data_SAD
#
_chem_comp.id SAD
_chem_comp.name "BETA-METHYLENE-SELENAZOLE-4-CARBOXYAMIDE-ADENINE DINUCLEOTIDE"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C20 H27 N7 O13 P2 Se"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 1999-07-08
_chem_comp.pdbx_modified_date 2011-06-04
_chem_comp.pdbx_ambiguous_flag N
_chem_comp.pdbx_release_status REL
_chem_comp.pdbx_replaced_by ?
_chem_comp.pdbx_replaces ?
_chem_comp.formula_weight 714.375
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code SAD
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag N
_chem_comp.pdbx_ideal_coordinates_details ?
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code 1ADG
_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
SAD PA AP P 0 1 N N R N N N 13.580 7.325 27.436 0.162 1.549 -1.759 PA SAD 1
SAD O1A AO1 O 0 1 N N N N N N 13.055 5.924 27.284 -1.110 2.124 -2.247 O1A SAD 2
SAD O2A AO2 O 0 1 N N N N N N 14.986 7.668 27.012 1.131 2.734 -1.260 O2A SAD 3
SAD O5B AO5* O 0 1 N N N N N N 13.292 7.734 28.978 0.877 0.739 -2.953 O5B SAD 4
SAD C5B AC5* C 0 1 N N N N N N 13.610 6.804 30.038 1.115 1.677 -4.004 C5B SAD 5
SAD C4B AC4* C 0 1 N N R N N N 14.996 7.119 30.622 1.797 0.967 -5.176 C4B SAD 6
SAD O4B AO4* O 0 1 N N N N N N 15.157 6.409 31.849 0.937 -0.063 -5.690 O4B SAD 7
SAD C3B AC3* C 0 1 N N R N N N 16.180 6.679 29.755 2.050 1.969 -6.319 C3B SAD 8
SAD O3B AO3* O 0 1 N N N N N N 17.100 7.778 29.593 3.446 2.066 -6.608 O3B SAD 9
SAD C2B AC2* C 0 1 N N S N N N 16.649 5.339 30.371 1.287 1.363 -7.527 C2B SAD 10
SAD O2B AO2* O 0 1 N N N N N N 18.022 5.037 30.105 2.048 1.497 -8.729 O2B SAD 11
SAD C1B AC1* C 0 1 N N R N N N 16.360 5.611 31.829 1.159 -0.125 -7.116 C1B SAD 12
SAD N9A AN9 N 0 1 Y N N N N N 16.260 4.476 32.796 0.019 -0.752 -7.788 N9A SAD 13
SAD C8A AC8 C 0 1 Y N N N N N 15.689 3.261 32.631 -1.276 -0.738 -7.363 C8A SAD 14
SAD N7A AN7 N 0 1 Y N N N N N 15.645 2.596 33.798 -2.026 -1.393 -8.201 N7A SAD 15
SAD C5A AC5 C 0 1 Y N N N N N 16.242 3.420 34.665 -1.262 -1.867 -9.215 C5A SAD 16
SAD C6A AC6 C 0 1 Y N N N N N 16.259 3.240 36.047 -1.514 -2.622 -10.373 C6A SAD 17
SAD N6A AN6 N 0 1 N N N N N N 15.850 2.127 36.656 -2.796 -3.049 -10.674 N6A SAD 18
SAD N1A AN1 N 0 1 Y N N N N N 16.765 4.281 36.734 -0.494 -2.917 -11.172 N1A SAD 19
SAD C2A AC2 C 0 1 Y N N N N N 17.230 5.387 36.147 0.731 -2.513 -10.892 C2A SAD 20
SAD N3A AN3 N 0 1 Y N N N N N 17.215 5.541 34.834 1.014 -1.804 -9.819 N3A SAD 21
SAD C4A AC4 C 0 1 Y N N N N N 16.685 4.574 34.063 0.058 -1.457 -8.965 C4A SAD 22
SAD C3 C3 C 0 1 N N N N N N 12.676 8.539 26.470 -0.174 0.415 -0.372 C3 SAD 23
SAD PN NP P 0 1 N N S N N N 12.143 10.049 27.299 -0.984 1.333 0.978 PN SAD 24
SAD O1N NO1 O 0 1 N N N N N N 12.158 11.076 26.224 -2.257 1.908 0.490 O1N SAD 25
SAD O2N NO2 O 0 1 N N N N N N 12.863 10.397 28.581 -0.016 2.518 1.478 O2N SAD 26
SAD O5D NO5* O 0 1 N N N N N N 10.603 9.752 27.642 -1.282 0.331 2.203 O5D SAD 27
SAD C5D NC5* C 0 1 N N N N N N 9.940 8.607 27.071 -1.914 1.106 3.225 C5D SAD 28
SAD C4D NC4* C 0 1 N N R N N N 10.147 7.379 27.968 -2.226 0.209 4.425 C4D SAD 29
SAD O4D NO4* O 0 1 N N N N N N 9.625 7.765 29.234 -1.007 -0.338 4.974 O4D SAD 30
SAD C3D NC3* C 0 1 N N S N N N 9.258 6.336 27.351 -2.839 1.039 5.575 C3D SAD 31
SAD O3D NO3* O 0 1 N N N N N N 10.073 5.457 26.546 -4.263 0.922 5.572 O3D SAD 32
SAD C2D NC2* C 0 1 N N S N N N 8.663 5.692 28.592 -2.244 0.406 6.854 C2D SAD 33
SAD O2D NO2* O 0 1 N N N N N N 9.517 4.676 29.132 -3.283 -0.119 7.683 O2D SAD 34
SAD C1D NC1* C 0 1 N N R N N N 8.538 6.883 29.550 -1.340 -0.728 6.324 C1D SAD 35
SAD C2N NC2 C 0 1 Y N N N N N 7.385 7.821 29.499 -0.092 -0.839 7.161 C2N SAD 36
SAD N3N NN3 N 0 1 Y N N N N N 6.140 7.439 29.182 0.405 -1.844 7.851 N3N SAD 37
SAD C4N NC4 C 0 1 Y N N N N N 5.415 8.559 29.206 1.531 -1.851 8.577 C4N SAD 38
SAD C5N NC5 C 0 1 Y N N N N N 6.077 9.719 29.446 2.379 -0.781 8.712 C5N SAD 39
SAD SE1N NSE1 SE 0 0 Y N N N N N 7.737 9.523 29.822 1.341 0.486 7.572 SE1N SAD 40
SAD C6N NC6 C 0 1 N N N N N N 3.952 8.461 29.001 1.888 -3.103 9.277 C6N SAD 41
SAD O6N NO6 O 0 1 N N N N N N 3.188 9.441 29.054 1.167 -4.077 9.186 O6N SAD 42
SAD N6N NN6 N 0 1 N N N N N N 3.574 7.213 28.767 3.013 -3.164 10.016 N6N SAD 43
SAD HOA2 2HOA H 0 0 N N N N N N 15.317 8.553 27.108 1.947 2.317 -0.951 HOA2 SAD 44
SAD H51A AH51 H 0 0 N N N N N N 12.820 6.784 30.825 0.166 2.098 -4.337 H51A SAD 45
SAD H52A AH52 H 0 0 N N N N N N 13.531 5.744 29.700 1.759 2.476 -3.639 H52A SAD 46
SAD H4B AH4* H 0 1 N N N N N N 15.014 8.229 30.718 2.741 0.533 -4.848 H4B SAD 47
SAD H3B AH3* H 0 1 N N N N N N 17.019 8.367 30.405 1.645 2.948 -6.065 H3B SAD 48
SAD HO3A AHO3 H 0 0 N N N N N N 17.834 7.505 29.055 3.534 2.658 -7.367 HO3A SAD 49
SAD H2B AH2* H 0 1 N N N N N N 18.592 5.786 30.427 0.305 1.822 -7.638 H2B SAD 50
SAD HO2A AHO2 H 0 0 N N N N N N 18.309 4.214 30.483 2.091 2.442 -8.929 HO2A SAD 51
SAD H1B AH1* H 0 1 N N N N N N 17.276 6.110 32.221 2.079 -0.665 -7.338 H1B SAD 52
SAD H8A AH8 H 0 1 N N N N N N 15.310 2.865 31.673 -1.627 -0.256 -6.463 H8A SAD 53
SAD H61A AH61 H 0 0 N N N N N N 15.494 1.370 36.108 -2.957 -3.570 -11.477 H61A SAD 54
SAD H62A AH62 H 0 0 N N N N N N 15.898 2.053 37.656 -3.532 -2.827 -10.084 H62A SAD 55
SAD H2A AH2 H 0 1 N N N N N N 17.640 6.201 36.767 1.531 -2.775 -11.568 H2A SAD 56
SAD H31 1H3 H 0 1 N N N N N N 13.273 8.807 25.567 0.762 -0.008 -0.013 H31 SAD 57
SAD H32 2H3 H 0 1 N N N N N N 11.792 8.048 25.999 -0.830 -0.386 -0.710 H32 SAD 58
SAD HON2 2HON H 0 0 N N N N N N 12.582 11.192 29.017 0.799 2.101 1.786 HON2 SAD 59
SAD H51N NH51 H 0 0 N N N N N N 8.860 8.804 26.875 -2.840 1.531 2.839 H51N SAD 60
SAD H52N NH52 H 0 0 N N N N N N 10.264 8.417 26.021 -1.247 1.910 3.536 H52N SAD 61
SAD H4D NH4* H 0 1 N N N N N N 11.196 7.016 28.069 -2.904 -0.592 4.132 H4D SAD 62
SAD H3D NH3* H 0 1 N N N N N N 8.462 6.689 26.654 -2.542 2.084 5.491 H3D SAD 63
SAD HO3N NHO3 H 0 0 N N N N N N 9.511 4.797 26.156 -4.588 1.458 6.308 HO3N SAD 64
SAD H2D NH2* H 0 1 N N N N N N 9.731 4.933 30.077 -1.652 1.138 7.404 H2D SAD 65
SAD HO2N NHO2 H 0 0 N N N N N N 9.145 4.273 29.907 -2.855 -0.499 8.462 HO2N SAD 66
SAD H1D NH1* H 0 1 N N N N N N 8.466 6.359 30.531 -1.881 -1.675 6.323 H1D SAD 67
SAD HN5 HN5 H 0 1 N N N N N N 5.425 10.604 29.357 3.304 -0.664 9.257 HN5 SAD 68
SAD H61N NH61 H 0 0 N N N N N N 4.295 6.523 28.735 3.247 -3.986 10.476 H61N SAD 69
SAD H62N NH62 H 0 0 N N N N N N 2.601 6.986 28.729 3.591 -2.388 10.086 H62N SAD 70
#
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
SAD PA O1A DOUB N N 1
SAD PA O2A SING N N 2
SAD PA O5B SING N N 3
SAD PA C3 SING N N 4
SAD O2A HOA2 SING N N 5
SAD O5B C5B SING N N 6
SAD C5B C4B SING N N 7
SAD C5B H51A SING N N 8
SAD C5B H52A SING N N 9
SAD C4B O4B SING N N 10
SAD C4B C3B SING N N 11
SAD C4B H4B SING N N 12
SAD O4B C1B SING N N 13
SAD C3B O3B SING N N 14
SAD C3B C2B SING N N 15
SAD C3B H3B SING N N 16
SAD O3B HO3A SING N N 17
SAD C2B O2B SING N N 18
SAD C2B C1B SING N N 19
SAD C2B H2B SING N N 20
SAD O2B HO2A SING N N 21
SAD C1B N9A SING N N 22
SAD C1B H1B SING N N 23
SAD N9A C8A SING Y N 24
SAD N9A C4A SING Y N 25
SAD C8A N7A DOUB Y N 26
SAD C8A H8A SING N N 27
SAD N7A C5A SING Y N 28
SAD C5A C6A SING Y N 29
SAD C5A C4A DOUB Y N 30
SAD C6A N6A SING N N 31
SAD C6A N1A DOUB Y N 32
SAD N6A H61A SING N N 33
SAD N6A H62A SING N N 34
SAD N1A C2A SING Y N 35
SAD C2A N3A DOUB Y N 36
SAD C2A H2A SING N N 37
SAD N3A C4A SING Y N 38
SAD C3 PN SING N N 39
SAD C3 H31 SING N N 40
SAD C3 H32 SING N N 41
SAD PN O1N DOUB N N 42
SAD PN O2N SING N N 43
SAD PN O5D SING N N 44
SAD O2N HON2 SING N N 45
SAD O5D C5D SING N N 46
SAD C5D C4D SING N N 47
SAD C5D H51N SING N N 48
SAD C5D H52N SING N N 49
SAD C4D O4D SING N N 50
SAD C4D C3D SING N N 51
SAD C4D H4D SING N N 52
SAD O4D C1D SING N N 53
SAD C3D O3D SING N N 54
SAD C3D C2D SING N N 55
SAD C3D H3D SING N N 56
SAD O3D HO3N SING N N 57
SAD C2D O2D SING N N 58
SAD C2D C1D SING N N 59
SAD C2D H2D SING N N 60
SAD O2D HO2N SING N N 61
SAD C1D C2N SING N N 62
SAD C1D H1D SING N N 63
SAD C2N N3N DOUB Y N 64
SAD C2N SE1N SING Y N 65
SAD N3N C4N SING Y N 66
SAD C4N C5N DOUB Y N 67
SAD C4N C6N SING N N 68
SAD C5N SE1N SING Y N 69
SAD C5N HN5 SING N N 70
SAD C6N O6N DOUB N N 71
SAD C6N N6N SING N N 72
SAD N6N H61N SING N N 73
SAD N6N H62N SING N N 74
#
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
SAD SMILES ACDLabs 10.04 O=P(O)(OCC3OC(n1c2ncnc(N)c2nc1)C(O)C3O)CP(=O)(O)OCC5OC(c4nc(c[se]4)C(=O)N)C(O)C5O
SAD SMILES_CANONICAL CACTVS 3.341 NC(=O)c1c[se]c(n1)[C@@H]2O[C@H](CO[P@](O)(=O)C[P@](O)(=O)OC[C@H]3O[C@H]([C@@H](O)[C@H]3O)n4cnc5c(N)ncnc45)[C@@H](O)[C@@H]2O
SAD SMILES CACTVS 3.341 NC(=O)c1c[se]c(n1)[CH]2O[CH](CO[P](O)(=O)C[P](O)(=O)OC[CH]3O[CH]([CH](O)[CH]3O)n4cnc5c(N)ncnc45)[CH](O)[CH]2O
SAD SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 c1c(nc([se]1)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@](=O)(C[P@@](=O)(O)OC[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4ncnc5N)O)O)O)O)O)C(=O)N
SAD SMILES "OpenEye OEToolkits" 1.5.0 c1c(nc([se]1)C2C(C(C(O2)COP(=O)(CP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)O)O)O)O)O)C(=O)N
SAD InChI InChI 1.03 InChI=1S/C20H27N7O13P2Se/c21-16-10-18(24-4-23-16)27(5-25-10)20-14(31)12(29)9(40-20)2-38-42(35,36)6-41(33,34)37-1-8-11(28)13(30)15(39-8)19-26-7(3-43-19)17(22)32/h3-5,8-9,11-15,20,28-31H,1-2,6H2,(H2,22,32)(H,33,34)(H,35,36)(H2,21,23,24)/t8-,9-,11-,12+,13+,14+,15-,20-/m1/s1
SAD InChIKey InChI 1.03 BQVYVGJIUMNETO-SFUJTQNPSA-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
SAD "SYSTEMATIC NAME" ACDLabs 10.04 "[(2R,3R,4S,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl [(2R,3S,4S,5R)-5-(4-carbamoyl-1,3-selenazol-2-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl methanediylbis[hydrogen (R,S)-phosphonate] (non-preferred name)"
SAD "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[[(2R,3S,4R,5R)-5-(4-aminocarbonyl-1,3-selenazol-2-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl]methyl-[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy]phosphinic 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
SAD 'Create component' 1999-07-08 RCSB
SAD 'Modify descriptor' 2011-06-04 RCSB
#
loop_
_software.name
_software.version
_software.description
rdkit 2025.03.3 'Core functionality.'
pdbeccdutils 1.0.0 'Wrapper to provide 2D templates and molecular fragments.'
#
loop_
_pdbe_chem_comp_atom_depiction.comp_id
_pdbe_chem_comp_atom_depiction.atom_id
_pdbe_chem_comp_atom_depiction.element
_pdbe_chem_comp_atom_depiction.model_Cartn_x
_pdbe_chem_comp_atom_depiction.model_Cartn_y
_pdbe_chem_comp_atom_depiction.pdbx_ordinal
SAD PA P -1.857 -2.850 1
SAD O1A O -2.667 -4.113 2
SAD O2A O -1.069 -1.593 3
SAD O5B O -3.110 -2.042 4
SAD C5B C -3.022 -0.545 5
SAD C4B C -4.268 0.275 6
SAD O4B O -4.344 1.771 7
SAD C3B C -5.669 -0.261 8
SAD O3B O -6.059 -1.708 9
SAD C2B C -6.610 0.906 10
SAD O2B O -8.110 0.830 11
SAD C1B C -5.792 2.163 12
SAD N9A N -6.326 3.563 13
SAD C8A C -5.508 4.819 14
SAD N7A N -6.450 5.987 15
SAD C5A C -7.850 5.450 16
SAD C6A C -9.189 6.135 17
SAD N6A N -9.264 7.632 18
SAD N1A N -10.446 5.317 19
SAD C2A C -10.371 3.820 20
SAD N3A N -9.032 3.139 21
SAD C4A C -7.776 3.953 22
SAD C3 C -0.578 -3.667 23
SAD PN P 0.782 -2.990 24
SAD O1N O 0.134 -1.655 25
SAD O2N O 1.451 -4.334 26
SAD O5D O 2.117 -2.324 27
SAD C5D C 3.362 -3.142 28
SAD C4D C 4.691 -2.465 29
SAD O4D O 6.028 -3.147 30
SAD C3D C 4.930 -0.983 31
SAD O3D O 3.870 0.080 32
SAD C2D C 6.412 -0.749 33
SAD O2D O 7.095 0.585 34
SAD C1D C 7.090 -2.089 35
SAD C2N C 8.571 -2.327 36
SAD N3N N 9.631 -1.266 37
SAD C4N C 10.967 -1.950 38
SAD C5N C 10.732 -3.430 39
SAD SE1N Se 9.249 -3.665 40
SAD C6N C 12.305 -1.269 41
SAD O6N O 12.386 0.229 42
SAD N6N N 13.562 -2.088 43
#
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
SAD PA O1A DOUBLE NONE 1
SAD PA O2A SINGLE BEGINWEDGE 2
SAD PA O5B SINGLE NONE 3
SAD PA C3 SINGLE NONE 4
SAD O5B C5B SINGLE NONE 5
SAD C4B C5B SINGLE BEGINDASH 6
SAD C4B O4B SINGLE NONE 7
SAD C4B C3B SINGLE NONE 8
SAD O4B C1B SINGLE NONE 9
SAD C3B O3B SINGLE BEGINWEDGE 10
SAD C3B C2B SINGLE NONE 11
SAD C2B O2B SINGLE BEGINWEDGE 12
SAD C2B C1B SINGLE NONE 13
SAD C1B N9A SINGLE BEGINDASH 14
SAD N9A C8A SINGLE NONE 15
SAD N9A C4A SINGLE NONE 16
SAD C8A N7A DOUBLE NONE 17
SAD N7A C5A SINGLE NONE 18
SAD C5A C6A DOUBLE NONE 19
SAD C5A C4A SINGLE NONE 20
SAD C6A N6A SINGLE NONE 21
SAD C6A N1A SINGLE NONE 22
SAD N1A C2A DOUBLE NONE 23
SAD C2A N3A SINGLE NONE 24
SAD N3A C4A DOUBLE NONE 25
SAD C3 PN SINGLE NONE 26
SAD PN O1N DOUBLE NONE 27
SAD PN O2N SINGLE BEGINDASH 28
SAD PN O5D SINGLE NONE 29
SAD O5D C5D SINGLE NONE 30
SAD C4D C5D SINGLE BEGINDASH 31
SAD C4D O4D SINGLE NONE 32
SAD C4D C3D SINGLE NONE 33
SAD O4D C1D SINGLE NONE 34
SAD C3D O3D SINGLE BEGINWEDGE 35
SAD C3D C2D SINGLE NONE 36
SAD C2D O2D SINGLE BEGINWEDGE 37
SAD C2D C1D SINGLE NONE 38
SAD C1D C2N SINGLE BEGINDASH 39
SAD C2N N3N DOUBLE NONE 40
SAD C2N SE1N SINGLE NONE 41
SAD N3N C4N SINGLE NONE 42
SAD C4N C5N DOUBLE NONE 43
SAD C4N C6N SINGLE NONE 44
SAD C5N SE1N SINGLE NONE 45
SAD C6N O6N DOUBLE NONE 46
SAD C6N N6N SINGLE NONE 47
#
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
SAD MurckoScaffold S1 scaffold 'O=[PH](C[PH](=O)OC[C@@H]1CC[C@H](n2cnc3cncnc32)O1)OC[C@@H]1CC[C@H](c2ncc[se]2)O1' InChI=1S/C19H25N5O6P2Se/c25-31(27-8-13-1-3-16(29-13)19-21-5-6-33-19)12-32(26)28-9-14-2-4-17(30-14)24-11-23-15-7-20-10-22-18(15)24/h5-7,10-11,13-14,16-17,31-32H,1-4,8-9,12H2/t13-,14-,16+,17+/m0/s1 ALWFMPDACXKTFZ-XJNFMUPTSA-N
SAD adenine F1 fragment 'Nc1ncnc2nc[nH]c12' InChI=1S/C5H5N5/c6-4-3-5(9-1-7-3)10-2-8-4/h1-2H,(H3,6,7,8,9,10) GFFGJBXGBJISGV-UHFFFAOYSA-N
SAD amide F2 fragment CC(N)=O InChI=1S/C2H5NO/c1-2(3)4/h1H3,(H2,3,4) DLFVBJFMPXGRIB-UHFFFAOYSA-N
SAD imidazole F3 fragment 'c1c[nH]cn1' InChI=1S/C3H4N2/c1-2-5-3-4-1/h1-3H,(H,4,5) RAXXELZNTBOGNW-UHFFFAOYSA-N
SAD 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
SAD pyrimidine F5 fragment c1cncnc1 InChI=1S/C4H4N2/c1-2-5-4-6-3-1/h1-4H CZPWVGJYEJSRLH-UHFFFAOYSA-N
SAD 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
SAD PA S1 1
SAD O1A S1 1
SAD O5B S1 1
SAD C5B S1 1
SAD C4B S1 1
SAD O4B S1 1
SAD C3B S1 1
SAD C2B S1 1
SAD C1B S1 1
SAD N9A S1 1
SAD C8A S1 1
SAD N7A S1 1
SAD C5A S1 1
SAD C6A S1 1
SAD N1A S1 1
SAD C2A S1 1
SAD N3A S1 1
SAD C4A S1 1
SAD C3 S1 1
SAD PN S1 1
SAD O1N S1 1
SAD O5D S1 1
SAD C5D S1 1
SAD C4D S1 1
SAD O4D S1 1
SAD C3D S1 1
SAD C2D S1 1
SAD C1D S1 1
SAD C2N S1 1
SAD N3N S1 1
SAD C4N S1 1
SAD C5N S1 1
SAD SE1N S1 1
SAD N1A F1 1
SAD C6A F1 1
SAD C5A F1 1
SAD C4A F1 1
SAD N3A F1 1
SAD C2A F1 1
SAD N9A F1 1
SAD C8A F1 1
SAD N7A F1 1
SAD N6A F1 1
SAD N6N F2 1
SAD C6N F2 1
SAD O6N F2 1
SAD C4N F2 1
SAD C5A F3 1
SAD C4A F3 1
SAD N9A F3 1
SAD C8A F3 1
SAD N7A F3 1
SAD N7A F4 1
SAD C8A F4 1
SAD N9A F4 1
SAD C4A F4 1
SAD C5A F4 1
SAD C6A F4 1
SAD N1A F4 1
SAD C2A F4 1
SAD N3A F4 1
SAD C5A F5 1
SAD C6A F5 1
SAD N1A F5 1
SAD C2A F5 1
SAD N3A F5 1
SAD C4A F5 1
SAD C2B F6 1
SAD C3B F6 1
SAD C4B F6 1
SAD O4B F6 1
SAD C1B F6 1
SAD C5B F6 1
SAD O5B F6 1
SAD O3B F6 1
SAD O2B F6 1
SAD C2D F6 2
SAD C3D F6 2
SAD C4D F6 2
SAD O4D F6 2
SAD C1D F6 2
SAD C5D F6 2
SAD O5D F6 2
SAD O3D F6 2
SAD O2D F6 2
#
_pdbe_chem_comp_rdkit_properties.comp_id SAD
_pdbe_chem_comp_rdkit_properties.exactmw 715.031
_pdbe_chem_comp_rdkit_properties.amw 714.380
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 20
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 10
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 18
_pdbe_chem_comp_rdkit_properties.NumHBD 8
_pdbe_chem_comp_rdkit_properties.NumHBA 19
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 43
_pdbe_chem_comp_rdkit_properties.NumAtoms 70
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 23
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 1
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.550
_pdbe_chem_comp_rdkit_properties.NumRings 5
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 3
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 2
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 2
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 5
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 3
_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 10
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 285.266
_pdbe_chem_comp_rdkit_properties.tpsa 318.040
_pdbe_chem_comp_rdkit_properties.CrippenClogP -4.116
_pdbe_chem_comp_rdkit_properties.CrippenMR 137.841
_pdbe_chem_comp_rdkit_properties.chi0v 23.242
_pdbe_chem_comp_rdkit_properties.chi1v 15.152
_pdbe_chem_comp_rdkit_properties.chi2v 8.886
_pdbe_chem_comp_rdkit_properties.chi3v 8.886
_pdbe_chem_comp_rdkit_properties.chi4v 6.291
_pdbe_chem_comp_rdkit_properties.chi0n 46.740
_pdbe_chem_comp_rdkit_properties.chi1n 23.092
_pdbe_chem_comp_rdkit_properties.chi2n 4.657
_pdbe_chem_comp_rdkit_properties.chi3n 4.657
_pdbe_chem_comp_rdkit_properties.chi4n 2.910
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -2.191
_pdbe_chem_comp_rdkit_properties.kappa1 12.542
_pdbe_chem_comp_rdkit_properties.kappa2 12.304
_pdbe_chem_comp_rdkit_properties.kappa3 6.752
_pdbe_chem_comp_rdkit_properties.Phi 3.589
#
#
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
SAD PA -1.955 -3.061 0.317 ETKDGv3 1
SAD O1A -2.775 -3.317 -0.929 ETKDGv3 2
SAD O2A -2.485 -4.091 1.553 ETKDGv3 3
SAD O5B -2.108 -1.428 0.789 ETKDGv3 4
SAD C5B -3.465 -1.162 1.049 ETKDGv3 5
SAD C4B -3.614 0.303 1.470 ETKDGv3 6
SAD O4B -3.148 1.148 0.442 ETKDGv3 7
SAD C3B -5.064 0.669 1.766 ETKDGv3 8
SAD O3B -5.401 0.421 3.107 ETKDGv3 9
SAD C2B -5.101 2.146 1.442 ETKDGv3 10
SAD O2B -4.948 2.951 2.589 ETKDGv3 11
SAD C1B -3.923 2.328 0.472 ETKDGv3 12
SAD N9A -4.402 2.632 -0.876 ETKDGv3 13
SAD C8A -4.864 3.921 -1.332 ETKDGv3 14
SAD N7A -5.640 3.892 -2.385 ETKDGv3 15
SAD C5A -5.769 2.516 -2.716 ETKDGv3 16
SAD C6A -6.538 1.917 -3.623 ETKDGv3 17
SAD N6A -7.344 2.659 -4.539 ETKDGv3 18
SAD N1A -6.551 0.471 -3.631 ETKDGv3 19
SAD C2A -5.860 -0.222 -2.755 ETKDGv3 20
SAD N3A -5.065 0.451 -1.751 ETKDGv3 21
SAD C4A -5.028 1.748 -1.786 ETKDGv3 22
SAD C3 -0.210 -3.405 -0.066 ETKDGv3 23
SAD PN 0.854 -3.052 1.372 ETKDGv3 24
SAD O1N 0.434 -3.934 2.525 ETKDGv3 25
SAD O2N 0.679 -1.431 1.830 ETKDGv3 26
SAD O5D 2.489 -3.386 1.015 ETKDGv3 27
SAD C5D 2.920 -2.520 -0.010 ETKDGv3 28
SAD C4D 4.436 -2.648 -0.181 ETKDGv3 29
SAD O4D 4.864 -1.830 -1.250 ETKDGv3 30
SAD C3D 5.196 -2.245 1.080 ETKDGv3 31
SAD O3D 5.428 -3.357 1.907 ETKDGv3 32
SAD C2D 6.471 -1.667 0.519 ETKDGv3 33
SAD O2D 7.430 -2.675 0.307 ETKDGv3 34
SAD C1D 6.009 -1.120 -0.829 ETKDGv3 35
SAD C2N 5.660 0.334 -0.735 ETKDGv3 36
SAD N3N 6.586 1.235 -0.699 ETKDGv3 37
SAD C4N 6.233 2.610 -0.599 ETKDGv3 38
SAD C5N 4.943 2.930 -0.543 ETKDGv3 39
SAD SE1N 5.202 2.150 -0.602 ETKDGv3 40
SAD C6N 7.294 3.641 -0.557 ETKDGv3 41
SAD O6N 6.992 4.862 -0.469 ETKDGv3 42
SAD N6N 8.672 3.269 -0.615 ETKDGv3 43
SAD HOA2 -2.216 -3.642 2.394 ETKDGv3 44
SAD H51A -3.839 -1.805 1.877 ETKDGv3 45
SAD H52A -4.080 -1.335 0.137 ETKDGv3 46
SAD H4B -2.990 0.477 2.378 ETKDGv3 47
SAD H3B -5.763 0.134 1.080 ETKDGv3 48
SAD HO3A -5.564 -0.555 3.181 ETKDGv3 49
SAD H2B -6.072 2.404 0.964 ETKDGv3 50
SAD HO2A -4.079 2.722 3.014 ETKDGv3 51
SAD H1B -3.270 3.164 0.807 ETKDGv3 52
SAD H8A -4.612 4.846 -0.830 ETKDGv3 53
SAD H61A -7.944 2.157 -5.230 ETKDGv3 54
SAD H62A -7.345 3.703 -4.536 ETKDGv3 55
SAD H2A -5.893 -1.302 -2.777 ETKDGv3 56
SAD H31 -0.099 -4.471 -0.353 ETKDGv3 57
SAD H32 0.094 -2.765 -0.918 ETKDGv3 58
SAD HON2 1.321 -1.308 2.574 ETKDGv3 59
SAD H51N 2.681 -1.454 0.214 ETKDGv3 60
SAD H52N 2.444 -2.806 -0.973 ETKDGv3 61
SAD H4D 4.677 -3.704 -0.441 ETKDGv3 62
SAD H3D 4.643 -1.451 1.638 ETKDGv3 63
SAD HO3N 5.774 -2.999 2.766 ETKDGv3 64
SAD H2D 6.883 -0.870 1.184 ETKDGv3 65
SAD HO2N 7.927 -2.782 1.160 ETKDGv3 66
SAD H1D 6.809 -1.242 -1.593 ETKDGv3 67
SAD HN5 4.603 3.955 -0.466 ETKDGv3 68
SAD H61N 8.964 2.269 -0.687 ETKDGv3 69
SAD H62N 9.414 4.003 -0.585 ETKDGv3 70
#