data_DND
#
_chem_comp.id DND
_chem_comp.name "NICOTINIC ACID ADENINE DINUCLEOTIDE"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C21 H27 N6 O15 P2"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms DEAMIDO-NAD+
_chem_comp.pdbx_formal_charge 1
_chem_comp.pdbx_initial_date 2001-04-16
_chem_comp.pdbx_modified_date 2020-06-17
_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 665.418
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code DND
_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 1KQO
_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
DND PN PN P 0 1 N N N N N N 9.531 43.089 14.197 1.491 -2.779 -1.073 PN DND 1
DND O11 O11 O 0 1 N N N N N N 9.848 44.197 13.283 1.036 -3.219 -2.411 O11 DND 2
DND O12 O12 O 0 1 N N N N N N 10.771 42.522 14.827 2.394 -3.934 -0.407 O12 DND 3
DND O3P O3P O 0 1 N N N N N N 8.645 41.888 13.598 0.211 -2.493 -0.139 O3P DND 4
DND O5D O5D O 0 1 N N N N N N 8.398 43.518 15.198 2.362 -1.433 -1.217 O5D DND 5
DND C5D C5D C 0 1 N N N N N N 8.575 44.670 16.012 3.505 -1.333 -2.068 C5D DND 6
DND C4D C4D C 0 1 N N R N N N 7.318 44.733 16.804 4.094 0.075 -1.969 C4D DND 7
DND O4D O4D O 0 1 N N N N N N 7.684 45.319 18.056 4.624 0.292 -0.650 O4D DND 8
DND C3D C3D C 0 1 N N S N N N 6.214 45.626 16.207 5.262 0.226 -2.962 C3D DND 9
DND O3D O3D O 0 1 N N N N N N 4.884 45.130 16.586 4.991 1.272 -3.898 O3D DND 10
DND C2D C2D C 0 1 N N R N N N 6.497 46.953 16.876 6.473 0.598 -2.071 C2D DND 11
DND O2D O2D O 0 1 N N N N N N 5.330 47.810 16.880 7.270 1.609 -2.690 O2D DND 12
DND C1D C1D C 0 1 N N R N N N 6.921 46.484 18.272 5.782 1.142 -0.795 C1D DND 13
DND N1N N1N N 1 1 Y N N N N N 7.677 47.529 18.973 6.666 1.012 0.366 N1N DND 14
DND C6N C6N C 0 1 Y N N N N N 9.016 47.909 18.640 6.840 -0.177 0.908 C6N DND 15
DND C5N C5N C 0 1 Y N N N N N 9.689 48.889 19.277 7.666 -0.348 2.005 C5N DND 16
DND C4N C4N C 0 1 Y N N N N N 9.036 49.678 20.415 8.318 0.749 2.539 C4N DND 17
DND C3N C3N C 0 1 Y N N N N N 7.641 49.275 20.759 8.113 1.999 1.941 C3N DND 18
DND C2N C2N C 0 1 Y N N N N N 7.026 48.204 20.013 7.268 2.086 0.834 C2N DND 19
DND C7N C7N C 0 1 N N N N N N 6.788 49.878 21.808 8.784 3.204 2.471 C7N DND 20
DND O7N O7N O 0 1 N N N N N N 5.533 49.483 22.097 8.599 4.283 1.944 O7N DND 21
DND O8N O8N O 0 1 N N N N N N 7.329 50.790 22.403 9.600 3.106 3.538 O8N DND 22
DND PA PA P 0 1 N N N N N N 9.061 40.513 12.883 -1.164 -3.279 0.146 PA DND 23
DND O13 O13 O 0 1 N N N N N N 8.038 40.320 11.838 -1.680 -3.846 -1.121 O13 DND 24
DND O14 O14 O 0 1 N N N N N N 10.471 40.510 12.352 -0.895 -4.470 1.196 O14 DND 25
DND O5B O5B O 0 1 N N N N N N 8.891 39.305 13.940 -2.249 -2.259 0.758 O5B DND 26
DND C5B C5B C 0 1 N N N N N N 7.576 39.005 14.542 -3.604 -2.630 1.020 C5B DND 27
DND C4B C4B C 0 1 N N R N N N 7.875 38.153 15.786 -4.359 -1.429 1.596 C4B DND 28
DND O4B O4B O 0 1 N N N N N N 8.748 37.021 15.472 -4.540 -0.416 0.583 O4B DND 29
DND C3B C3B C 0 1 N N S N N N 8.591 38.909 16.912 -5.791 -1.840 2.004 C3B DND 30
DND O3B O3B O 0 1 N N N N N N 7.867 38.790 18.163 -5.858 -2.095 3.408 O3B DND 31
DND C2B C2B C 0 1 N N R N N N 9.975 38.255 16.846 -6.653 -0.611 1.636 C2B DND 32
DND O2B O2B O 0 1 N N N N N N 10.700 38.368 18.082 -7.278 -0.071 2.802 O2B DND 33
DND C1B C1B C 0 1 N N R N N N 9.622 36.802 16.468 -5.639 0.396 1.049 C1B DND 34
DND N9A N9A N 0 1 Y N N N N N 10.748 36.079 15.888 -6.239 1.131 -0.067 N9A DND 35
DND C4A C4A C 0 1 Y N N N N N 11.193 34.853 16.273 -6.963 2.293 0.022 C4A DND 36
DND N3A N3A N 0 1 Y N N N N N 10.690 34.069 17.252 -7.343 3.088 1.017 N3A DND 37
DND C2A C2A C 0 1 Y N N N N N 11.351 32.929 17.374 -8.055 4.169 0.777 C2A DND 38
DND N1A N1A N 0 1 Y N N N N N 12.433 32.502 16.636 -8.424 4.519 -0.441 N1A DND 39
DND C6A C6A C 0 1 Y N N N N N 12.928 33.326 15.642 -8.090 3.787 -1.499 C6A DND 40
DND C5A C5A C 0 1 Y N N N N N 12.276 34.579 15.444 -7.330 2.623 -1.294 C5A DND 41
DND N7A N7A N 0 1 Y N N N N N 12.525 35.601 14.552 -6.822 1.662 -2.103 N7A DND 42
DND C8A C8A C 0 1 Y N N N N N 11.565 36.485 14.865 -6.176 0.789 -1.385 C8A DND 43
DND N6A N6A N 0 1 N N N N N N 13.982 32.905 14.923 -8.483 4.161 -2.772 N6A DND 44
DND H1 H1 H 0 1 N N N N N N 11.532 42.994 14.510 2.727 -3.713 0.474 H1 DND 45
DND H2 H2 H 0 1 N N N N N N 9.449 44.556 16.670 4.254 -2.063 -1.758 H2 DND 46
DND H3 H3 H 0 1 N N N N N N 8.696 45.572 15.395 3.210 -1.532 -3.099 H3 DND 47
DND H4 H4 H 0 1 N N N N N N 6.919 43.719 16.952 3.323 0.815 -2.184 H4 DND 48
DND H5 H5 H 0 1 N N N N N N 6.324 45.702 15.115 5.444 -0.714 -3.484 H5 DND 49
DND H6 H6 H 0 1 N N N N N N 4.217 45.692 16.210 5.694 1.410 -4.548 H6 DND 50
DND H7 H7 H 0 1 N N N N N N 7.344 47.449 16.380 7.073 -0.283 -1.844 H7 DND 51
DND H8 H8 H 0 1 N N N N N N 5.542 48.632 17.306 7.651 1.345 -3.539 H8 DND 52
DND H9 H9 H 0 1 N N N N N N 6.016 46.242 18.848 5.480 2.180 -0.935 H9 DND 53
DND H10 H10 H 0 1 N N N N N N 9.513 47.384 17.838 6.330 -1.032 0.489 H10 DND 54
DND H11 H11 H 0 1 N N N N N N 10.701 49.120 18.981 7.800 -1.327 2.440 H11 DND 55
DND H12 H12 H 0 1 N N N N N N 9.551 50.473 20.934 8.968 0.645 3.396 H12 DND 56
DND H13 H13 H 0 1 N N N N N N 6.019 47.910 20.268 7.103 3.042 0.360 H13 DND 57
DND H14 H14 H 0 1 N N N N N N 6.735 51.138 23.058 10.016 3.922 3.848 H14 DND 58
DND H15 H15 H 0 1 N N N N N N 10.455 40.381 11.411 -0.555 -4.171 2.050 H15 DND 59
DND H16 H16 H 0 1 N N N N N N 7.064 39.935 14.828 -4.081 -2.947 0.093 H16 DND 60
DND H17 H17 H 0 1 N N N N N N 6.949 38.444 13.834 -3.624 -3.450 1.738 H17 DND 61
DND H18 H18 H 0 1 N N N N N N 6.920 37.774 16.179 -3.822 -1.020 2.452 H18 DND 62
DND H19 H19 H 0 1 N N N N N N 8.683 39.968 16.629 -6.112 -2.717 1.442 H19 DND 63
DND H20 H20 H 0 1 N N N N N N 8.329 39.265 18.843 -6.735 -2.357 3.720 H20 DND 64
DND H21 H21 H 0 1 N N N N N N 10.548 38.709 16.024 -7.402 -0.880 0.891 H21 DND 65
DND H22 H22 H 0 1 N N N N N N 10.886 39.283 18.258 -7.880 -0.684 3.245 H22 DND 66
DND H23 H23 H 0 1 N N N N N N 9.192 36.270 17.330 -5.300 1.087 1.821 H23 DND 67
DND H24 H24 H 0 1 N N N N N N 11.001 32.255 18.142 -8.347 4.793 1.609 H24 DND 68
DND H25 H25 H 0 1 N N N N N N 11.447 37.431 14.357 -5.671 -0.082 -1.776 H25 DND 69
DND H26 H26 H 0 1 N N N N N N 14.263 31.999 15.241 -9.007 4.967 -2.900 H26 DND 70
DND H27 H27 H 0 1 N N N N N N 13.728 32.855 13.957 -8.233 3.618 -3.536 H27 DND 71
#
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
DND O13 PA DOUB N N 1
DND O14 PA SING N N 2
DND PA O3P SING N N 3
DND PA O5B SING N N 4
DND O11 PN DOUB N N 5
DND O3P PN SING N N 6
DND O5B C5B SING N N 7
DND PN O12 SING N N 8
DND PN O5D SING N N 9
DND C5B C4B SING N N 10
DND N7A C8A DOUB Y N 11
DND N7A C5A SING Y N 12
DND C8A N9A SING Y N 13
DND N6A C6A SING N N 14
DND O5D C5D SING N N 15
DND C5A C6A SING Y N 16
DND C5A C4A DOUB Y N 17
DND O4B C4B SING N N 18
DND O4B C1B SING N N 19
DND C6A N1A DOUB Y N 20
DND C4B C3B SING N N 21
DND N9A C4A SING Y N 22
DND N9A C1B SING N N 23
DND C5D C4D SING N N 24
DND C3D O3D SING N N 25
DND C3D C4D SING N N 26
DND C3D C2D SING N N 27
DND C4A N3A SING Y N 28
DND C1B C2B SING N N 29
DND N1A C2A SING Y N 30
DND C4D O4D SING N N 31
DND C2B C3B SING N N 32
DND C2B O2B SING N N 33
DND C2D O2D SING N N 34
DND C2D C1D SING N N 35
DND C3B O3B SING N N 36
DND N3A C2A DOUB Y N 37
DND O4D C1D SING N N 38
DND C1D N1N SING N N 39
DND C6N N1N DOUB Y N 40
DND C6N C5N SING Y N 41
DND N1N C2N SING Y N 42
DND C5N C4N DOUB Y N 43
DND C2N C3N DOUB Y N 44
DND C4N C3N SING Y N 45
DND C3N C7N SING N N 46
DND C7N O7N DOUB N N 47
DND C7N O8N SING N N 48
DND O12 H1 SING N N 49
DND C5D H2 SING N N 50
DND C5D H3 SING N N 51
DND C4D H4 SING N N 52
DND C3D H5 SING N N 53
DND O3D H6 SING N N 54
DND C2D H7 SING N N 55
DND O2D H8 SING N N 56
DND C1D H9 SING N N 57
DND C6N H10 SING N N 58
DND C5N H11 SING N N 59
DND C4N H12 SING N N 60
DND C2N H13 SING N N 61
DND O8N H14 SING N N 62
DND O14 H15 SING N N 63
DND C5B H16 SING N N 64
DND C5B H17 SING N N 65
DND C4B H18 SING N N 66
DND C3B H19 SING N N 67
DND O3B H20 SING N N 68
DND C2B H21 SING N N 69
DND O2B H22 SING N N 70
DND C1B H23 SING N N 71
DND C2A H24 SING N N 72
DND C8A H25 SING N N 73
DND N6A H26 SING N N 74
DND N6A H27 SING N N 75
#
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
DND InChI InChI 1.03 InChI=1S/C21H26N6O15P2/c22-17-12-18(24-7-23-17)27(8-25-12)20-16(31)14(29)11(41-20)6-39-44(36,37)42-43(34,35)38-5-10-13(28)15(30)19(40-10)26-3-1-2-9(4-26)21(32)33/h1-4,7-8,10-11,13-16,19-20,28-31H,5-6H2,(H4-,22,23,24,32,33,34,35,36,37)/p+1/t10-,11-,13-,14-,15-,16-,19-,20-/m1/s1
DND InChIKey InChI 1.03 SENPVEZBRZQVST-HISDBWNOSA-O
DND SMILES_CANONICAL CACTVS 3.385 Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)OC[C@H]4O[C@H]([C@H](O)[C@@H]4O)[n+]5cccc(c5)C(O)=O)[C@@H](O)[C@H]3O
DND SMILES CACTVS 3.385 Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]4O[CH]([CH](O)[CH]4O)[n+]5cccc(c5)C(O)=O)[CH](O)[CH]3O
DND SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 c1cc(c[n+](c1)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)OP(=O)(O)OC[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4ncnc5N)O)O)O)O)C(=O)O
DND SMILES "OpenEye OEToolkits" 1.7.6 c1cc(c[n+](c1)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)O)O)O)O)C(=O)O
#
_pdbx_chem_comp_identifier.comp_id DND
_pdbx_chem_comp_identifier.type "SYSTEMATIC NAME"
_pdbx_chem_comp_identifier.program "OpenEye OEToolkits"
_pdbx_chem_comp_identifier.program_version 1.7.6
_pdbx_chem_comp_identifier.identifier
"1-[(2R,3R,4S,5R)-5-[[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxymethyl]-3,4-bis(oxidanyl)oxolan-2-yl]pyridin-1-ium-3-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
DND 'Create component' 2001-04-16 RCSB
DND 'Modify descriptor' 2011-06-04 RCSB
DND 'Other modification' 2014-10-13 RCSB
DND 'Modify synonyms' 2020-06-05 PDBE
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id DND
_pdbx_chem_comp_synonyms.name DEAMIDO-NAD+
_pdbx_chem_comp_synonyms.provenance ?
_pdbx_chem_comp_synonyms.type ?
#
_pdbe_chem_comp_drugbank_details.comp_id DND
_pdbe_chem_comp_drugbank_details.drugbank_id DB04099
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name Deamido-Nad+
_pdbe_chem_comp_drugbank_details.description ?
_pdbe_chem_comp_drugbank_details.cas_number ?
_pdbe_chem_comp_drugbank_details.mechanism_of_action ?
#
loop_
_pdbe_chem_comp_synonyms.comp_id
_pdbe_chem_comp_synonyms.name
_pdbe_chem_comp_synonyms.provenance
_pdbe_chem_comp_synonyms.type
DND DEAMIDO-NAD+ wwPDB ?
DND Deamido-Nad+ DrugBank ?
#
_pdbe_chem_comp_drugbank_classification.comp_id DND
_pdbe_chem_comp_drugbank_classification.drugbank_id DB04099
_pdbe_chem_comp_drugbank_classification.parent "(5'->5')-dinucleotides"
_pdbe_chem_comp_drugbank_classification.kingdom 'Organic compounds'
_pdbe_chem_comp_drugbank_classification.class "(5'->5')-dinucleotides"
_pdbe_chem_comp_drugbank_classification.superclass 'Nucleosides, nucleotides, and analogues'
_pdbe_chem_comp_drugbank_classification.description
"This compound belongs to the class of organic compounds known as (5'->5')-dinucleotides. These are dinucleotides where the two bases are connected via a (5'->5')-phosphodiester linkage."
#
loop_
_pdbe_chem_comp_drugbank_targets.comp_id
_pdbe_chem_comp_drugbank_targets.drugbank_id
_pdbe_chem_comp_drugbank_targets.name
_pdbe_chem_comp_drugbank_targets.organism
_pdbe_chem_comp_drugbank_targets.uniprot_id
_pdbe_chem_comp_drugbank_targets.pharmacologically_active
_pdbe_chem_comp_drugbank_targets.ordinal
DND DB04099 'NH(3)-dependent NAD(+) synthetase' 'Escherichia coli (strain K12)' P18843 unknown 1
DND DB04099 'NH(3)-dependent NAD(+) synthetase' 'Bacillus subtilis (strain 168)' P08164 unknown 2
DND DB04099 'Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 1' Humans Q9HAN9 unknown 3
DND DB04099 'Nicotinate-nucleotide adenylyltransferase' 'Bacillus subtilis (strain 168)' P54455 unknown 4
DND DB04099 'Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3' Humans Q96T66 unknown 5
DND DB04099 'NH(3)-dependent NAD(+) synthetase' 'Helicobacter pylori (strain ATCC 700392 / 26695)' O25096 unknown 6
#
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
DND PN P 8.116 3.562 1
DND O11 O 7.003 4.568 2
DND O12 O 9.229 2.557 3
DND O3P O 7.110 2.449 4
DND O5D O 9.121 4.675 5
DND C5D C 8.660 6.103 6
DND C4D C 9.666 7.216 7
DND O4D O 11.157 7.056 8
DND C3D C 9.357 8.684 9
DND O3D O 7.987 9.296 10
DND C2D C 10.657 9.431 11
DND O2D O 10.816 10.923 12
DND C1D C 11.770 8.426 13
DND N1N N 13.238 8.735 14
DND C6N C 13.704 10.161 15
DND C5N C 15.171 10.470 16
DND C4N C 16.173 9.354 17
DND C3N C 15.707 7.928 18
DND C2N C 14.239 7.619 19
DND C7N C 16.709 6.811 20
DND O7N O 18.177 7.121 21
DND O8N O 16.243 5.386 22
DND PA P 7.571 1.022 23
DND O13 O 8.998 1.483 24
DND O14 O 6.144 0.561 25
DND O5B O 8.032 -0.405 26
DND C5B C 7.027 -1.518 27
DND C4B C 7.487 -2.946 28
DND O4B O 6.604 -4.158 29
DND C3B C 8.913 -3.412 30
DND O3B O 10.129 -2.532 31
DND C2B C 8.911 -4.912 32
DND O2B O 10.123 -5.796 33
DND C1B C 7.483 -5.373 34
DND N9A N 7.018 -6.799 35
DND C4A C 5.598 -7.256 36
DND N3A N 4.299 -6.506 37
DND C2A C 3.000 -7.256 38
DND N1A N 3.000 -8.756 39
DND C6A C 4.299 -9.506 40
DND C5A C 5.598 -8.756 41
DND N7A N 7.018 -9.213 42
DND C8A C 7.893 -8.006 43
DND N6A N 4.299 -11.006 44
#
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
DND O13 PA DOUBLE NONE 1
DND PA O14 SINGLE BEGINWEDGE 2
DND PA O3P SINGLE NONE 3
DND PA O5B SINGLE NONE 4
DND O11 PN DOUBLE NONE 5
DND O3P PN SINGLE NONE 6
DND O5B C5B SINGLE NONE 7
DND PN O12 SINGLE BEGINDASH 8
DND PN O5D SINGLE NONE 9
DND C4B C5B SINGLE BEGINDASH 10
DND N7A C8A DOUBLE NONE 11
DND N7A C5A SINGLE NONE 12
DND C8A N9A SINGLE NONE 13
DND N6A C6A SINGLE NONE 14
DND O5D C5D SINGLE NONE 15
DND C5A C6A DOUBLE NONE 16
DND C5A C4A SINGLE NONE 17
DND O4B C4B SINGLE NONE 18
DND O4B C1B SINGLE NONE 19
DND C6A N1A SINGLE NONE 20
DND C4B C3B SINGLE NONE 21
DND N9A C4A SINGLE NONE 22
DND C1B N9A SINGLE BEGINDASH 23
DND C4D C5D SINGLE BEGINDASH 24
DND C3D O3D SINGLE BEGINWEDGE 25
DND C3D C4D SINGLE NONE 26
DND C3D C2D SINGLE NONE 27
DND C4A N3A DOUBLE NONE 28
DND C1B C2B SINGLE NONE 29
DND N1A C2A DOUBLE NONE 30
DND C4D O4D SINGLE NONE 31
DND C2B C3B SINGLE NONE 32
DND C2B O2B SINGLE BEGINWEDGE 33
DND C2D O2D SINGLE BEGINWEDGE 34
DND C2D C1D SINGLE NONE 35
DND C3B O3B SINGLE BEGINWEDGE 36
DND N3A C2A SINGLE NONE 37
DND O4D C1D SINGLE NONE 38
DND C1D N1N SINGLE BEGINDASH 39
DND C6N N1N DOUBLE NONE 40
DND C6N C5N SINGLE NONE 41
DND N1N C2N SINGLE NONE 42
DND C5N C4N DOUBLE NONE 43
DND C2N C3N DOUBLE NONE 44
DND C4N C3N SINGLE NONE 45
DND C3N C7N SINGLE NONE 46
DND C7N O7N DOUBLE NONE 47
DND C7N O8N SINGLE NONE 48
#
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
DND MurckoScaffold S1 scaffold 'O=[PH](OC[C@@H]1CC[C@H](n2cnc3cncnc32)O1)O[PH](=O)OC[C@@H]1CC[C@H]([n+]2ccccc2)O1' InChI=1S/C20H26N5O7P2/c26-33(28-11-15-4-6-18(30-15)24-8-2-1-3-9-24)32-34(27)29-12-16-5-7-19(31-16)25-14-23-17-10-21-13-22-20(17)25/h1-3,8-10,13-16,18-19,33-34H,4-7,11-12H2/q+1/t15-,16-,18+,19+/m0/s1 NEQSZHPXWRKWHT-RNIPGJKVSA-N
DND 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
DND imidazole F2 fragment 'c1c[nH]cn1' InChI=1S/C3H4N2/c1-2-5-3-4-1/h1-3H,(H,4,5) RAXXELZNTBOGNW-UHFFFAOYSA-N
DND 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
DND 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
DND pyridine F5 fragment c1ccncc1 InChI=1S/C5H5N/c1-2-4-6-5-3-1/h1-5H JUJWROOIHBZHMG-UHFFFAOYSA-N
DND pyrimidine F6 fragment c1cncnc1 InChI=1S/C4H4N2/c1-2-5-4-6-3-1/h1-4H CZPWVGJYEJSRLH-UHFFFAOYSA-N
DND ribose F7 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
DND PN S1 1
DND O11 S1 1
DND O3P S1 1
DND O5D S1 1
DND C5D S1 1
DND C4D S1 1
DND O4D S1 1
DND C3D S1 1
DND C2D S1 1
DND C1D S1 1
DND N1N S1 1
DND C6N S1 1
DND C5N S1 1
DND C4N S1 1
DND C3N S1 1
DND C2N S1 1
DND PA S1 1
DND O13 S1 1
DND O5B S1 1
DND C5B S1 1
DND C4B S1 1
DND O4B S1 1
DND C3B S1 1
DND C2B S1 1
DND C1B S1 1
DND N9A S1 1
DND C4A S1 1
DND N3A S1 1
DND C2A S1 1
DND N1A S1 1
DND C6A S1 1
DND C5A S1 1
DND N7A S1 1
DND C8A S1 1
DND N1A F1 1
DND C6A F1 1
DND C5A F1 1
DND C4A F1 1
DND N3A F1 1
DND C2A F1 1
DND N9A F1 1
DND C8A F1 1
DND N7A F1 1
DND N6A F1 1
DND C4A F2 1
DND C5A F2 1
DND N7A F2 1
DND C8A F2 1
DND N9A F2 1
DND O12 F3 1
DND PN F3 1
DND O11 F3 1
DND O3P F3 1
DND O5D F3 1
DND O3P F3 2
DND PA F3 2
DND O13 F3 2
DND O14 F3 2
DND O5B F3 2
DND N7A F4 1
DND C8A F4 1
DND N9A F4 1
DND C4A F4 1
DND C5A F4 1
DND C6A F4 1
DND N1A F4 1
DND C2A F4 1
DND N3A F4 1
DND C6N F5 1
DND C5N F5 1
DND C4N F5 1
DND C3N F5 1
DND C2N F5 1
DND N1N F5 1
DND C5A F6 1
DND C6A F6 1
DND N1A F6 1
DND C2A F6 1
DND N3A F6 1
DND C4A F6 1
DND C2D F7 1
DND C3D F7 1
DND C4D F7 1
DND O4D F7 1
DND C1D F7 1
DND C5D F7 1
DND O5D F7 1
DND O3D F7 1
DND O2D F7 1
DND C2B F7 2
DND C3B F7 2
DND C4B F7 2
DND O4B F7 2
DND C1B F7 2
DND C5B F7 2
DND O5B F7 2
DND O3B F7 2
DND O2B F7 2
#
_pdbe_chem_comp_rdkit_properties.comp_id DND
_pdbe_chem_comp_rdkit_properties.exactmw 665.100
_pdbe_chem_comp_rdkit_properties.amw 665.422
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 21
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 9
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 18
_pdbe_chem_comp_rdkit_properties.NumHBD 8
_pdbe_chem_comp_rdkit_properties.NumHBA 20
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 44
_pdbe_chem_comp_rdkit_properties.NumAtoms 71
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 23
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.476
_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 284.066
_pdbe_chem_comp_rdkit_properties.tpsa 312.470
_pdbe_chem_comp_rdkit_properties.CrippenClogP -3.280
_pdbe_chem_comp_rdkit_properties.CrippenMR 134.522
_pdbe_chem_comp_rdkit_properties.chi0v 21.990
_pdbe_chem_comp_rdkit_properties.chi1v 13.488
_pdbe_chem_comp_rdkit_properties.chi2v 6.939
_pdbe_chem_comp_rdkit_properties.chi3v 6.939
_pdbe_chem_comp_rdkit_properties.chi4v 4.577
_pdbe_chem_comp_rdkit_properties.chi0n 47.201
_pdbe_chem_comp_rdkit_properties.chi1n 23.319
_pdbe_chem_comp_rdkit_properties.chi2n 4.709
_pdbe_chem_comp_rdkit_properties.chi3n 4.709
_pdbe_chem_comp_rdkit_properties.chi4n 2.941
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -3.010
_pdbe_chem_comp_rdkit_properties.kappa1 12.648
_pdbe_chem_comp_rdkit_properties.kappa2 12.410
_pdbe_chem_comp_rdkit_properties.kappa3 6.650
_pdbe_chem_comp_rdkit_properties.Phi 3.568
#
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
DND UniChem DrugBank DB04099
DND UniChem 'KEGG LIGAND' C00857
DND UniChem ChEBI 18304
DND UniChem ZINC ZINC000008216447
DND UniChem HMDB HMDB0001179
DND UniChem 'PubChem TPHARMA' 57280724
DND UniChem PubChem 165491
DND UniChem NMRShiftDB 60020891
DND UniChem Nikkaji J2.686.411I
DND UniChem Nikkaji J667.336H
DND UniChem Nikkaji J713.045G
DND UniChem MetaboLights MTBLC18304
DND UniChem BRENDA 1300
DND UniChem BRENDA 136900
DND UniChem BRENDA 1467
DND UniChem BRENDA 20434
DND UniChem BRENDA 208342
DND UniChem BRENDA 51843
DND UniChem BRENDA 6713
DND UniChem 'Probes And Drugs' PD059385
#
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
DND PN -1.424 0.534 2.741 ETKDGv3 1
DND O11 -0.902 1.646 1.859 ETKDGv3 2
DND O12 -1.957 1.195 4.207 ETKDGv3 3
DND O3P -0.211 -0.634 3.016 ETKDGv3 4
DND O5D -2.731 -0.204 1.934 ETKDGv3 5
DND C5D -3.275 -1.197 2.772 ETKDGv3 6
DND C4D -4.349 -1.986 2.015 ETKDGv3 7
DND O4D -5.330 -1.108 1.513 ETKDGv3 8
DND C3D -3.778 -2.779 0.844 ETKDGv3 9
DND O3D -3.335 -4.051 1.243 ETKDGv3 10
DND C2D -4.960 -2.866 -0.099 ETKDGv3 11
DND O2D -5.642 -4.095 0.005 ETKDGv3 12
DND C1D -5.854 -1.691 0.336 ETKDGv3 13
DND N1N -5.948 -0.679 -0.733 ETKDGv3 14
DND C6N -4.947 0.131 -0.979 ETKDGv3 15
DND C5N -5.030 1.121 -2.065 ETKDGv3 16
DND C4N -6.130 1.182 -2.817 ETKDGv3 17
DND C3N -7.255 0.255 -2.559 ETKDGv3 18
DND C2N -7.140 -0.633 -1.553 ETKDGv3 19
DND C7N -8.469 0.313 -3.402 ETKDGv3 20
DND O7N -9.435 -0.471 -3.195 ETKDGv3 21
DND O8N -8.554 1.241 -4.437 ETKDGv3 22
DND PA 1.169 0.168 3.613 ETKDGv3 23
DND O13 0.826 0.965 4.852 ETKDGv3 24
DND O14 2.331 -0.991 4.030 ETKDGv3 25
DND O5B 1.819 1.216 2.435 ETKDGv3 26
DND C5B 2.160 0.450 1.304 ETKDGv3 27
DND C4B 2.691 1.381 0.211 ETKDGv3 28
DND O4B 3.851 2.043 0.668 ETKDGv3 29
DND C3B 3.036 0.624 -1.067 ETKDGv3 30
DND O3B 1.937 0.543 -1.938 ETKDGv3 31
DND C2B 4.150 1.459 -1.650 ETKDGv3 32
DND O2B 3.678 2.401 -2.587 ETKDGv3 33
DND C1B 4.748 2.151 -0.418 ETKDGv3 34
DND N9A 6.027 1.542 -0.053 ETKDGv3 35
DND C4A 7.271 1.761 -0.688 ETKDGv3 36
DND N3A 7.585 2.696 -1.531 ETKDGv3 37
DND C2A 8.896 2.630 -2.142 ETKDGv3 38
DND N1A 9.699 1.622 -1.888 ETKDGv3 39
DND C6A 9.305 0.555 -0.995 ETKDGv3 40
DND C5A 8.114 0.658 -0.406 ETKDGv3 41
DND N7A 7.401 -0.279 0.388 ETKDGv3 42
DND C8A 6.218 0.250 0.564 ETKDGv3 43
DND N6A 10.153 -0.575 -0.790 ETKDGv3 44
DND H1 -1.934 0.444 4.852 ETKDGv3 45
DND H2 -2.496 -1.913 3.123 ETKDGv3 46
DND H3 -3.759 -0.726 3.657 ETKDGv3 47
DND H4 -4.839 -2.684 2.733 ETKDGv3 48
DND H5 -2.956 -2.219 0.337 ETKDGv3 49
DND H6 -2.445 -3.921 1.663 ETKDGv3 50
DND H7 -4.613 -2.750 -1.150 ETKDGv3 51
DND H8 -5.945 -4.203 0.945 ETKDGv3 52
DND H9 -6.875 -2.064 0.581 ETKDGv3 53
DND H10 -4.037 0.085 -0.394 ETKDGv3 54
DND H11 -4.202 1.793 -2.252 ETKDGv3 55
DND H12 -6.188 1.910 -3.616 ETKDGv3 56
DND H13 -7.948 -1.327 -1.351 ETKDGv3 57
DND H14 -9.379 1.293 -5.023 ETKDGv3 58
DND H15 1.858 -1.617 4.634 ETKDGv3 59
DND H16 2.951 -0.292 1.559 ETKDGv3 60
DND H17 1.267 -0.082 0.904 ETKDGv3 61
DND H18 1.915 2.149 -0.008 ETKDGv3 62
DND H19 3.433 -0.394 -0.839 ETKDGv3 63
DND H20 1.349 -0.174 -1.584 ETKDGv3 64
DND H21 4.893 0.806 -2.160 ETKDGv3 65
DND H22 3.027 2.996 -2.129 ETKDGv3 66
DND H23 4.920 3.231 -0.625 ETKDGv3 67
DND H24 9.211 3.411 -2.820 ETKDGv3 68
DND H25 5.438 -0.260 1.112 ETKDGv3 69
DND H26 9.873 -1.354 -0.154 ETKDGv3 70
DND H27 11.074 -0.630 -1.279 ETKDGv3 71
#