data_ZKD
#
_chem_comp.id ZKD
_chem_comp.name URIDINE-DIPHOSPHATE-1-DEOXY-1-THIO-N-ACETYLGLUCOSAMINE
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C17 H27 N3 O16 P2 S"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2010-06-07
_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 623.419
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code ZKD
_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 2XGO
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site EBI
#
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
ZKD N1 N1 N 0 1 N N N N N N 29.895 7.661 2.333 6.448 -1.004 -0.148 N1 ZKD 1
ZKD C2 C2 C 0 1 N N N N N N 30.263 7.945 3.681 7.119 -2.076 0.310 C2 ZKD 2
ZKD O2 O2 O 0 1 N N N N N N 30.207 9.104 4.104 7.244 -2.239 1.508 O2 ZKD 3
ZKD N3 N3 N 0 1 N N N N N N 30.716 6.897 4.531 7.654 -2.972 -0.541 N3 ZKD 4
ZKD C4 C4 C 0 1 N N N N N N 30.787 5.571 4.049 7.523 -2.807 -1.872 C4 ZKD 5
ZKD O4 O4 O 0 1 N N N N N N 31.161 4.662 4.795 8.007 -3.617 -2.643 O4 ZKD 6
ZKD C5 C5 C 0 1 N N N N N N 30.405 5.304 2.726 6.819 -1.683 -2.367 C5 ZKD 7
ZKD C6 C6 C 0 1 N N N N N N 29.956 6.325 1.866 6.293 -0.800 -1.492 C6 ZKD 8
ZKD PA PA P 0 1 N N N N N N 27.752 8.170 -4.222 0.564 1.922 -0.568 PA ZKD 9
ZKD PB PB P 0 1 N N N N N N 25.130 7.189 -4.459 -2.262 1.038 -0.431 PB ZKD 10
ZKD "C1'" "C1'" C 0 1 N N R N N N 24.101 6.078 -1.408 -4.939 -0.428 0.010 "C1'" ZKD 11
ZKD O1A O1A O 0 1 N N N N N N 28.104 6.715 -4.213 0.863 1.862 -2.149 O1A ZKD 12
ZKD C1B C1B C 0 1 N N R N N N 29.410 8.782 1.466 5.871 -0.049 0.802 C1B ZKD 13
ZKD O1B O1B O 0 1 N N N N N N 25.567 6.013 -5.269 -2.560 1.159 -1.875 O1B ZKD 14
ZKD "N2'" "N2'" N 0 1 N N N N N N 21.753 6.072 -2.450 -5.570 -1.380 2.174 "N2'" ZKD 15
ZKD "O2'" "O2'" O 0 1 N N N N N N 31.018 10.491 0.744 7.718 1.450 1.409 "O2'" ZKD 16
ZKD "C2'" "C2'" C 0 1 N N S N N N 22.836 6.732 -1.937 -5.771 -1.494 0.728 "C2'" ZKD 17
ZKD O2A O2A O 0 1 N N N N N N 28.627 9.166 -4.913 0.221 3.309 -0.184 O2A ZKD 18
ZKD C2B C2B C 0 1 N N R N N N 30.179 9.448 0.311 6.522 1.348 0.635 C2B ZKD 19
ZKD O2B O2B O 0 1 N N N N N N 23.814 7.820 -4.720 -2.834 2.328 0.345 O2B ZKD 20
ZKD "C3'" "C3'" C 0 1 N N R N N N 22.888 8.256 -1.740 -7.252 -1.283 0.398 "C3'" ZKD 21
ZKD "O3'" "O3'" O 0 1 N N N N N N 21.794 8.902 -2.373 -7.675 -0.012 0.895 "O3'" ZKD 22
ZKD O3A O3A O 0 1 N N N N N N 26.231 8.321 -4.755 -0.668 0.947 -0.218 O3A ZKD 23
ZKD C3B C3B C 0 1 N N S N N N 28.987 10.119 -0.340 5.422 2.286 1.189 C3B ZKD 24
ZKD O3B O3B O 0 1 N N N N N N 28.407 11.103 0.537 5.700 2.633 2.547 O3B ZKD 25
ZKD "C4'" "C4'" C 0 1 N N S N N N 22.874 8.442 -0.215 -7.437 -1.327 -1.122 "C4'" ZKD 26
ZKD "O4'" "O4'" O 0 1 N N N N N N 22.729 9.801 0.184 -7.075 -2.621 -1.609 "O4'" ZKD 27
ZKD C4B C4B C 0 1 N N R N N N 28.012 8.960 -0.418 4.131 1.449 1.099 C4B ZKD 28
ZKD O4B O4B O 0 1 N N N N N N 28.242 8.216 0.803 4.478 0.186 0.505 O4B ZKD 29
ZKD "C5'" "C5'" C 0 1 N N R N N N 24.135 7.799 0.413 -6.541 -0.267 -1.768 "C5'" ZKD 30
ZKD "O5'" "O5'" O 0 1 N N N N N N 24.303 6.378 0.010 -5.182 -0.504 -1.396 "O5'" ZKD 31
ZKD C5B C5B C 0 1 N N N N N N 28.418 8.239 -1.684 3.103 2.172 0.227 C5B ZKD 32
ZKD O5B O5B O 0 1 N N N N N N 27.562 8.670 -2.722 1.871 1.448 0.244 O5B ZKD 33
ZKD "C6'" "C6'" C 0 1 N N N N N N 24.088 7.872 1.964 -6.967 1.122 -1.288 "C6'" ZKD 34
ZKD "O6'" "O6'" O 0 1 N N N N N N 24.170 9.243 2.419 -6.236 2.118 -2.006 "O6'" ZKD 35
ZKD "C7'" "C7'" C 0 1 N N N N N N 21.515 4.755 -2.661 -4.520 -1.991 2.759 "C7'" ZKD 36
ZKD "O7'" "O7'" O 0 1 N N N N N N 20.475 4.351 -3.170 -3.742 -2.635 2.088 "O7'" ZKD 37
ZKD "C8'" "C8'" C 0 1 N N N N N N 22.569 3.715 -2.271 -4.313 -1.873 4.247 "C8'" ZKD 38
ZKD "S1'" "S1'" S 0 1 N N N N N N 25.542 6.816 -2.252 -3.178 -0.713 0.337 "S1'" ZKD 39
ZKD H5 H5 H 0 1 N N N N N N 30.456 4.290 2.358 6.705 -1.533 -3.431 H5 ZKD 40
ZKD H6 H6 H 0 1 N N N N N N 29.659 6.090 0.854 5.752 0.064 -1.851 H6 ZKD 41
ZKD "H1'" "H1'" H 0 1 N N N N N N 24.002 4.995 -1.573 -5.222 0.560 0.375 "H1'" ZKD 42
ZKD HO1A HO1A H 0 0 N N N N N N 28.179 6.401 -5.107 1.096 0.980 -2.472 HO1A ZKD 43
ZKD H1B H1B H 0 1 N N N N N N 29.384 9.604 2.197 5.990 -0.408 1.825 H1B ZKD 44
ZKD "HO2'" "HO2'" H 0 0 N N N N N N 31.207 10.383 1.669 8.162 2.306 1.337 "HO2'" ZKD 45
ZKD H2B H2B H 0 1 N N N N N N 30.812 8.758 -0.266 6.721 1.560 -0.416 H2B ZKD 46
ZKD HO2B HO2B H 0 0 N N N N N N 23.358 7.955 -3.897 -2.674 2.316 1.299 HO2B ZKD 47
ZKD "H3'" "H3'" H 0 1 N N N N N N 23.779 8.710 -2.198 -7.845 -2.072 0.861 "H3'" ZKD 48
ZKD "HO3'" "HO3'" H 0 0 N N N N N N 21.101 9.046 -1.739 -8.605 0.188 0.721 "HO3'" ZKD 49
ZKD H3B H3B H 0 1 N N N N N N 29.235 10.621 -1.287 5.342 3.183 0.576 H3B ZKD 50
ZKD HO3B HO3B H 0 0 N N N N N N 28.279 10.724 1.399 6.532 3.111 2.669 HO3B ZKD 51
ZKD "H4'" "H4'" H 0 1 N N N N N N 21.981 7.924 0.165 -8.479 -1.124 -1.368 "H4'" ZKD 52
ZKD "HO4'" "HO4'" H 0 0 N N N N N N 22.697 9.851 1.132 -7.168 -2.720 -2.567 "HO4'" ZKD 53
ZKD H4B H4B H 0 1 N N N N N N 26.937 9.187 -0.476 3.725 1.287 2.098 H4B ZKD 54
ZKD "H5'" "H5'" H 0 1 N N N N N N 24.992 8.377 0.036 -6.637 -0.322 -2.852 "H5'" ZKD 55
ZKD H5B H5B H 0 1 N N N N N N 29.462 8.477 -1.934 2.939 3.177 0.615 H5B ZKD 56
ZKD H5BA H5BA H 0 0 N N N N N N 28.336 7.151 -1.548 3.474 2.234 -0.796 H5BA ZKD 57
ZKD "H6'" "H6'" H 0 1 N N N N N N 23.142 7.434 2.315 -8.034 1.256 -1.466 "H6'" ZKD 58
ZKD "H6'A" "H6'A" H 0 0 N N N N N N 24.945 7.315 2.369 -6.761 1.217 -0.222 "H6'A" ZKD 59
ZKD "HO6'" "HO6'" H 0 0 N N N N N N 24.188 9.261 3.369 -6.455 3.026 -1.753 "HO6'" ZKD 60
ZKD "H8'" "H8'" H 0 1 N N N N N N 23.182 3.466 -3.150 -5.106 -1.262 4.677 "H8'" ZKD 61
ZKD "H8'A" "H8'A" H 0 0 N N N N N N 23.213 4.125 -1.480 -4.337 -2.866 4.697 "H8'A" ZKD 62
ZKD "H8'B" "H8'B" H 0 0 N N N N N N 22.069 2.807 -1.903 -3.348 -1.408 4.444 "H8'B" ZKD 63
ZKD HN3 HN3 H 0 1 N N N N N N 30.985 7.100 5.473 8.135 -3.740 -0.194 HN3 ZKD 64
ZKD "HN2'" "HN2'" H 0 0 N N N N N N 20.999 6.671 -2.718 -6.192 -0.865 2.711 "HN2'" ZKD 65
ZKD "H2'" "H2'" H 0 1 N N N N N N 22.281 6.152 -2.689 -5.460 -2.484 0.394 "H2'" ZKD 66
#
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
ZKD C1B N1 SING N N 1
ZKD C6 N1 SING N N 2
ZKD N1 C2 SING N N 3
ZKD C2 O2 DOUB N N 4
ZKD C2 N3 SING N N 5
ZKD C4 N3 SING N N 6
ZKD C5 C4 SING N N 7
ZKD C4 O4 DOUB N N 8
ZKD C6 C5 DOUB N N 9
ZKD C5 H5 SING N N 10
ZKD C6 H6 SING N N 11
ZKD O2A PA DOUB N N 12
ZKD O3A PA SING N N 13
ZKD PA O1A SING N N 14
ZKD PA O5B SING N N 15
ZKD O1B PB DOUB N N 16
ZKD O3A PB SING N N 17
ZKD O2B PB SING N N 18
ZKD PB "S1'" SING N N 19
ZKD "S1'" "C1'" SING N N 20
ZKD "C2'" "C1'" SING N N 21
ZKD "C1'" "O5'" SING N N 22
ZKD "C1'" "H1'" SING N N 23
ZKD O1A HO1A SING N N 24
ZKD C2B C1B SING N N 25
ZKD O4B C1B SING N N 26
ZKD C1B H1B SING N N 27
ZKD "C7'" "N2'" SING N N 28
ZKD "N2'" "C2'" SING N N 29
ZKD C2B "O2'" SING N N 30
ZKD "O2'" "HO2'" SING N N 31
ZKD "C2'" "C3'" SING N N 32
ZKD C3B C2B SING N N 33
ZKD C2B H2B SING N N 34
ZKD O2B HO2B SING N N 35
ZKD "O3'" "C3'" SING N N 36
ZKD "C3'" "C4'" SING N N 37
ZKD "C3'" "H3'" SING N N 38
ZKD "O3'" "HO3'" SING N N 39
ZKD C4B C3B SING N N 40
ZKD C3B O3B SING N N 41
ZKD C3B H3B SING N N 42
ZKD O3B HO3B SING N N 43
ZKD "C4'" "O4'" SING N N 44
ZKD "C4'" "C5'" SING N N 45
ZKD "C4'" "H4'" SING N N 46
ZKD "O4'" "HO4'" SING N N 47
ZKD C5B C4B SING N N 48
ZKD C4B O4B SING N N 49
ZKD C4B H4B SING N N 50
ZKD "O5'" "C5'" SING N N 51
ZKD "C5'" "C6'" SING N N 52
ZKD "C5'" "H5'" SING N N 53
ZKD O5B C5B SING N N 54
ZKD C5B H5B SING N N 55
ZKD C5B H5BA SING N N 56
ZKD "C6'" "O6'" SING N N 57
ZKD "C6'" "H6'" SING N N 58
ZKD "C6'" "H6'A" SING N N 59
ZKD "O6'" "HO6'" SING N N 60
ZKD "O7'" "C7'" DOUB N N 61
ZKD "C7'" "C8'" SING N N 62
ZKD "C8'" "H8'" SING N N 63
ZKD "C8'" "H8'A" SING N N 64
ZKD "C8'" "H8'B" SING N N 65
ZKD N3 HN3 SING N N 66
ZKD "N2'" "HN2'" SING N N 67
ZKD "C2'" "H2'" SING N N 68
#
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
ZKD SMILES ACDLabs 10.04 O=P(SC1OC(C(O)C(O)C1NC(=O)C)CO)(O)OP(=O)(O)OCC3OC(N2C=CC(=O)NC2=O)C(O)C3O
ZKD SMILES_CANONICAL CACTVS 3.352 CC(=O)N[C@H]1[C@@H](O)[C@H](O)[C@@H](CO)O[C@@H]1S[P](O)(=O)O[P](O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)N3C=CC(=O)NC3=O
ZKD SMILES CACTVS 3.352 CC(=O)N[CH]1[CH](O)[CH](O)[CH](CO)O[CH]1S[P](O)(=O)O[P](O)(=O)OC[CH]2O[CH]([CH](O)[CH]2O)N3C=CC(=O)NC3=O
ZKD SMILES_CANONICAL "OpenEye OEToolkits" 1.6.1 CC(=O)NC1[C@H]([C@@H]([C@H](O[C@@H]1S[P@@](=O)(O)O[P@](=O)(O)OC[C@@H]2[C@H]([C@H]([C@@H](O2)N3C=CC(=O)NC3=O)O)O)CO)O)O
ZKD SMILES "OpenEye OEToolkits" 1.6.1 CC(=O)NC1C(C(C(OC1SP(=O)(O)OP(=O)(O)OCC2C(C(C(O2)N3C=CC(=O)NC3=O)O)O)CO)O)O
ZKD InChI InChI 1.03 InChI=1S/C17H27N3O16P2S/c1-6(22)18-10-13(26)11(24)7(4-21)35-16(10)39-38(31,32)36-37(29,30)33-5-8-12(25)14(27)15(34-8)20-3-2-9(23)19-17(20)28/h2-3,7-8,10-16,21,24-27H,4-5H2,1H3,(H,18,22)(H,29,30)(H,31,32)(H,19,23,28)/t7-,8-,10+,11-,12-,13-,14-,15-,16-/m1/s1
ZKD InChIKey InChI 1.03 NBABRWVWQSKDQY-ZYQOOJPVSA-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
ZKD "SYSTEMATIC NAME" ACDLabs 10.04 "S-[(2R,3S,4R,5S,6R)-3-(acetylamino)-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl] O-{[(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl} dihydrogen thiodiphosphate (non-preferred name)"
ZKD "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.6.1 "[(2R,4R,5S,6R)-3-acetamido-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]sulfanyl-[[(2R,3S,4R,5R)-5-(2,4-dioxopyrimidin-1-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl]oxy-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
ZKD 'Create component' 2010-06-07 EBI
ZKD '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
ZKD N1 N 16.765 4.242 1
ZKD C2 C 17.375 2.872 2
ZKD O2 O 16.493 1.658 3
ZKD N3 N 18.866 2.715 4
ZKD C4 C 19.748 3.929 5
ZKD O4 O 21.240 3.772 6
ZKD C5 C 19.138 5.299 7
ZKD C6 C 17.646 5.456 8
ZKD PA P 10.301 0.894 9
ZKD PB P 9.002 -1.356 10
ZKD "C1'" C 7.702 -3.606 11
ZKD O1A O 11.051 -0.405 12
ZKD C1B C 15.273 4.399 13
ZKD O1B O 10.502 -1.356 14
ZKD "N2'" N 9.002 -5.856 15
ZKD "O2'" O 15.133 7.068 16
ZKD "C2'" C 7.702 -5.106 17
ZKD O2A O 9.551 2.193 18
ZKD C2B C 14.523 5.698 19
ZKD O2B O 7.502 -1.356 20
ZKD "C3'" C 6.404 -5.856 21
ZKD "O3'" O 6.404 -7.356 22
ZKD O3A O 9.002 0.144 23
ZKD C3B C 13.055 5.386 24
ZKD O3B O 11.941 6.390 25
ZKD "C4'" C 5.104 -5.106 26
ZKD "O4'" O 3.805 -5.856 27
ZKD C4B C 12.899 3.894 28
ZKD O4B O 14.269 3.284 29
ZKD "C5'" C 5.104 -3.606 30
ZKD "O5'" O 6.404 -2.856 31
ZKD C5B C 11.600 3.144 32
ZKD O5B O 11.600 1.644 33
ZKD "C6'" C 3.805 -2.856 34
ZKD "O6'" O 3.805 -1.356 35
ZKD "C7'" C 10.301 -5.106 36
ZKD "O7'" O 10.301 -3.606 37
ZKD "C8'" C 11.600 -5.856 38
ZKD "S1'" S 9.002 -2.856 39
#
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
ZKD C1B N1 SINGLE BEGINDASH 1
ZKD C6 N1 SINGLE NONE 2
ZKD N1 C2 SINGLE NONE 3
ZKD C2 O2 DOUBLE NONE 4
ZKD C2 N3 SINGLE NONE 5
ZKD C4 N3 SINGLE NONE 6
ZKD C5 C4 SINGLE NONE 7
ZKD C4 O4 DOUBLE NONE 8
ZKD C6 C5 DOUBLE NONE 9
ZKD O2A PA DOUBLE NONE 10
ZKD O3A PA SINGLE NONE 11
ZKD PA O1A SINGLE BEGINDASH 12
ZKD PA O5B SINGLE NONE 13
ZKD O1B PB DOUBLE NONE 14
ZKD O3A PB SINGLE NONE 15
ZKD PB O2B SINGLE BEGINDASH 16
ZKD PB "S1'" SINGLE NONE 17
ZKD "C1'" "S1'" SINGLE BEGINDASH 18
ZKD "C2'" "C1'" SINGLE NONE 19
ZKD "C1'" "O5'" SINGLE NONE 20
ZKD C2B C1B SINGLE NONE 21
ZKD O4B C1B SINGLE NONE 22
ZKD "C7'" "N2'" SINGLE NONE 23
ZKD "C2'" "N2'" SINGLE BEGINWEDGE 24
ZKD C2B "O2'" SINGLE BEGINWEDGE 25
ZKD "C2'" "C3'" SINGLE NONE 26
ZKD C3B C2B SINGLE NONE 27
ZKD "C3'" "O3'" SINGLE BEGINWEDGE 28
ZKD "C3'" "C4'" SINGLE NONE 29
ZKD C4B C3B SINGLE NONE 30
ZKD C3B O3B SINGLE BEGINWEDGE 31
ZKD "C4'" "O4'" SINGLE BEGINDASH 32
ZKD "C4'" "C5'" SINGLE NONE 33
ZKD C4B C5B SINGLE BEGINDASH 34
ZKD C4B O4B SINGLE NONE 35
ZKD "O5'" "C5'" SINGLE NONE 36
ZKD "C5'" "C6'" SINGLE BEGINWEDGE 37
ZKD O5B C5B SINGLE NONE 38
ZKD "C6'" "O6'" SINGLE NONE 39
ZKD "O7'" "C7'" DOUBLE NONE 40
ZKD "C7'" "C8'" SINGLE NONE 41
#
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
ZKD MurckoScaffold S1 scaffold 'O=c1ccn([C@H]2CC[C@@H](CO[PH](=O)O[PH](=O)S[C@@H]3CCCCO3)O2)c(=O)[nH]1' InChI=1S/C14H22N2O8P2S/c17-11-6-7-16(14(18)15-11)12-5-4-10(23-12)9-22-25(19)24-26(20)27-13-3-1-2-8-21-13/h6-7,10,12-13,25-26H,1-5,8-9H2,(H,15,17,18)/t10-,12+,13+/m0/s1 DLOARBBQQJXLRY-CYZMBNFOSA-N
ZKD amide F1 fragment CC(N)=O InChI=1S/C2H5NO/c1-2(3)4/h1H3,(H2,3,4) DLFVBJFMPXGRIB-UHFFFAOYSA-N
ZKD 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
ZKD pyrimidine F3 fragment c1cncnc1 InChI=1S/C4H4N2/c1-2-5-4-6-3-1/h1-4H CZPWVGJYEJSRLH-UHFFFAOYSA-N
ZKD ribose F4 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
ZKD N1 S1 1
ZKD C2 S1 1
ZKD O2 S1 1
ZKD N3 S1 1
ZKD C4 S1 1
ZKD O4 S1 1
ZKD C5 S1 1
ZKD C6 S1 1
ZKD PA S1 1
ZKD PB S1 1
ZKD "C1'" S1 1
ZKD C1B S1 1
ZKD O1B S1 1
ZKD "C2'" S1 1
ZKD O2A S1 1
ZKD C2B S1 1
ZKD "C3'" S1 1
ZKD O3A S1 1
ZKD C3B S1 1
ZKD "C4'" S1 1
ZKD C4B S1 1
ZKD O4B S1 1
ZKD "C5'" S1 1
ZKD "O5'" S1 1
ZKD C5B S1 1
ZKD O5B S1 1
ZKD "S1'" S1 1
ZKD "N2'" F1 1
ZKD "C7'" F1 1
ZKD "O7'" F1 1
ZKD "C8'" F1 1
ZKD O1A F2 1
ZKD PA F2 1
ZKD O2A F2 1
ZKD O3A F2 1
ZKD O5B F2 1
ZKD C5 F3 1
ZKD C4 F3 1
ZKD N3 F3 1
ZKD C2 F3 1
ZKD N1 F3 1
ZKD C6 F3 1
ZKD C2B F4 1
ZKD C3B F4 1
ZKD C4B F4 1
ZKD O4B F4 1
ZKD C1B F4 1
ZKD C5B F4 1
ZKD O5B F4 1
ZKD O3B F4 1
ZKD "O2'" F4 1
#
_pdbe_chem_comp_rdkit_properties.comp_id ZKD
_pdbe_chem_comp_rdkit_properties.exactmw 623.059
_pdbe_chem_comp_rdkit_properties.amw 623.423
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 19
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 9
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 18
_pdbe_chem_comp_rdkit_properties.NumHBD 9
_pdbe_chem_comp_rdkit_properties.NumHBA 18
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 39
_pdbe_chem_comp_rdkit_properties.NumAtoms 66
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 22
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 1
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.706
_pdbe_chem_comp_rdkit_properties.NumRings 3
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 1
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 2
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 2
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 3
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 1
_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 260.403
_pdbe_chem_comp_rdkit_properties.tpsa 296.630
_pdbe_chem_comp_rdkit_properties.CrippenClogP -2.134
_pdbe_chem_comp_rdkit_properties.CrippenMR 127.106
_pdbe_chem_comp_rdkit_properties.chi0v 20.282
_pdbe_chem_comp_rdkit_properties.chi1v 13.308
_pdbe_chem_comp_rdkit_properties.chi2v 7.987
_pdbe_chem_comp_rdkit_properties.chi3v 7.987
_pdbe_chem_comp_rdkit_properties.chi4v 6.235
_pdbe_chem_comp_rdkit_properties.chi0n 44.676
_pdbe_chem_comp_rdkit_properties.chi1n 21.636
_pdbe_chem_comp_rdkit_properties.chi2n 3.638
_pdbe_chem_comp_rdkit_properties.chi3n 3.638
_pdbe_chem_comp_rdkit_properties.chi4n 2.230
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.480
_pdbe_chem_comp_rdkit_properties.kappa1 11.309
_pdbe_chem_comp_rdkit_properties.kappa2 12.580
_pdbe_chem_comp_rdkit_properties.kappa3 7.837
_pdbe_chem_comp_rdkit_properties.Phi 3.648
#
_pdbe_chem_comp_external_mappings.comp_id ZKD
_pdbe_chem_comp_external_mappings.source UniChem
_pdbe_chem_comp_external_mappings.resource PDBe
_pdbe_chem_comp_external_mappings.resource_id ZKD
#
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
ZKD N1 6.272 0.626 -0.160 ETKDGv3 1
ZKD C2 7.522 1.317 -0.367 ETKDGv3 2
ZKD O2 8.393 0.857 -1.154 ETKDGv3 3
ZKD N3 7.778 2.537 0.332 ETKDGv3 4
ZKD C4 6.808 3.029 1.257 ETKDGv3 5
ZKD O4 7.015 4.103 1.881 ETKDGv3 6
ZKD C5 5.570 2.272 1.483 ETKDGv3 7
ZKD C6 5.337 1.139 0.814 ETKDGv3 8
ZKD PA 0.336 -1.195 -0.785 ETKDGv3 9
ZKD PB -1.215 0.685 0.540 ETKDGv3 10
ZKD "C1'" -4.127 0.073 1.061 ETKDGv3 11
ZKD O1A -0.277 -2.598 -0.059 ETKDGv3 12
ZKD C1B 6.005 -0.656 -0.834 ETKDGv3 13
ZKD O1B -1.691 1.309 -0.752 ETKDGv3 14
ZKD "N2'" -4.868 -1.407 -0.801 ETKDGv3 15
ZKD "O2'" 7.250 -2.735 -0.614 ETKDGv3 16
ZKD "C2'" -4.707 -0.011 -0.375 ETKDGv3 17
ZKD O2A -0.515 -0.850 -1.987 ETKDGv3 18
ZKD C2B 6.409 -1.832 0.068 ETKDGv3 19
ZKD O2B -1.167 1.890 1.726 ETKDGv3 20
ZKD "C3'" -6.056 0.743 -0.445 ETKDGv3 21
ZKD "O3'" -7.112 -0.094 -0.039 ETKDGv3 22
ZKD O3A 0.370 0.091 0.339 ETKDGv3 23
ZKD C3B 5.084 -2.455 0.447 ETKDGv3 24
ZKD O3B 5.169 -3.855 0.522 ETKDGv3 25
ZKD "C4'" -6.056 2.009 0.449 ETKDGv3 26
ZKD "O4'" -6.688 3.065 -0.228 ETKDGv3 27
ZKD C4B 4.171 -2.004 -0.688 ETKDGv3 28
ZKD O4B 4.631 -0.756 -1.155 ETKDGv3 29
ZKD "C5'" -4.613 2.413 0.844 ETKDGv3 30
ZKD "O5'" -3.970 1.388 1.589 ETKDGv3 31
ZKD C5B 2.712 -1.883 -0.237 ETKDGv3 32
ZKD O5B 1.923 -1.487 -1.335 ETKDGv3 33
ZKD "C6'" -4.596 3.690 1.701 ETKDGv3 34
ZKD "O6'" -4.967 4.815 0.950 ETKDGv3 35
ZKD "C7'" -4.988 -1.777 -2.181 ETKDGv3 36
ZKD "O7'" -4.947 -0.899 -3.084 ETKDGv3 37
ZKD "C8'" -5.141 -3.215 -2.555 ETKDGv3 38
ZKD "S1'" -2.544 -0.851 1.193 ETKDGv3 39
ZKD H5 4.844 2.631 2.202 ETKDGv3 40
ZKD H6 4.419 0.602 1.018 ETKDGv3 41
ZKD "H1'" -4.837 -0.459 1.731 ETKDGv3 42
ZKD HO1A 0.034 -2.558 0.880 ETKDGv3 43
ZKD H1B 6.569 -0.696 -1.792 ETKDGv3 44
ZKD "HO2'" 6.777 -3.044 -1.430 ETKDGv3 45
ZKD H2B 6.940 -1.485 0.982 ETKDGv3 46
ZKD HO2B -0.870 1.423 2.547 ETKDGv3 47
ZKD "H3'" -6.209 1.056 -1.506 ETKDGv3 48
ZKD "HO3'" -7.436 -0.574 -0.846 ETKDGv3 49
ZKD H3B 4.753 -2.028 1.424 ETKDGv3 50
ZKD HO3B 4.342 -4.164 0.977 ETKDGv3 51
ZKD "H4'" -6.606 1.795 1.397 ETKDGv3 52
ZKD "HO4'" -7.662 2.869 -0.215 ETKDGv3 53
ZKD H4B 4.225 -2.736 -1.527 ETKDGv3 54
ZKD "H5'" -4.019 2.621 -0.074 ETKDGv3 55
ZKD H5B 2.659 -1.135 0.587 ETKDGv3 56
ZKD H5BA 2.375 -2.875 0.137 ETKDGv3 57
ZKD "H6'" -5.295 3.581 2.557 ETKDGv3 58
ZKD "H6'A" -3.577 3.844 2.126 ETKDGv3 59
ZKD "HO6'" -4.192 5.040 0.373 ETKDGv3 60
ZKD "H8'" -4.207 -3.762 -2.308 ETKDGv3 61
ZKD "H8'A" -5.344 -3.318 -3.642 ETKDGv3 62
ZKD "H8'B" -5.986 -3.660 -1.989 ETKDGv3 63
ZKD HN3 8.670 3.058 0.177 ETKDGv3 64
ZKD "HN2'" -4.889 -2.167 -0.082 ETKDGv3 65
ZKD "H2'" -3.992 0.482 -1.066 ETKDGv3 66
#