data_9XR
#
_chem_comp.id 9XR
_chem_comp.name
"[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl [(2R,3S,4R,5S)-5-(3-carbamoylanilino)-3,4-dihydroxyoxolan-2-yl]methyl dihydrogen diphosphate (non-preferred name)"
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C22 H29 N7 O14 P2"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2021-11-01
_chem_comp.pdbx_modified_date 2022-04-08
_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 677.452
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code 9XR
_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 7SNE
_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
9XR O7N O1 O 0 1 N N N N N N -2.951 56.542 21.053 -7.658 -2.933 1.185 O7N 9XR 1
9XR C7N C1 C 0 1 N N N N N N -4.058 56.037 20.827 -7.814 -3.447 0.095 C7N 9XR 2
9XR N7N N1 N 0 1 N N N N N N -5.177 56.719 21.017 -8.223 -4.728 0.006 N7N 9XR 3
9XR C3N C2 C 0 1 Y N N N N N -4.086 54.627 20.339 -7.561 -2.664 -1.134 C3N 9XR 4
9XR C2N C3 C 0 1 Y N N N N N -5.154 54.152 19.584 -7.133 -1.340 -1.045 C2N 9XR 5
9XR C4N C4 C 0 1 Y N N N N N -3.027 53.794 20.658 -7.745 -3.251 -2.388 C4N 9XR 6
9XR C5N C5 C 0 1 Y N N N N N -3.019 52.489 20.208 -7.508 -2.519 -3.533 C5N 9XR 7
9XR C6N C6 C 0 1 Y N N N N N -4.072 52.015 19.432 -7.089 -1.204 -3.445 C6N 9XR 8
9XR C1N C7 C 0 1 Y N N N N N -5.130 52.859 19.106 -6.893 -0.615 -2.202 C1N 9XR 9
9XR C1D C8 C 0 1 N N S N N N -7.516 52.886 18.484 -6.405 1.381 -0.816 C1D 9XR 10
9XR O4D O2 O 0 1 N N N N N N -7.728 53.769 17.379 -5.079 1.279 -0.282 O4D 9XR 11
9XR C2D C9 C 0 1 N N R N N N -8.670 51.870 18.447 -6.728 2.882 -0.977 C2D 9XR 12
9XR O2D O3 O 0 1 N N N N N N -8.303 50.563 18.072 -6.489 3.312 -2.319 O2D 9XR 13
9XR C3D C10 C 0 1 N N S N N N -9.622 52.426 17.411 -5.724 3.544 0.006 C3D 9XR 14
9XR O3D O4 O 0 1 N N N N N N -9.483 51.755 16.170 -5.387 4.867 -0.414 O3D 9XR 15
9XR C4D C11 C 0 1 N N R N N N -9.148 53.848 17.239 -4.511 2.589 -0.126 C4D 9XR 16
9XR C5D C12 C 0 1 N N N N N N -9.736 54.751 18.319 -3.650 2.647 1.137 C5D 9XR 17
9XR O5D O5 O 0 1 N N N N N N -9.011 55.969 18.377 -2.510 1.800 0.976 O5D 9XR 18
9XR PN P1 P 0 1 N N N N N N -8.842 56.721 19.777 -1.386 1.617 2.114 PN 9XR 19
9XR O1N O6 O 0 1 N N N N N N -8.272 55.812 20.822 -0.621 3.016 2.342 O1N 9XR 20
9XR O2N O7 O 0 1 N N N N N N -8.156 58.030 19.479 -2.027 1.193 3.379 O2N 9XR 21
9XR O3 O8 O 0 1 N N N N N N -10.385 56.988 20.076 -0.327 0.497 1.647 O3 9XR 22
9XR PA P2 P 0 1 N N N N N N -11.122 57.811 21.265 0.741 -0.424 2.423 PA 9XR 23
9XR O1A O9 O 0 1 N N N N N N -10.776 57.171 22.576 -0.016 -1.680 3.088 O1A 9XR 24
9XR O2A O10 O 0 1 N N N N N N -12.573 57.912 20.880 1.401 0.371 3.483 O2A 9XR 25
9XR O5B O11 O 0 1 N N N N N N -10.407 59.251 21.236 1.848 -0.955 1.382 O5B 9XR 26
9XR C5B C13 C 0 1 N N N N N N -10.578 60.144 20.150 2.992 -1.713 1.781 C5B 9XR 27
9XR C4B C14 C 0 1 N N R N N N -10.827 61.523 20.734 3.833 -2.054 0.549 C4B 9XR 28
9XR C3B C15 C 0 1 N N S N N N -9.826 61.990 21.790 5.011 -2.961 0.954 C3B 9XR 29
9XR O3B O12 O 0 1 N N N N N N -8.617 62.547 21.276 4.941 -4.210 0.262 O3B 9XR 30
9XR C2B C16 C 0 1 N N R N N N -10.609 63.079 22.481 6.267 -2.169 0.518 C2B 9XR 31
9XR O2B O13 O 0 1 N N N N N N -10.741 64.251 21.658 7.241 -3.038 -0.065 O2B 9XR 32
9XR C1B C17 C 0 1 N N R N N N -11.976 62.452 22.538 5.688 -1.199 -0.542 C1B 9XR 33
9XR O4B O14 O 0 1 N N N N N N -12.105 61.575 21.393 4.391 -0.853 -0.009 O4B 9XR 34
9XR N9A N2 N 0 1 Y N N N N N -12.339 61.639 23.720 6.530 -0.006 -0.665 N9A 9XR 35
9XR C4A C18 C 0 1 Y N N N N N -13.148 62.051 24.681 7.646 0.122 -1.452 C4A 9XR 36
9XR C5A C19 C 0 1 Y N N N N N -13.332 60.884 25.535 8.118 1.429 -1.247 C5A 9XR 37
9XR N7A N3 N 0 1 Y N N N N N -12.674 59.843 25.001 7.280 2.021 -0.361 N7A 9XR 38
9XR C8A C20 C 0 1 Y N N N N N -12.078 60.323 23.901 6.345 1.182 -0.023 C8A 9XR 39
9XR N3A N4 N 0 1 Y N N N N N -13.708 63.238 24.999 8.301 -0.677 -2.289 N3A 9XR 40
9XR C2A C21 C 0 1 Y N N N N N -14.455 63.294 26.101 9.377 -0.252 -2.918 C2A 9XR 41
9XR N1A N5 N 0 1 Y N N N N N -14.677 62.255 26.929 9.857 0.967 -2.757 N1A 9XR 42
9XR C6A C22 C 0 1 Y N N N N N -14.161 61.040 26.716 9.270 1.836 -1.941 C6A 9XR 43
9XR N6A N6 N 0 1 N N N N N N -14.381 60.025 27.554 9.781 3.112 -1.778 N6A 9XR 44
9XR N8N N7 N 0 1 N N N N N N -6.193 52.309 18.430 -6.469 0.714 -2.118 N8N 9XR 45
9XR H71N H1 H 0 0 N N N N N N -5.138 57.661 21.349 -8.392 -5.240 0.812 H71N 9XR 46
9XR H72N H2 H 0 0 N N N N N N -6.061 56.292 20.828 -8.347 -5.138 -0.864 H72N 9XR 47
9XR H2N H3 H 0 1 N N N N N N -5.997 54.793 19.374 -6.990 -0.881 -0.078 H2N 9XR 48
9XR H4N H4 H 0 1 N N N N N N -2.209 54.165 21.258 -8.072 -4.277 -2.461 H4N 9XR 49
9XR H5N H5 H 0 1 N N N N N N -2.196 51.836 20.458 -7.650 -2.974 -4.502 H5N 9XR 50
9XR H6N1 H6 H 0 0 N N N N N N -4.069 50.993 19.083 -6.904 -0.637 -4.345 H6N1 9XR 51
9XR H1D H7 H 0 1 N N N N N N -7.611 53.459 19.418 -7.116 0.922 -0.129 H1D 9XR 52
9XR H2D H8 H 0 1 N N N N N N -9.168 51.865 19.428 -7.756 3.092 -0.682 H2D 9XR 53
9XR HO2N H9 H 0 0 N N N N N N -7.705 50.204 18.717 -7.034 2.862 -2.979 HO2N 9XR 54
9XR H3D H10 H 0 1 N N N N N N -10.657 52.402 17.782 -6.114 3.545 1.024 H3D 9XR 55
9XR HO3N H11 H 0 0 N N N N N N -9.778 50.856 16.261 -6.141 5.472 -0.450 HO3N 9XR 56
9XR H4D H12 H 0 1 N N N N N N -9.430 54.223 16.244 -3.917 2.851 -1.002 H4D 9XR 57
9XR H51N H13 H 0 0 N N N N N N -10.789 54.964 18.083 -3.319 3.672 1.305 H51N 9XR 58
9XR H52N H14 H 0 0 N N N N N N -9.674 54.243 19.293 -4.235 2.310 1.992 H52N 9XR 59
9XR H1 H15 H 0 1 N N N N N N -7.491 56.206 21.193 -0.177 3.354 1.553 H1 9XR 60
9XR H2 H16 H 0 1 N N N N N N -11.573 56.898 23.015 -0.472 -2.247 2.451 H2 9XR 61
9XR H52A H17 H 0 0 N N N N N N -11.438 59.833 19.539 3.590 -1.128 2.479 H52A 9XR 62
9XR H51A H18 H 0 0 N N N N N N -9.671 60.157 19.527 2.667 -2.634 2.265 H51A 9XR 63
9XR H4B H19 H 0 1 N N N N N N -10.816 62.251 19.909 3.214 -2.556 -0.195 H4B 9XR 64
9XR H3B H20 H 0 1 N N N N N N -9.619 61.171 22.494 5.016 -3.122 2.032 H3B 9XR 65
9XR HO3A H21 H 0 0 N N N N N N -8.057 62.809 21.997 5.659 -4.820 0.479 HO3A 9XR 66
9XR H2B H22 H 0 1 N N N N N N -10.213 63.298 23.484 6.692 -1.620 1.358 H2B 9XR 67
9XR HO2A H23 H 0 0 N N N N N N -11.238 64.912 22.125 7.568 -3.722 0.536 HO2A 9XR 68
9XR H1B H24 H 0 1 N N N N N N -12.717 63.259 22.441 5.588 -1.698 -1.506 H1B 9XR 69
9XR H8A H25 H 0 1 N N N N N N -11.463 59.731 23.239 5.541 1.395 0.667 H8A 9XR 70
9XR H2A H26 H 0 1 N N N N N N -14.915 64.239 26.348 9.885 -0.926 -3.591 H2A 9XR 71
9XR H61A H27 H 0 0 N N N N N N -14.961 60.334 28.308 9.344 3.737 -1.179 H61A 9XR 72
9XR H62A H28 H 0 0 N N N N N N -14.838 59.282 27.065 10.577 3.381 -2.263 H62A 9XR 73
9XR HN8N H29 H 0 0 N N N N N N -6.283 51.371 18.765 -6.218 1.195 -2.922 HN8N 9XR 74
#
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
9XR O3D C3D SING N N 1
9XR C4D O4D SING N N 2
9XR C4D C3D SING N N 3
9XR C4D C5D SING N N 4
9XR O4D C1D SING N N 5
9XR C3D C2D SING N N 6
9XR O2D C2D SING N N 7
9XR C5D O5D SING N N 8
9XR O5D PN SING N N 9
9XR N8N C1D SING N N 10
9XR N8N C1N SING N N 11
9XR C2D C1D SING N N 12
9XR C1N C6N DOUB Y N 13
9XR C1N C2N SING Y N 14
9XR C6N C5N SING Y N 15
9XR O2N PN DOUB N N 16
9XR C2N C3N DOUB Y N 17
9XR PN O3 SING N N 18
9XR PN O1N SING N N 19
9XR O3 PA SING N N 20
9XR C5B C4B SING N N 21
9XR C5B O5B SING N N 22
9XR C5N C4N DOUB Y N 23
9XR C3N C4N SING Y N 24
9XR C3N C7N SING N N 25
9XR C4B O4B SING N N 26
9XR C4B C3B SING N N 27
9XR C7N N7N SING N N 28
9XR C7N O7N DOUB N N 29
9XR O2A PA DOUB N N 30
9XR O5B PA SING N N 31
9XR PA O1A SING N N 32
9XR O3B C3B SING N N 33
9XR O4B C1B SING N N 34
9XR O2B C2B SING N N 35
9XR C3B C2B SING N N 36
9XR C2B C1B SING N N 37
9XR C1B N9A SING N N 38
9XR N9A C8A SING Y N 39
9XR N9A C4A SING Y N 40
9XR C8A N7A DOUB Y N 41
9XR C4A N3A DOUB Y N 42
9XR C4A C5A SING Y N 43
9XR N3A C2A SING Y N 44
9XR N7A C5A SING Y N 45
9XR C5A C6A DOUB Y N 46
9XR C2A N1A DOUB Y N 47
9XR C6A N1A SING Y N 48
9XR C6A N6A SING N N 49
9XR N7N H71N SING N N 50
9XR N7N H72N SING N N 51
9XR C2N H2N SING N N 52
9XR C4N H4N SING N N 53
9XR C5N H5N SING N N 54
9XR C6N H6N1 SING N N 55
9XR C1D H1D SING N N 56
9XR C2D H2D SING N N 57
9XR O2D HO2N SING N N 58
9XR C3D H3D SING N N 59
9XR O3D HO3N SING N N 60
9XR C4D H4D SING N N 61
9XR C5D H51N SING N N 62
9XR C5D H52N SING N N 63
9XR O1N H1 SING N N 64
9XR O1A H2 SING N N 65
9XR C5B H52A SING N N 66
9XR C5B H51A SING N N 67
9XR C4B H4B SING N N 68
9XR C3B H3B SING N N 69
9XR O3B HO3A SING N N 70
9XR C2B H2B SING N N 71
9XR O2B HO2A SING N N 72
9XR C1B H1B SING N N 73
9XR C8A H8A SING N N 74
9XR C2A H2A SING N N 75
9XR N6A H61A SING N N 76
9XR N6A H62A SING N N 77
9XR N8N HN8N SING N N 78
#
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
9XR SMILES ACDLabs 12.01 NC(=O)c1cc(ccc1)NC1OC(COP(=O)(O)OP(=O)(O)OCC2OC(n3cnc4c(N)ncnc43)C(O)C2O)C(O)C1O
9XR InChI InChI 1.03 InChI=1S/C22H29N7O14P2/c23-18-13-20(26-7-25-18)29(8-27-13)22-17(33)15(31)12(42-22)6-40-45(37,38)43-44(35,36)39-5-11-14(30)16(32)21(41-11)28-10-3-1-2-9(4-10)19(24)34/h1-4,7-8,11-12,14-17,21-22,28,30-33H,5-6H2,(H2,24,34)(H,35,36)(H,37,38)(H2,23,25,26)/t11-,12-,14-,15-,16-,17-,21+,22-/m1/s1
9XR InChIKey InChI 1.03 OJEGJAIQKNCBOQ-ZLPBMXMUSA-N
9XR SMILES_CANONICAL CACTVS 3.385 NC(=O)c1cccc(N[C@H]2O[C@H](CO[P](O)(=O)O[P](O)(=O)OC[C@H]3O[C@H]([C@H](O)[C@@H]3O)n4cnc5c(N)ncnc45)[C@@H](O)[C@H]2O)c1
9XR SMILES CACTVS 3.385 NC(=O)c1cccc(N[CH]2O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O)[CH]3O)n4cnc5c(N)ncnc45)[CH](O)[CH]2O)c1
9XR SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 c1cc(cc(c1)N[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)N
9XR SMILES "OpenEye OEToolkits" 2.0.7 c1cc(cc(c1)NC2C(C(C(O2)COP(=O)(O)OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)O)O)O)O)C(=O)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
9XR "SYSTEMATIC NAME" ACDLabs 12.01 "[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl [(2R,3S,4R,5S)-5-(3-carbamoylanilino)-3,4-dihydroxyoxolan-2-yl]methyl dihydrogen diphosphate (non-preferred name)"
9XR "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "[[(2~{R},3~{S},4~{R},5~{S})-5-[(3-aminocarbonylphenyl)amino]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate"
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
9XR 'Create component' 2021-11-01 RCSB
9XR 'Initial release' 2022-04-13 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
9XR O7N O 23.421 -0.434 1
9XR C7N C 23.109 -1.902 2
9XR N7N N 24.224 -2.905 3
9XR C3N C 21.682 -2.365 4
9XR C2N C 21.370 -3.833 5
9XR C4N C 20.568 -1.361 6
9XR C5N C 19.141 -1.825 7
9XR C6N C 18.829 -3.292 8
9XR C1N C 19.944 -4.296 9
9XR C1D C 18.206 -6.227 10
9XR O4D O 16.992 -5.345 11
9XR C2D C 17.742 -7.653 12
9XR O2D O 18.624 -8.867 13
9XR C3D C 16.242 -7.653 14
9XR O3D O 15.360 -8.867 15
9XR C4D C 15.778 -6.227 16
9XR C5D C 14.352 -5.763 17
9XR O5D O 14.040 -4.296 18
9XR PN P 12.614 -3.833 19
9XR O1N O 12.150 -5.259 20
9XR O2N O 13.077 -2.406 21
9XR O3 O 11.187 -3.369 22
9XR PA P 10.875 -1.902 23
9XR O1A O 12.342 -1.590 24
9XR O2A O 9.408 -2.214 25
9XR O5B O 10.563 -0.434 26
9XR C5B C 9.136 0.029 27
9XR C4B C 8.825 1.496 28
9XR C3B C 9.828 2.611 29
9XR O3B O 11.320 2.454 30
9XR C2B C 9.078 3.910 31
9XR O2B O 9.688 5.280 32
9XR C1B C 7.611 3.598 33
9XR O4B O 7.454 2.107 34
9XR N9A N 6.496 4.602 35
9XR C4A C 6.654 6.085 36
9XR C5A C 5.282 6.692 37
9XR N7A N 4.289 5.580 38
9XR C8A C 5.038 4.291 39
9XR N3A N 7.865 6.968 40
9XR C2A C 7.706 8.460 41
9XR N1A N 6.335 9.068 42
9XR C6A C 5.123 8.184 43
9XR N6A N 3.752 8.792 44
9XR N8N N 19.632 -5.763 45
#
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
9XR C3D O3D SINGLE BEGINDASH 1
9XR C4D O4D SINGLE NONE 2
9XR C4D C3D SINGLE NONE 3
9XR C4D C5D SINGLE BEGINWEDGE 4
9XR O4D C1D SINGLE NONE 5
9XR C3D C2D SINGLE NONE 6
9XR C2D O2D SINGLE BEGINDASH 7
9XR C5D O5D SINGLE NONE 8
9XR O5D PN SINGLE NONE 9
9XR C1D N8N SINGLE BEGINDASH 10
9XR N8N C1N SINGLE NONE 11
9XR C2D C1D SINGLE NONE 12
9XR C1N C6N DOUBLE NONE 13
9XR C1N C2N SINGLE NONE 14
9XR C6N C5N SINGLE NONE 15
9XR O2N PN DOUBLE NONE 16
9XR C2N C3N DOUBLE NONE 17
9XR PN O3 SINGLE NONE 18
9XR PN O1N SINGLE BEGINWEDGE 19
9XR O3 PA SINGLE NONE 20
9XR C4B C5B SINGLE BEGINWEDGE 21
9XR C5B O5B SINGLE NONE 22
9XR C5N C4N DOUBLE NONE 23
9XR C3N C4N SINGLE NONE 24
9XR C3N C7N SINGLE NONE 25
9XR C4B O4B SINGLE NONE 26
9XR C4B C3B SINGLE NONE 27
9XR C7N N7N SINGLE NONE 28
9XR C7N O7N DOUBLE NONE 29
9XR O2A PA DOUBLE NONE 30
9XR O5B PA SINGLE NONE 31
9XR PA O1A SINGLE BEGINWEDGE 32
9XR C3B O3B SINGLE BEGINDASH 33
9XR O4B C1B SINGLE NONE 34
9XR C2B O2B SINGLE BEGINDASH 35
9XR C3B C2B SINGLE NONE 36
9XR C2B C1B SINGLE NONE 37
9XR C1B N9A SINGLE BEGINWEDGE 38
9XR N9A C8A SINGLE NONE 39
9XR N9A C4A SINGLE NONE 40
9XR C8A N7A DOUBLE NONE 41
9XR C4A N3A SINGLE NONE 42
9XR C4A C5A DOUBLE NONE 43
9XR N3A C2A DOUBLE NONE 44
9XR N7A C5A SINGLE NONE 45
9XR C5A C6A SINGLE NONE 46
9XR C2A N1A SINGLE NONE 47
9XR C6A N1A DOUBLE NONE 48
9XR C6A N6A SINGLE NONE 49
#
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
9XR MurckoScaffold S1 scaffold 'O=[PH](OC[C@@H]1CC[C@@H](Nc2ccccc2)O1)O[PH](=O)OC[C@@H]1CC[C@H](n2cnc3cncnc32)O1' InChI=1S/C21H27N5O7P2/c27-34(29-11-16-6-8-19(31-16)25-15-4-2-1-3-5-15)33-35(28)30-12-17-7-9-20(32-17)26-14-24-18-10-22-13-23-21(18)26/h1-5,10,13-14,16-17,19-20,25,34-35H,6-9,11-12H2/t16-,17-,19-,20+/m0/s1 LWITWSGXTYOBMF-QGZVKYPTSA-N
9XR 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
9XR amide F2 fragment CC(N)=O InChI=1S/C2H5NO/c1-2(3)4/h1H3,(H2,3,4) DLFVBJFMPXGRIB-UHFFFAOYSA-N
9XR imidazole F3 fragment 'c1c[nH]cn1' InChI=1S/C3H4N2/c1-2-5-3-4-1/h1-3H,(H,4,5) RAXXELZNTBOGNW-UHFFFAOYSA-N
9XR phenyl F4 fragment c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-UHFFFAOYSA-N
9XR phosphate F5 fragment O=P(O)(O)O InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4) NBIIXXVUZAFLBC-UHFFFAOYSA-N
9XR purine F6 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
9XR pyrimidine F7 fragment c1cncnc1 InChI=1S/C4H4N2/c1-2-5-4-6-3-1/h1-4H CZPWVGJYEJSRLH-UHFFFAOYSA-N
9XR ribose F8 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
9XR C3N S1 1
9XR C2N S1 1
9XR C4N S1 1
9XR C5N S1 1
9XR C6N S1 1
9XR C1N S1 1
9XR C1D S1 1
9XR O4D S1 1
9XR C2D S1 1
9XR C3D S1 1
9XR C4D S1 1
9XR C5D S1 1
9XR O5D S1 1
9XR PN S1 1
9XR O2N S1 1
9XR O3 S1 1
9XR PA S1 1
9XR O2A S1 1
9XR O5B S1 1
9XR C5B S1 1
9XR C4B S1 1
9XR C3B S1 1
9XR C2B S1 1
9XR C1B S1 1
9XR O4B S1 1
9XR N9A S1 1
9XR C4A S1 1
9XR C5A S1 1
9XR N7A S1 1
9XR C8A S1 1
9XR N3A S1 1
9XR C2A S1 1
9XR N1A S1 1
9XR C6A S1 1
9XR N8N S1 1
9XR N1A F1 1
9XR C6A F1 1
9XR C5A F1 1
9XR C4A F1 1
9XR N3A F1 1
9XR C2A F1 1
9XR N9A F1 1
9XR C8A F1 1
9XR N7A F1 1
9XR N6A F1 1
9XR N7N F2 1
9XR C7N F2 1
9XR O7N F2 1
9XR C3N F2 1
9XR C4A F3 1
9XR C5A F3 1
9XR N7A F3 1
9XR C8A F3 1
9XR N9A F3 1
9XR C3N F4 1
9XR C2N F4 1
9XR C1N F4 1
9XR C6N F4 1
9XR C5N F4 1
9XR C4N F4 1
9XR O5D F5 1
9XR PN F5 1
9XR O2N F5 1
9XR O3 F5 1
9XR O1N F5 1
9XR O3 F5 2
9XR PA F5 2
9XR O2A F5 2
9XR O5B F5 2
9XR O1A F5 2
9XR N7A F6 1
9XR C8A F6 1
9XR N9A F6 1
9XR C4A F6 1
9XR C5A F6 1
9XR C6A F6 1
9XR N1A F6 1
9XR C2A F6 1
9XR N3A F6 1
9XR C5A F7 1
9XR C4A F7 1
9XR N3A F7 1
9XR C2A F7 1
9XR N1A F7 1
9XR C6A F7 1
9XR C2D F8 1
9XR C3D F8 1
9XR C4D F8 1
9XR O4D F8 1
9XR C1D F8 1
9XR C5D F8 1
9XR O5D F8 1
9XR O3D F8 1
9XR O2D F8 1
9XR C2B F8 2
9XR C3B F8 2
9XR C4B F8 2
9XR O4B F8 2
9XR C1B F8 2
9XR C5B F8 2
9XR O5B F8 2
9XR O3B F8 2
9XR O2B F8 2
#
_pdbe_chem_comp_rdkit_properties.comp_id 9XR
_pdbe_chem_comp_rdkit_properties.exactmw 677.125
_pdbe_chem_comp_rdkit_properties.amw 677.457
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 21
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 11
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 19
_pdbe_chem_comp_rdkit_properties.NumHBD 9
_pdbe_chem_comp_rdkit_properties.NumHBA 20
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 45
_pdbe_chem_comp_rdkit_properties.NumAtoms 74
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 23
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 1
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.455
_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 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 293.629
_pdbe_chem_comp_rdkit_properties.tpsa 326.410
_pdbe_chem_comp_rdkit_properties.CrippenClogP -3.308
_pdbe_chem_comp_rdkit_properties.CrippenMR 143.436
_pdbe_chem_comp_rdkit_properties.chi0v 22.529
_pdbe_chem_comp_rdkit_properties.chi1v 13.784
_pdbe_chem_comp_rdkit_properties.chi2v 6.992
_pdbe_chem_comp_rdkit_properties.chi3v 6.992
_pdbe_chem_comp_rdkit_properties.chi4v 4.589
_pdbe_chem_comp_rdkit_properties.chi0n 49.740
_pdbe_chem_comp_rdkit_properties.chi1n 24.548
_pdbe_chem_comp_rdkit_properties.chi2n 4.762
_pdbe_chem_comp_rdkit_properties.chi3n 4.762
_pdbe_chem_comp_rdkit_properties.chi4n 2.954
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -3.140
_pdbe_chem_comp_rdkit_properties.kappa1 12.471
_pdbe_chem_comp_rdkit_properties.kappa2 12.929
_pdbe_chem_comp_rdkit_properties.kappa3 7.312
_pdbe_chem_comp_rdkit_properties.Phi 3.583
#
_pdbe_chem_comp_external_mappings.comp_id 9XR
_pdbe_chem_comp_external_mappings.source UniChem
_pdbe_chem_comp_external_mappings.resource PubChem
_pdbe_chem_comp_external_mappings.resource_id 163183782
#
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
9XR O7N 9.955 -3.662 -1.267 ETKDGv3 1
9XR C7N 8.868 -3.264 -1.766 ETKDGv3 2
9XR N7N 8.550 -3.635 -3.110 ETKDGv3 3
9XR C3N 7.945 -2.446 -0.942 ETKDGv3 4
9XR C2N 7.028 -1.634 -1.503 ETKDGv3 5
9XR C4N 8.049 -2.496 0.537 ETKDGv3 6
9XR C5N 7.231 -1.763 1.297 ETKDGv3 7
9XR C6N 6.218 -0.890 0.675 ETKDGv3 8
9XR C1N 6.120 -0.807 -0.667 ETKDGv3 9
9XR C1D 4.454 1.210 -0.808 ETKDGv3 10
9XR O4D 3.829 0.956 0.428 ETKDGv3 11
9XR C2D 5.362 2.431 -0.679 ETKDGv3 12
9XR O2D 6.682 2.095 -0.315 ETKDGv3 13
9XR C3D 4.642 3.227 0.387 ETKDGv3 14
9XR O3D 5.535 3.974 1.172 ETKDGv3 15
9XR C4D 3.934 2.135 1.205 ETKDGv3 16
9XR C5D 2.544 2.570 1.683 ETKDGv3 17
9XR O5D 1.693 2.749 0.574 ETKDGv3 18
9XR PN 0.161 3.241 1.139 ETKDGv3 19
9XR O1N -0.442 2.083 2.219 ETKDGv3 20
9XR O2N 0.289 4.574 1.842 ETKDGv3 21
9XR O3 -0.865 3.402 -0.212 ETKDGv3 22
9XR PA -2.447 3.682 0.358 ETKDGv3 23
9XR O1A -3.448 4.019 -0.965 ETKDGv3 24
9XR O2A -2.473 4.873 1.291 ETKDGv3 25
9XR O5B -3.044 2.313 1.181 ETKDGv3 26
9XR C5B -3.089 1.237 0.274 ETKDGv3 27
9XR C4B -3.521 -0.027 1.020 ETKDGv3 28
9XR C3B -3.540 -1.250 0.109 ETKDGv3 29
9XR O3B -2.302 -1.914 0.100 ETKDGv3 30
9XR C2B -4.624 -2.101 0.726 ETKDGv3 31
9XR O2B -4.109 -3.047 1.636 ETKDGv3 32
9XR C1B -5.511 -1.071 1.438 ETKDGv3 33
9XR O4B -4.813 0.152 1.558 ETKDGv3 34
9XR N9A -6.749 -0.849 0.692 ETKDGv3 35
9XR C4A -7.866 -1.718 0.645 ETKDGv3 36
9XR C5A -8.546 -1.514 -0.450 ETKDGv3 37
9XR N7A -7.929 -0.509 -1.247 ETKDGv3 38
9XR C8A -6.885 -0.152 -0.556 ETKDGv3 39
9XR N3A -8.145 -2.817 1.521 ETKDGv3 40
9XR C2A -9.136 -3.616 1.223 ETKDGv3 41
9XR N1A -9.913 -3.406 0.017 ETKDGv3 42
9XR C6A -9.649 -2.418 -0.797 ETKDGv3 43
9XR N6A -10.411 -2.238 -1.990 ETKDGv3 44
9XR N8N 5.141 0.019 -1.333 ETKDGv3 45
9XR H71N 9.246 -4.161 -3.683 ETKDGv3 46
9XR H72N 7.602 -3.476 -3.516 ETKDGv3 47
9XR H2N 6.956 -1.540 -2.578 ETKDGv3 48
9XR H4N 8.783 -3.134 1.013 ETKDGv3 49
9XR H5N 7.307 -1.809 2.376 ETKDGv3 50
9XR H6N1 5.572 -0.336 1.334 ETKDGv3 51
9XR H1D 3.646 1.477 -1.528 ETKDGv3 52
9XR H2D 5.393 2.997 -1.636 ETKDGv3 53
9XR HO2N 6.679 1.765 0.620 ETKDGv3 54
9XR H3D 3.908 3.906 -0.111 ETKDGv3 55
9XR HO3N 4.979 4.572 1.737 ETKDGv3 56
9XR H4D 4.548 1.897 2.102 ETKDGv3 57
9XR H51N 2.152 1.772 2.353 ETKDGv3 58
9XR H52N 2.651 3.514 2.265 ETKDGv3 59
9XR H1 -0.351 1.220 1.742 ETKDGv3 60
9XR H2 -2.992 4.755 -1.445 ETKDGv3 61
9XR H52A -2.085 1.052 -0.172 ETKDGv3 62
9XR H51A -3.823 1.445 -0.537 ETKDGv3 63
9XR H4B -2.813 -0.201 1.863 ETKDGv3 64
9XR H3B -3.846 -0.976 -0.929 ETKDGv3 65
9XR HO3A -1.704 -1.387 -0.491 ETKDGv3 66
9XR H2B -5.180 -2.649 -0.067 ETKDGv3 67
9XR HO2A -3.627 -2.557 2.354 ETKDGv3 68
9XR H1B -5.776 -1.426 2.458 ETKDGv3 69
9XR H8A -6.176 0.583 -0.911 ETKDGv3 70
9XR H2A -9.368 -4.449 1.872 ETKDGv3 71
9XR H61A -11.190 -2.893 -2.224 ETKDGv3 72
9XR H62A -10.202 -1.449 -2.641 ETKDGv3 73
9XR HN8N 4.940 -0.211 -2.333 ETKDGv3 74
#