 3
UD0 P OP4 SINGLE NONE 4
UD0 C1 OA1 SINGLE BEGINWEDGE 5
UD0 O1 C1 SINGLE NONE 6
UD0 C1 C2 SINGLE NONE 7
UD0 "C1'" N1 DOUBLE NONE 8
UD0 "C6'" N1 SINGLE NONE 9
UD0 O1 C5 SINGLE NONE 10
UD0 C2 N2A SINGLE BEGINWEDGE 11
UD0 C2 C3 SINGLE NONE 12
UD0 C4 C3 SINGLE NONE 13
UD0 C3 N3A SINGLE BEGINDASH 14
UD0 C5 C4 SINGLE NONE 15
UD0 C4 O4A SINGLE BEGINWEDGE 16
UD0 C5 C6 SINGLE BEGINDASH 17
UD0 O6A C6 DOUBLE NONE 18
UD0 C6 O6B SINGLE NONE 19
UD0 OA3 PA DOUBLE NONE 20
UD0 PA OA2 SINGLE BEGINWEDGE 21
UD0 PA OB4 SINGLE NONE 22
UD0 PA OA1 SINGLE NONE 23
UD0 "O5'" PB SINGLE NONE 24
UD0 OB1 PB DOUBLE NONE 25
UD0 PB OB2 SINGLE BEGINDASH 26
UD0 PB OB4 SINGLE NONE 27
UD0 "C2'" "C1'" SINGLE NONE 28
UD0 "C1'" C1A SINGLE NONE 29
UD0 "O1'" "C2'" SINGLE NONE 30
UD0 "C1'A" NBZ SINGLE BEGINWEDGE 31
UD0 "C2'A" "C1'A" SINGLE NONE 32
UD0 "C1'A" "O4'" SINGLE NONE 33
UD0 "C3'" "C2'" DOUBLE NONE 34
UD0 "C2'A" "O2'" SINGLE BEGINWEDGE 35
UD0 "C2'A" "C3'A" SINGLE NONE 36
UD0 N2A C2A SINGLE NONE 37
UD0 C2B C2A SINGLE NONE 38
UD0 C2A O2A DOUBLE NONE 39
UD0 "C4'" "C3'" SINGLE ENDUPRIGHT 40
UD0 "C3'" "C5'" SINGLE NONE 41
UD0 "C3'A" "O3'" SINGLE BEGINWEDGE 42
UD0 "C3'A" "C4'A" SINGLE NONE 43
UD0 N3A "C4'" DOUBLE NONE 44
UD0 "O4'" "C4'A" SINGLE NONE 45
UD0 "C4'A" "C5'A" SINGLE BEGINDASH 46
UD0 "C7'" "C5'" SINGLE NONE 47
UD0 "C5'" "C6'" DOUBLE NONE 48
UD0 "C5'A" "O5'" SINGLE NONE 49
UD0 OP4 "C7'" SINGLE NONE 50
UD0 OAE CBO DOUBLE NONE 51
UD0 OAF CBP DOUBLE NONE 52
UD0 CBO CAT SINGLE NONE 53
UD0 CAT CAU DOUBLE NONE 54
UD0 NBZ CAU SINGLE NONE 55
UD0 NBB CBP SINGLE NONE 56
UD0 NBB CBO SINGLE NONE 57
UD0 CBP NBZ SINGLE NONE 58
#
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
UD0 MurckoScaffold S1 scaffold 'O=c1ccn([C@H]2CC[C@H](CO[PH](=O)O[PH](=O)O[C@@H]3C[C@@H](/N=C/c4ccncc4)CCO3)O2)c(=O)[nH]1' InChI=1S/C20H26N4O9P2/c25-17-5-9-24(20(26)23-17)18-2-1-16(31-18)13-30-34(27)33-35(28)32-19-11-15(6-10-29-19)22-12-14-3-7-21-8-4-14/h3-5,7-9,12,15-16,18-19,34-35H,1-2,6,10-11,13H2,(H,23,25,26)/b22-12+/t15-,16+,18+,19+/m0/s1 OBXAHNLFXPFEOH-SHGQFXBPSA-N
UD0 amide F1 fragment CC(N)=O InChI=1S/C2H5NO/c1-2(3)4/h1H3,(H2,3,4) DLFVBJFMPXGRIB-UHFFFAOYSA-N
UD0 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
UD0 pyranose F3 fragment OC1CCCCO1 InChI=1S/C5H10O2/c6-5-3-1-2-4-7-5/h5-6H,1-4H2 CELWCAITJAEQNL-UHFFFAOYSA-N
UD0 pyridine F4 fragment c1ccncc1 InChI=1S/C5H5N/c1-2-4-6-5-3-1/h1-5H JUJWROOIHBZHMG-UHFFFAOYSA-N
UD0 pyrimidine F5 fragment c1cncnc1 InChI=1S/C4H4N2/c1-2-5-4-6-3-1/h1-4H CZPWVGJYEJSRLH-UHFFFAOYSA-N
UD0 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
UD0 C1 S1 1
UD0 N1 S1 1
UD0 O1 S1 1
UD0 C2 S1 1
UD0 C3 S1 1
UD0 C4 S1 1
UD0 C5 S1 1
UD0 PA S1 1
UD0 PB S1 1
UD0 "C1'" S1 1
UD0 "C1'A" S1 1
UD0 "C2'" S1 1
UD0 "C2'A" S1 1
UD0 "C3'" S1 1
UD0 "C3'A" S1 1
UD0 N3A S1 1
UD0 "C4'" S1 1
UD0 "C4'A" S1 1
UD0 "O4'" S1 1
UD0 "C5'" S1 1
UD0 "C5'A" S1 1
UD0 "O5'" S1 1
UD0 "C6'" S1 1
UD0 OA1 S1 1
UD0 OA3 S1 1
UD0 OAE S1 1
UD0 OAF S1 1
UD0 CAT S1 1
UD0 CAU S1 1
UD0 OB1 S1 1
UD0 OB4 S1 1
UD0 NBB S1 1
UD0 CBO S1 1
UD0 CBP S1 1
UD0 NBZ S1 1
UD0 N2A F1 1
UD0 C2A F1 1
UD0 O2A F1 1
UD0 C2B F1 1
UD0 "O5'" F2 1
UD0 PB F2 1
UD0 OB1 F2 1
UD0 OB2 F2 1
UD0 OB4 F2 1
UD0 OA1 F2 2
UD0 PA F2 2
UD0 OA3 F2 2
UD0 OA2 F2 2
UD0 OB4 F2 2
UD0 OP1 F2 3
UD0 P F2 3
UD0 OP2 F2 3
UD0 OP3 F2 3
UD0 OP4 F2 3
UD0 C4 F3 1
UD0 C5 F3 1
UD0 O1 F3 1
UD0 C1 F3 1
UD0 C2 F3 1
UD0 C3 F3 1
UD0 OA1 F3 1
UD0 "C1'" F4 1
UD0 "C2'" F4 1
UD0 "C3'" F4 1
UD0 "C5'" F4 1
UD0 "C6'" F4 1
UD0 N1 F4 1
UD0 CAT F5 1
UD0 CBO F5 1
UD0 NBB F5 1
UD0 CBP F5 1
UD0 NBZ F5 1
UD0 CAU F5 1
UD0 "C2'A" F6 1
UD0 "C3'A" F6 1
UD0 "C4'A" F6 1
UD0 "O4'" F6 1
UD0 "C1'A" F6 1
UD0 "C5'A" F6 1
UD0 "O5'" F6 1
UD0 "O3'" F6 1
UD0 "O2'" F6 1
#
_pdbe_chem_comp_rdkit_properties.comp_id UD0
_pdbe_chem_comp_rdkit_properties.exactmw 849.091
_pdbe_chem_comp_rdkit_properties.amw 849.482
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 27
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 11
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 25
_pdbe_chem_comp_rdkit_properties.NumHBD 11
_pdbe_chem_comp_rdkit_properties.NumHBA 25
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 55
_pdbe_chem_comp_rdkit_properties.NumAtoms 89
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 30
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 1
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.520
_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 354.419
_pdbe_chem_comp_rdkit_properties.tpsa 414.940
_pdbe_chem_comp_rdkit_properties.CrippenClogP -2.239
_pdbe_chem_comp_rdkit_properties.CrippenMR 172.589
_pdbe_chem_comp_rdkit_properties.chi0v 27.742
_pdbe_chem_comp_rdkit_properties.chi1v 17.048
_pdbe_chem_comp_rdkit_properties.chi2v 7.879
_pdbe_chem_comp_rdkit_properties.chi3v 7.879
_pdbe_chem_comp_rdkit_properties.chi4v 5.227
_pdbe_chem_comp_rdkit_properties.chi0n 59.059
_pdbe_chem_comp_rdkit_properties.chi1n 28.735
_pdbe_chem_comp_rdkit_properties.chi2n 5.260
_pdbe_chem_comp_rdkit_properties.chi3n 5.260
_pdbe_chem_comp_rdkit_properties.chi4n 3.256
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -3.590
_pdbe_chem_comp_rdkit_properties.kappa1 16.714
_pdbe_chem_comp_rdkit_properties.kappa2 17.273
_pdbe_chem_comp_rdkit_properties.kappa3 11.264
_pdbe_chem_comp_rdkit_properties.Phi 5.249
#
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
UD0 UniChem PDBe UD0
UD0 UniChem ZINC ZINC000263620550
#
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
UD0 P -5.574 0.375 -4.541 ETKDGv3 1
UD0 C1 -0.671 1.046 1.339 ETKDGv3 2
UD0 N1 -8.619 -1.335 -1.194 ETKDGv3 3
UD0 O1 -0.822 2.199 2.148 ETKDGv3 4
UD0 C2 -1.827 0.975 0.304 ETKDGv3 5
UD0 C3 -3.162 1.489 0.901 ETKDGv3 6
UD0 C4 -3.155 1.335 2.437 ETKDGv3 7
UD0 C5 -1.934 2.098 3.035 ETKDGv3 8
UD0 C6 -1.513 1.513 4.356 ETKDGv3 9
UD0 PA 1.352 -0.378 0.638 ETKDGv3 10
UD0 PB 2.646 -2.261 2.183 ETKDGv3 11
UD0 "C1'" -8.875 -0.488 -0.240 ETKDGv3 12
UD0 "O1'" -8.035 1.292 1.314 ETKDGv3 13
UD0 "C1'A" 6.907 -0.549 0.789 ETKDGv3 14
UD0 C1A -10.243 -0.471 0.368 ETKDGv3 15
UD0 "C2'" -7.799 0.415 0.251 ETKDGv3 16
UD0 "C2'A" 6.323 -0.933 -0.578 ETKDGv3 17
UD0 "O2'" 7.115 -0.475 -1.647 ETKDGv3 18
UD0 C2A -1.498 1.212 -2.219 ETKDGv3 19
UD0 N2A -1.496 1.758 -0.893 ETKDGv3 20
UD0 O2A -1.758 -0.006 -2.414 ETKDGv3 21
UD0 C2B -1.177 2.091 -3.383 ETKDGv3 22
UD0 "C3'" -6.576 0.360 -0.318 ETKDGv3 23
UD0 "C3'A" 6.236 -2.444 -0.534 ETKDGv3 24
UD0 "O3'" 7.303 -3.023 -1.242 ETKDGv3 25
UD0 N3A -4.273 0.740 0.311 ETKDGv3 26
UD0 "C4'" -5.487 1.192 0.243 ETKDGv3 27
UD0 "C4'A" 6.358 -2.762 0.958 ETKDGv3 28
UD0 "O4'" 7.009 -1.694 1.609 ETKDGv3 29
UD0 O4A -4.358 1.786 3.010 ETKDGv3 30
UD0 "C5'" -6.346 -0.568 -1.476 ETKDGv3 31
UD0 "C5'A" 4.998 -3.032 1.620 ETKDGv3 32
UD0 "O5'" 4.178 -1.890 1.525 ETKDGv3 33
UD0 "C6'" -7.337 -1.406 -1.831 ETKDGv3 34
UD0 O6A -2.282 1.597 5.352 ETKDGv3 35
UD0 O6B -0.285 0.870 4.486 ETKDGv3 36
UD0 "C7'" -5.031 -0.587 -2.234 ETKDGv3 37
UD0 OA1 0.575 1.142 0.673 ETKDGv3 38
UD0 OA2 0.340 -1.513 -0.107 ETKDGv3 39
UD0 OA3 2.630 -0.239 -0.161 ETKDGv3 40
UD0 OAE 11.755 2.140 0.210 ETKDGv3 41
UD0 OAF 9.437 -1.885 0.434 ETKDGv3 42
UD0 CAT 9.409 2.228 0.508 ETKDGv3 43
UD0 CAU 8.261 1.560 0.657 ETKDGv3 44
UD0 OB1 2.811 -2.766 3.599 ETKDGv3 45
UD0 OB2 1.882 -3.465 1.266 ETKDGv3 46
UD0 OB4 1.694 -0.851 2.239 ETKDGv3 47
UD0 NBB 10.676 0.077 0.324 ETKDGv3 48
UD0 CBO 10.675 1.505 0.341 ETKDGv3 49
UD0 CBP 9.442 -0.626 0.476 ETKDGv3 50
UD0 NBZ 8.218 0.117 0.672 ETKDGv3 51
UD0 OP1 -5.867 -0.138 -6.126 ETKDGv3 52
UD0 OP2 -6.807 1.071 -4.010 ETKDGv3 53
UD0 OP3 -4.271 1.455 -4.544 ETKDGv3 54
UD0 OP4 -5.196 -0.987 -3.580 ETKDGv3 55
UD0 H1 -0.733 0.141 1.996 ETKDGv3 56
UD0 H2 -1.946 -0.099 0.036 ETKDGv3 57
UD0 H3 -3.274 2.572 0.657 ETKDGv3 58
UD0 H4 -3.062 0.250 2.667 ETKDGv3 59
UD0 H5 -2.252 3.144 3.240 ETKDGv3 60
UD0 "HO1'" -8.931 1.357 1.780 ETKDGv3 61
UD0 "H1'" 6.192 0.143 1.290 ETKDGv3 62
UD0 H1A -10.682 0.544 0.277 ETKDGv3 63
UD0 H1AA -10.180 -0.756 1.440 ETKDGv3 64
UD0 H1AB -10.914 -1.191 -0.148 ETKDGv3 65
UD0 "H2'" 5.298 -0.504 -0.663 ETKDGv3 66
UD0 "HO2'" 6.575 -0.598 -2.471 ETKDGv3 67
UD0 HN2A -1.279 2.774 -0.775 ETKDGv3 68
UD0 H2B -0.138 2.470 -3.285 ETKDGv3 69
UD0 H2BA -1.267 1.528 -4.336 ETKDGv3 70
UD0 H2BB -1.880 2.949 -3.405 ETKDGv3 71
UD0 "H3'" 5.265 -2.784 -0.966 ETKDGv3 72
UD0 "HO3'" 7.075 -3.982 -1.363 ETKDGv3 73
UD0 "H4'" -5.726 2.159 0.669 ETKDGv3 74
UD0 "H4'A" 6.976 -3.678 1.094 ETKDGv3 75
UD0 HO4A -4.473 2.741 2.763 ETKDGv3 76
UD0 "H5'" 5.184 -3.288 2.687 ETKDGv3 77
UD0 "H5'A" 4.533 -3.909 1.115 ETKDGv3 78
UD0 "H6'" -7.202 -2.120 -2.633 ETKDGv3 79
UD0 HO6B 0.001 0.469 5.371 ETKDGv3 80
UD0 "H7'" -4.371 -1.328 -1.737 ETKDGv3 81
UD0 "H7'A" -4.506 0.390 -2.160 ETKDGv3 82
UD0 HOA2 0.313 -1.242 -1.059 ETKDGv3 83
UD0 HAT 9.404 3.311 0.505 ETKDGv3 84
UD0 HAU 7.345 2.128 0.768 ETKDGv3 85
UD0 HOB2 2.248 -3.364 0.351 ETKDGv3 86
UD0 HOP1 -6.577 -0.823 -6.042 ETKDGv3 87
UD0 HOP3 -4.543 2.179 -5.162 ETKDGv3 88
UD0 HNBB 11.570 -0.448 0.195 ETKDGv3 89
#