data_XYQ
#
_chem_comp.id XYQ
_chem_comp.name
'(2R,3R,4S,5R)-5-({[(R)-{[(R)-{[(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHOXY}(HYDROXY)PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]OXY}METHYL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL ACETATE'
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula 'C17 H25 N5 O15 P2'
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ACETYL-RIBOSYL-ADP
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2006-07-13
_chem_comp.pdbx_modified_date 2024-09-27
_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 601.352
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code XYQ
_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 ?
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site RCSB
_chem_comp.pdbx_pcm Y
#
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
XYQ O5 O5 O 0 1 N N N N N N -0.359 39.124 84.350 -7.889 1.042 -3.134 O5 XYQ 1
XYQ CH CH C 0 1 N N N N N N -0.456 39.139 85.683 -8.361 1.931 -2.464 CH XYQ 2
XYQ CH3 CH3 C 0 1 N N N N N N 0.730 39.155 86.487 -8.775 3.226 -3.115 CH3 XYQ 3
XYQ OH OH O 0 1 N N N N N N -1.698 39.087 86.328 -8.516 1.764 -1.142 OH XYQ 4
XYQ C1N C1N C 0 1 N N R N N N -1.665 38.933 87.761 -8.118 0.517 -0.515 C1N XYQ 5
XYQ C2N C2N C 0 1 N N R N N N -1.907 37.439 87.981 -8.619 0.480 0.945 C2N XYQ 6
XYQ C3N C3N C 0 1 N N S N N N -3.392 37.345 88.015 -7.425 -0.186 1.685 C3N XYQ 7
XYQ O3N O3N O 0 1 N N N N N N -3.869 36.983 86.685 -7.363 0.237 3.049 O3N XYQ 8
XYQ O2N O2N O 0 1 N N N N N N -1.223 36.535 87.161 -8.852 1.800 1.439 O2N XYQ 9
XYQ O4N O4N O 0 1 N N N N N N -2.827 39.638 88.009 -6.689 0.422 -0.486 O4N XYQ 10
XYQ C4N C4N C 0 1 N N R N N N -3.903 38.715 88.222 -6.228 0.370 0.873 C4N XYQ 11
XYQ C5N C5N C 0 1 N N N N N N -4.349 38.784 89.699 -5.024 -0.568 0.990 C5N XYQ 12
XYQ O5N O5N O 0 1 N N N N N N -5.606 38.139 89.849 -3.917 -0.012 0.277 O5N XYQ 13
XYQ PN PN P 0 1 N N R N N N -5.873 37.012 90.997 -2.693 -1.045 0.442 PN XYQ 14
XYQ ON2 ON2 O 0 1 N N N N N N -4.740 36.078 91.073 -3.059 -2.432 -0.289 ON2 XYQ 15
XYQ ON1 ON1 O 0 1 N N N N N N -7.255 36.600 90.834 -2.447 -1.294 1.880 ON1 XYQ 16
XYQ ON3 ON3 O 0 1 N N N N N N -5.681 37.923 92.320 -1.369 -0.419 -0.228 ON3 XYQ 17
XYQ PA PA P 0 1 N N R N N N -6.798 38.912 92.951 -0.122 -1.286 0.307 PA XYQ 18
XYQ OA2 OA2 O 0 1 N N N N N N -6.003 39.618 93.994 0.193 -0.887 1.834 OA2 XYQ 19
XYQ O5A O5A O 0 1 N N N N N N -7.927 37.989 93.523 1.170 -0.986 -0.605 O5A XYQ 20
XYQ C5A C5A C 0 1 N N N N N N -7.730 37.201 94.708 2.204 -1.866 -0.159 C5A XYQ 21
XYQ C4A C4A C 0 1 N N R N N N -9.048 36.584 95.072 3.468 -1.631 -0.988 C4A XYQ 22
XYQ O4A O4A O 0 1 N N N N N N -8.893 35.536 96.052 3.994 -0.321 -0.716 O4A XYQ 23
XYQ C1A C1A C 0 1 N N R N N N -9.618 35.894 97.258 5.432 -0.419 -0.801 C1A XYQ 24
XYQ N9 N9 N 0 1 Y N N N N N -8.875 35.334 98.387 6.068 0.680 -0.070 N9 XYQ 25
XYQ C8 C8 C 0 1 Y N N N N N -7.735 35.780 98.970 5.516 1.397 0.949 C8 XYQ 26
XYQ N7 N7 N 0 1 Y N N N N N -7.350 34.875 99.932 6.359 2.296 1.368 N7 XYQ 27
XYQ C5 C5 C 0 1 Y N N N N N -8.245 33.889 99.883 7.502 2.214 0.645 C5 XYQ 28
XYQ C4 C4 C 0 1 Y N N N N N -9.130 34.152 98.899 7.331 1.172 -0.283 C4 XYQ 29
XYQ N3 N3 N 0 1 Y N N N N N -10.227 33.291 98.602 8.319 0.890 -1.125 N3 XYQ 30
XYQ C2 C2 C 0 1 Y N N N N N -10.320 32.122 99.275 9.448 1.567 -1.088 C2 XYQ 31
XYQ N1 N1 N 0 1 Y N N N N N -9.374 31.868 100.211 9.656 2.550 -0.231 N1 XYQ 32
XYQ C6 C6 C 0 1 Y N N N N N -8.382 32.698 100.519 8.724 2.908 0.646 C6 XYQ 33
XYQ N6 N6 N 0 1 N N N N N N -7.391 32.465 101.428 8.952 3.939 1.541 N6 XYQ 34
XYQ C2A C2A C 0 1 N N R N N N -10.053 37.374 97.173 5.743 -1.780 -0.127 C2A XYQ 35
XYQ C3A C3A C 0 1 N N S N N N -9.898 37.678 95.682 4.551 -2.654 -0.595 C3A XYQ 36
XYQ O3A O3A O 0 1 N N N N N N -11.187 37.406 95.070 4.927 -3.451 -1.720 O3A XYQ 37
XYQ O2A O2A O 0 1 N N N N N N -11.319 37.542 97.718 6.982 -2.312 -0.600 O2A XYQ 38
XYQ OA1 OA1 O 0 1 N N N N N N -7.472 39.767 91.881 -0.455 -2.726 0.231 OA1 XYQ 39
XYQ HH31 1HH3 H 0 0 N N N N N N 0.751 38.261 87.127 -8.574 3.175 -4.185 HH31 XYQ 40
XYQ HH32 2HH3 H 0 0 N N N N N N 0.734 40.057 87.116 -9.840 3.390 -2.952 HH32 XYQ 41
XYQ HH33 3HH3 H 0 0 N N N N N N 1.616 39.159 85.835 -8.210 4.049 -2.678 HH33 XYQ 42
XYQ H1N H1N H 0 1 N N N N N N -0.783 39.244 88.340 -8.532 -0.325 -1.070 H1N XYQ 43
XYQ H2N H2N H 0 1 N N N N N N -1.444 37.086 88.914 -9.518 -0.130 1.033 H2N XYQ 44
XYQ H3N H3N H 0 1 N N N N N N -3.707 36.625 88.785 -7.477 -1.272 1.615 H3N XYQ 45
XYQ HO3N HO3N H 0 0 N N N N N N -4.816 36.904 86.698 -8.133 -0.142 3.494 HO3N XYQ 46
XYQ HO2N HO2N H 0 0 N N N N N N -1.068 36.932 86.312 -9.601 2.157 0.942 HO2N XYQ 47
XYQ H4N H4N H 0 1 N N N N N N -4.730 38.960 87.539 -5.964 1.368 1.222 H4N XYQ 48
XYQ H5N1 1H5N H 0 0 N N N N N N -4.440 39.837 90.004 -4.757 -0.688 2.040 H5N1 XYQ 49
XYQ H5N2 2H5N H 0 0 N N N N N N -3.602 38.281 90.330 -5.278 -1.540 0.566 H5N2 XYQ 50
XYQ HON2 HON2 H 0 0 N N N N N N -4.436 35.877 90.196 -3.211 -2.226 -1.221 HON2 XYQ 51
XYQ HOA2 HOA2 H 0 0 N N N N N N -5.122 39.768 93.673 0.404 0.056 1.839 HOA2 XYQ 52
XYQ H5A1 1H5A H 0 0 N N N N N N -7.361 37.831 95.531 2.418 -1.672 0.893 H5A1 XYQ 53
XYQ H5A2 2H5A H 0 0 N N N N N N -6.985 36.414 94.518 1.878 -2.899 -0.279 H5A2 XYQ 54
XYQ H4A H4A H 0 1 N N N N N N -9.503 36.146 94.171 3.237 -1.724 -2.049 H4A XYQ 55
XYQ H1A H1A H 0 1 N N N N N N -10.610 35.445 97.414 5.755 -0.424 -1.842 H1A XYQ 56
XYQ H8 H8 H 0 1 N N N N N N -7.216 36.694 98.721 4.526 1.241 1.351 H8 XYQ 57
XYQ H2 H2 H 0 1 N N N N N N -11.116 31.420 99.075 10.232 1.309 -1.784 H2 XYQ 58
XYQ HN61 1HN6 H 0 0 N N N N N N -7.365 33.213 102.092 8.263 4.190 2.176 HN61 XYQ 59
XYQ HN62 2HN6 H 0 0 N N N N N N -6.511 32.408 100.956 9.799 4.410 1.532 HN62 XYQ 60
XYQ H2A H2A H 0 1 N N N N N N -9.461 38.089 97.763 5.753 -1.682 0.959 H2A XYQ 61
XYQ H3A H3A H 0 1 N N N N N N -9.506 38.696 95.544 4.199 -3.288 0.219 H3A XYQ 62
XYQ HO3A HO3A H 0 0 N N N N N N -11.852 37.347 95.745 5.646 -4.027 -1.427 HO3A XYQ 63
XYQ HO2A HO2A H 0 0 N N N N N N -11.254 37.580 98.665 7.116 -3.154 -0.144 HO2A XYQ 64
#
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
XYQ O5 CH DOUB N N 1
XYQ CH CH3 SING N N 2
XYQ CH OH SING N N 3
XYQ CH3 HH31 SING N N 4
XYQ CH3 HH32 SING N N 5
XYQ CH3 HH33 SING N N 6
XYQ OH C1N SING N N 7
XYQ C1N C2N SING N N 8
XYQ C1N O4N SING N N 9
XYQ C1N H1N SING N N 10
XYQ C2N C3N SING N N 11
XYQ C2N O2N SING N N 12
XYQ C2N H2N SING N N 13
XYQ C3N O3N SING N N 14
XYQ C3N C4N SING N N 15
XYQ C3N H3N SING N N 16
XYQ O3N HO3N SING N N 17
XYQ O2N HO2N SING N N 18
XYQ O4N C4N SING N N 19
XYQ C4N C5N SING N N 20
XYQ C4N H4N SING N N 21
XYQ C5N O5N SING N N 22
XYQ C5N H5N1 SING N N 23
XYQ C5N H5N2 SING N N 24
XYQ O5N PN SING N N 25
XYQ PN ON2 SING N N 26
XYQ PN ON1 DOUB N N 27
XYQ PN ON3 SING N N 28
XYQ ON2 HON2 SING N N 29
XYQ ON3 PA SING N N 30
XYQ PA OA2 SING N N 31
XYQ PA O5A SING N N 32
XYQ PA OA1 DOUB N N 33
XYQ OA2 HOA2 SING N N 34
XYQ O5A C5A SING N N 35
XYQ C5A C4A SING N N 36
XYQ C5A H5A1 SING N N 37
XYQ C5A H5A2 SING N N 38
XYQ C4A O4A SING N N 39
XYQ C4A C3A SING N N 40
XYQ C4A H4A SING N N 41
XYQ O4A C1A SING N N 42
XYQ C1A N9 SING N N 43
XYQ C1A C2A SING N N 44
XYQ C1A H1A SING N N 45
XYQ N9 C8 SING Y N 46
XYQ N9 C4 SING Y N 47
XYQ C8 N7 DOUB Y N 48
XYQ C8 H8 SING N N 49
XYQ N7 C5 SING Y N 50
XYQ C5 C4 SING Y N 51
XYQ C5 C6 DOUB Y N 52
XYQ C4 N3 DOUB Y N 53
XYQ N3 C2 SING Y N 54
XYQ C2 N1 DOUB Y N 55
XYQ C2 H2 SING N N 56
XYQ N1 C6 SING Y N 57
XYQ C6 N6 SING N N 58
XYQ N6 HN61 SING N N 59
XYQ N6 HN62 SING N N 60
XYQ C2A C3A SING N N 61
XYQ C2A O2A SING N N 62
XYQ C2A H2A SING N N 63
XYQ C3A O3A SING N N 64
XYQ C3A H3A SING N N 65
XYQ O3A HO3A SING N N 66
XYQ O2A HO2A SING N N 67
#
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
XYQ SMILES ACDLabs 10.04 'O=C(OC1OC(C(O)C1O)COP(=O)(O)OP(=O)(O)OCC4OC(n2c3ncnc(N)c3nc2)C(O)C4O)C'
XYQ SMILES_CANONICAL CACTVS 3.341 'CC(=O)O[C@H]1O[C@H](CO[P@](O)(=O)O[P@@](O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)n3cnc4c(N)ncnc34)[C@@H](O)[C@H]1O'
XYQ SMILES CACTVS 3.341 'CC(=O)O[CH]1O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]2O[CH]([CH](O)[CH]2O)n3cnc4c(N)ncnc34)[CH](O)[CH]1O'
XYQ SMILES_CANONICAL 'OpenEye OEToolkits' 1.5.0 'CC(=O)O[C@@H]1[C@@H]([C@@H]([C@H](O1)CO[P@@](=O)(O)O[P@](=O)(O)OC[C@@H]2[C@H]([C@H]([C@@H](O2)n3cnc4c3ncnc4N)O)O)O)O'
XYQ SMILES 'OpenEye OEToolkits' 1.5.0 'CC(=O)OC1C(C(C(O1)COP(=O)(O)OP(=O)(O)OCC2C(C(C(O2)n3cnc4c3ncnc4N)O)O)O)O'
XYQ InChI InChI 1.03 'InChI=1S/C17H25N5O15P2/c1-6(23)34-17-13(27)11(25)8(36-17)3-33-39(30,31)37-38(28,29)32-2-7-10(24)12(26)16(35-7)22-5-21-9-14(18)19-4-20-15(9)22/h4-5,7-8,10-13,16-17,24-27H,2-3H2,1H3,(H,28,29)(H,30,31)(H2,18,19,20)/t7-,8-,10-,11-,12-,13-,16-,17+/m1/s1'
XYQ InChIKey InChI 1.03 IJOUKWCBVUMMCR-DLFWLGJNSA-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
XYQ 'SYSTEMATIC NAME' ACDLabs 10.04 '(2R,3R,4S,5R)-5-({[(R)-{[(R)-{[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}methyl)-3,4-dihydroxytetrahydrofuran-2-yl acetate (non-preferred name)'
XYQ 'SYSTEMATIC NAME' 'OpenEye OEToolkits' 1.5.0 '[(2R,3R,4S,5R)-5-[[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl]oxy-hydroxy-phosphoryl]oxymethyl]-3,4-dihydroxy-oxolan-2-yl] ethanoate'
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
XYQ 'Create component' 2006-07-13 RCSB
XYQ 'Modify descriptor' 2011-06-04 RCSB
XYQ 'Modify synonyms' 2021-03-01 PDBE
XYQ 'Modify PCM' 2024-09-27 PDBE
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id XYQ
_pdbx_chem_comp_synonyms.name ACETYL-RIBOSYL-ADP
_pdbx_chem_comp_synonyms.provenance ?
_pdbx_chem_comp_synonyms.type ?
#
_pdbx_chem_comp_pcm.pcm_id 1
_pdbx_chem_comp_pcm.comp_id XYQ
_pdbx_chem_comp_pcm.modified_residue_id LYS
_pdbx_chem_comp_pcm.type None
_pdbx_chem_comp_pcm.category 'Covalent chemical modification'
_pdbx_chem_comp_pcm.position 'Amino-acid side chain'
_pdbx_chem_comp_pcm.polypeptide_position 'Any position'
_pdbx_chem_comp_pcm.comp_id_linking_atom CH
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom NZ
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession ?
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession ?
#
_pdbe_chem_comp_synonyms.comp_id XYQ
_pdbe_chem_comp_synonyms.name ACETYL-RIBOSYL-ADP
_pdbe_chem_comp_synonyms.provenance wwPDB
_pdbe_chem_comp_synonyms.type ?
#
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
XYQ O5 O 18.829 -3.292 1
XYQ CH C 19.944 -4.296 2
XYQ CH3 C 21.370 -3.833 3
XYQ OH O 19.632 -5.763 4
XYQ C1N C 18.206 -6.227 5
XYQ C2N C 17.742 -7.653 6
XYQ C3N C 16.242 -7.653 7
XYQ O3N O 15.360 -8.867 8
XYQ O2N O 18.624 -8.867 9
XYQ O4N O 16.992 -5.345 10
XYQ C4N C 15.778 -6.227 11
XYQ C5N C 14.352 -5.763 12
XYQ O5N O 14.040 -4.296 13
XYQ PN P 12.614 -3.833 14
XYQ ON2 O 13.077 -2.406 15
XYQ ON1 O 12.150 -5.259 16
XYQ ON3 O 11.187 -3.369 17
XYQ PA P 10.875 -1.902 18
XYQ OA2 O 9.408 -2.214 19
XYQ O5A O 10.563 -0.434 20
XYQ C5A C 9.136 0.029 21
XYQ C4A C 8.825 1.496 22
XYQ O4A O 7.454 2.107 23
XYQ C1A C 7.611 3.598 24
XYQ N9 N 6.496 4.602 25
XYQ C8 C 5.038 4.291 26
XYQ N7 N 4.289 5.580 27
XYQ C5 C 5.282 6.692 28
XYQ C4 C 6.654 6.085 29
XYQ N3 N 7.865 6.968 30
XYQ C2 C 7.706 8.460 31
XYQ N1 N 6.335 9.068 32
XYQ C6 C 5.123 8.184 33
XYQ N6 N 3.752 8.792 34
XYQ C2A C 9.078 3.910 35
XYQ C3A C 9.828 2.611 36
XYQ O3A O 11.320 2.454 37
XYQ O2A O 9.688 5.280 38
XYQ OA1 O 12.342 -1.590 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
XYQ O5 CH DOUBLE NONE 1
XYQ CH CH3 SINGLE NONE 2
XYQ CH OH SINGLE NONE 3
XYQ C1N OH SINGLE BEGINDASH 4
XYQ C1N C2N SINGLE NONE 5
XYQ C1N O4N SINGLE NONE 6
XYQ C2N C3N SINGLE NONE 7
XYQ C2N O2N SINGLE BEGINDASH 8
XYQ C3N O3N SINGLE BEGINDASH 9
XYQ C3N C4N SINGLE NONE 10
XYQ O4N C4N SINGLE NONE 11
XYQ C4N C5N SINGLE BEGINWEDGE 12
XYQ C5N O5N SINGLE NONE 13
XYQ O5N PN SINGLE NONE 14
XYQ PN ON2 SINGLE BEGINWEDGE 15
XYQ PN ON1 DOUBLE NONE 16
XYQ PN ON3 SINGLE NONE 17
XYQ ON3 PA SINGLE NONE 18
XYQ PA OA2 SINGLE BEGINWEDGE 19
XYQ PA O5A SINGLE NONE 20
XYQ PA OA1 DOUBLE NONE 21
XYQ O5A C5A SINGLE NONE 22
XYQ C4A C5A SINGLE BEGINWEDGE 23
XYQ C4A O4A SINGLE NONE 24
XYQ C4A C3A SINGLE NONE 25
XYQ O4A C1A SINGLE NONE 26
XYQ C1A N9 SINGLE BEGINWEDGE 27
XYQ C1A C2A SINGLE NONE 28
XYQ N9 C8 SINGLE NONE 29
XYQ N9 C4 SINGLE NONE 30
XYQ C8 N7 DOUBLE NONE 31
XYQ N7 C5 SINGLE NONE 32
XYQ C5 C4 DOUBLE NONE 33
XYQ C5 C6 SINGLE NONE 34
XYQ C4 N3 SINGLE NONE 35
XYQ N3 C2 DOUBLE NONE 36
XYQ C2 N1 SINGLE NONE 37
XYQ N1 C6 DOUBLE NONE 38
XYQ C6 N6 SINGLE NONE 39
XYQ C2A C3A SINGLE NONE 40
XYQ C2A O2A SINGLE BEGINDASH 41
XYQ C3A O3A SINGLE BEGINDASH 42
#
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
XYQ MurckoScaffold S1 scaffold 'O=[PH](OC[C@@H]1CCCO1)O[PH](=O)OC[C@@H]1CC[C@H](n2cnc3cncnc32)O1' InChI=1S/C15H22N4O7P2/c20-27(23-7-11-2-1-5-22-11)26-28(21)24-8-12-3-4-14(25-12)19-10-18-13-6-16-9-17-15(13)19/h6,9-12,14,27-28H,1-5,7-8H2/t11-,12-,14+/m0/s1 UJUHCPFOMLEXIT-SGMGOOAPSA-N
XYQ 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
XYQ furanose F2 fragment OC1CCCO1 InChI=1S/C4H8O2/c5-4-2-1-3-6-4/h4-5H,1-3H2 JNODDICFTDYODH-UHFFFAOYSA-N
XYQ imidazole F3 fragment 'c1c[nH]cn1' InChI=1S/C3H4N2/c1-2-5-3-4-1/h1-3H,(H,4,5) RAXXELZNTBOGNW-UHFFFAOYSA-N
XYQ phosphate F4 fragment O=P(O)(O)O InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4) NBIIXXVUZAFLBC-UHFFFAOYSA-N
XYQ purine F5 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
XYQ pyrimidine F6 fragment c1cncnc1 InChI=1S/C4H4N2/c1-2-5-4-6-3-1/h1-4H CZPWVGJYEJSRLH-UHFFFAOYSA-N
XYQ 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
XYQ C1N S1 1
XYQ C2N S1 1
XYQ C3N S1 1
XYQ O4N S1 1
XYQ C4N S1 1
XYQ C5N S1 1
XYQ O5N S1 1
XYQ PN S1 1
XYQ ON1 S1 1
XYQ ON3 S1 1
XYQ PA S1 1
XYQ O5A S1 1
XYQ C5A S1 1
XYQ C4A S1 1
XYQ O4A S1 1
XYQ C1A S1 1
XYQ N9 S1 1
XYQ C8 S1 1
XYQ N7 S1 1
XYQ C5 S1 1
XYQ C4 S1 1
XYQ N3 S1 1
XYQ C2 S1 1
XYQ N1 S1 1
XYQ C6 S1 1
XYQ C2A S1 1
XYQ C3A S1 1
XYQ OA1 S1 1
XYQ N1 F1 1
XYQ C6 F1 1
XYQ C5 F1 1
XYQ C4 F1 1
XYQ N3 F1 1
XYQ C2 F1 1
XYQ N9 F1 1
XYQ C8 F1 1
XYQ N7 F1 1
XYQ N6 F1 1
XYQ C3N F2 1
XYQ C4N F2 1
XYQ O4N F2 1
XYQ C1N F2 1
XYQ C2N F2 1
XYQ OH F2 1
XYQ C5 F3 1
XYQ C4 F3 1
XYQ N9 F3 1
XYQ C8 F3 1
XYQ N7 F3 1
XYQ O5N F4 1
XYQ PN F4 1
XYQ ON1 F4 1
XYQ ON2 F4 1
XYQ ON3 F4 1
XYQ ON3 F4 2
XYQ PA F4 2
XYQ OA1 F4 2
XYQ OA2 F4 2
XYQ O5A F4 2
XYQ N7 F5 1
XYQ C8 F5 1
XYQ N9 F5 1
XYQ C4 F5 1
XYQ C5 F5 1
XYQ C6 F5 1
XYQ N1 F5 1
XYQ C2 F5 1
XYQ N3 F5 1
XYQ C5 F6 1
XYQ C4 F6 1
XYQ N3 F6 1
XYQ C2 F6 1
XYQ N1 F6 1
XYQ C6 F6 1
XYQ C2N F7 1
XYQ C3N F7 1
XYQ C4N F7 1
XYQ O4N F7 1
XYQ C1N F7 1
XYQ C5N F7 1
XYQ O5N F7 1
XYQ O3N F7 1
XYQ O2N F7 1
XYQ C2A F7 2
XYQ C3A F7 2
XYQ C4A F7 2
XYQ O4A F7 2
XYQ C1A F7 2
XYQ C5A F7 2
XYQ O5A F7 2
XYQ O3A F7 2
XYQ O2A F7 2
#
_pdbe_chem_comp_rdkit_properties.comp_id XYQ
_pdbe_chem_comp_rdkit_properties.exactmw 601.082
_pdbe_chem_comp_rdkit_properties.amw 601.355
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 20
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 8
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 18
_pdbe_chem_comp_rdkit_properties.NumHBD 7
_pdbe_chem_comp_rdkit_properties.NumHBA 20
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 39
_pdbe_chem_comp_rdkit_properties.NumAtoms 64
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 22
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.647
_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 10
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 253.366
_pdbe_chem_comp_rdkit_properties.tpsa 297.590
_pdbe_chem_comp_rdkit_properties.CrippenClogP -3.521
_pdbe_chem_comp_rdkit_properties.CrippenMR 117.709
_pdbe_chem_comp_rdkit_properties.chi0v 19.543
_pdbe_chem_comp_rdkit_properties.chi1v 12.021
_pdbe_chem_comp_rdkit_properties.chi2v 6.126
_pdbe_chem_comp_rdkit_properties.chi3v 6.126
_pdbe_chem_comp_rdkit_properties.chi4v 4.061
_pdbe_chem_comp_rdkit_properties.chi0n 42.754
_pdbe_chem_comp_rdkit_properties.chi1n 20.944
_pdbe_chem_comp_rdkit_properties.chi2n 3.896
_pdbe_chem_comp_rdkit_properties.chi3n 3.896
_pdbe_chem_comp_rdkit_properties.chi4n 2.425
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -2.160
_pdbe_chem_comp_rdkit_properties.kappa1 11.256
_pdbe_chem_comp_rdkit_properties.kappa2 11.376
_pdbe_chem_comp_rdkit_properties.kappa3 6.603
_pdbe_chem_comp_rdkit_properties.Phi 3.283
#
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
XYQ UniChem ZINC ZINC000058661159
XYQ UniChem PubChem 49867878
#
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
XYQ O5 7.490 0.592 1.909 ETKDGv3 1
XYQ CH 7.947 0.910 0.778 ETKDGv3 2
XYQ CH3 8.956 2.002 0.670 ETKDGv3 3
XYQ OH 7.488 0.280 -0.383 ETKDGv3 4
XYQ C1N 6.499 -0.748 -0.368 ETKDGv3 5
XYQ C2N 6.286 -1.317 -1.765 ETKDGv3 6
XYQ C3N 4.844 -1.758 -1.706 ETKDGv3 7
XYQ O3N 4.220 -1.653 -2.960 ETKDGv3 8
XYQ O2N 6.506 -0.350 -2.769 ETKDGv3 9
XYQ O4N 5.272 -0.237 0.105 ETKDGv3 10
XYQ C4N 4.238 -0.791 -0.684 ETKDGv3 11
XYQ C5N 3.209 -1.481 0.217 ETKDGv3 12
XYQ O5N 2.646 -0.525 1.083 ETKDGv3 13
XYQ PN 1.516 -1.310 2.096 ETKDGv3 14
XYQ ON2 2.324 -2.453 3.047 ETKDGv3 15
XYQ ON1 0.468 -2.017 1.264 ETKDGv3 16
XYQ ON3 0.753 -0.195 3.134 ETKDGv3 17
XYQ PA 0.386 1.197 2.223 ETKDGv3 18
XYQ OA2 -0.666 2.175 3.121 ETKDGv3 19
XYQ O5A -0.331 0.785 0.731 ETKDGv3 20
XYQ C5A -1.667 0.407 0.965 ETKDGv3 21
XYQ C4A -2.260 -0.184 -0.317 ETKDGv3 22
XYQ O4A -3.592 -0.580 -0.082 ETKDGv3 23
XYQ C1A -4.342 -0.320 -1.253 ETKDGv3 24
XYQ N9 -5.511 0.488 -0.906 ETKDGv3 25
XYQ C8 -5.497 1.800 -0.318 ETKDGv3 26
XYQ N7 -6.558 2.077 0.384 ETKDGv3 27
XYQ C5 -7.346 0.897 0.299 ETKDGv3 28
XYQ C4 -6.742 -0.012 -0.416 ETKDGv3 29
XYQ N3 -7.227 -1.357 -0.502 ETKDGv3 30
XYQ C2 -8.324 -1.668 0.138 ETKDGv3 31
XYQ N1 -9.017 -0.675 0.935 ETKDGv3 32
XYQ C6 -8.570 0.550 1.032 ETKDGv3 33
XYQ N6 -9.253 1.510 1.836 ETKDGv3 34
XYQ C2A -3.460 0.398 -2.288 ETKDGv3 35
XYQ C3A -2.257 0.819 -1.473 ETKDGv3 36
XYQ O3A -1.056 0.834 -2.211 ETKDGv3 37
XYQ O2A -3.114 -0.458 -3.353 ETKDGv3 38
XYQ OA1 1.655 1.978 1.962 ETKDGv3 39
XYQ HH31 9.526 1.901 -0.277 ETKDGv3 40
XYQ HH32 8.440 2.985 0.681 ETKDGv3 41
XYQ HH33 9.666 1.951 1.523 ETKDGv3 42
XYQ H1N 6.831 -1.567 0.311 ETKDGv3 43
XYQ H2N 6.959 -2.183 -1.946 ETKDGv3 44
XYQ H3N 4.809 -2.813 -1.343 ETKDGv3 45
XYQ HO3N 3.338 -2.099 -2.872 ETKDGv3 46
XYQ HO2N 5.926 0.434 -2.580 ETKDGv3 47
XYQ H4N 3.733 0.044 -1.221 ETKDGv3 48
XYQ H5N1 3.724 -2.282 0.795 ETKDGv3 49
XYQ H5N2 2.424 -1.930 -0.432 ETKDGv3 50
XYQ HON2 1.627 -2.821 3.647 ETKDGv3 51
XYQ HOA2 -0.218 2.290 3.997 ETKDGv3 52
XYQ H5A1 -2.273 1.290 1.271 ETKDGv3 53
XYQ H5A2 -1.734 -0.373 1.759 ETKDGv3 54
XYQ H4A -1.677 -1.093 -0.587 ETKDGv3 55
XYQ H1A -4.696 -1.289 -1.670 ETKDGv3 56
XYQ H8 -4.674 2.494 -0.420 ETKDGv3 57
XYQ H2 -8.710 -2.676 0.084 ETKDGv3 58
XYQ HN61 -8.898 2.488 1.915 ETKDGv3 59
XYQ HN62 -10.121 1.244 2.354 ETKDGv3 60
XYQ H2A -3.967 1.291 -2.714 ETKDGv3 61
XYQ H3A -2.438 1.846 -1.084 ETKDGv3 62
XYQ HO3A -0.780 -0.101 -2.394 ETKDGv3 63
XYQ HO2A -2.731 -1.292 -2.973 ETKDGv3 64
#