data_YG8
#
_chem_comp.id YG8
_chem_comp.name
"[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{R})-5-imidazol-1-yl-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate"
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C18 H25 N7 O13 P2"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2023-12-04
_chem_comp.pdbx_modified_date 2024-06-07
_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 609.378
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code YG8
_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 8V6S
_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_n_terminal_atom_flag
_chem_comp_atom.pdbx_backbone_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
YG8 C11 C1 C 0 1 N N R N N N 8.993 -4.938 17.924 5.848 1.243 1.073 C11 YG8 1
YG8 C10 C2 C 0 1 N N R N N N 10.333 -5.623 18.108 5.014 -0.056 0.940 C10 YG8 2
YG8 C3 C3 C 0 1 Y N N N N N 13.500 -6.305 21.698 7.747 -3.372 -1.411 C3 YG8 3
YG8 C4 C4 C 0 1 Y N N N N N 12.334 -5.784 21.097 6.748 -2.396 -1.256 C4 YG8 4
YG8 C8 C5 C 0 1 Y N N N N N 10.530 -4.826 20.525 5.135 -0.955 -1.415 C8 YG8 5
YG8 C5 C6 C 0 1 Y N N N N N 12.100 -6.164 19.779 6.579 -1.816 0.013 C5 YG8 6
YG8 C1 C7 C 0 1 Y N N N N N 13.917 -7.394 19.700 8.278 -3.135 0.822 C1 YG8 7
YG8 C12 C8 C 0 1 N N S N N N 8.964 -4.828 16.403 4.828 2.220 1.706 C12 YG8 8
YG8 C13 C9 C 0 1 N N R N N N 10.434 -4.532 16.065 3.456 1.602 1.374 C13 YG8 9
YG8 C15 C10 C 0 1 N N N N N N 10.717 -3.081 15.782 2.617 2.599 0.572 C15 YG8 10
YG8 C25 C11 C 0 1 N N N N N N 9.317 2.593 15.194 -4.990 0.965 -1.136 C25 YG8 11
YG8 C26 C12 C 0 1 N N R N N N 9.521 3.973 14.618 -5.485 -0.483 -1.136 C26 YG8 12
YG8 C27 C13 C 0 1 N N S N N N 10.898 4.562 14.906 -6.939 -0.554 -1.651 C27 YG8 13
YG8 C28 C14 C 0 1 N N R N N N 10.621 5.495 16.082 -7.593 -1.651 -0.782 C28 YG8 14
YG8 C29 C15 C 0 1 N N R N N N 9.225 5.993 15.718 -6.456 -2.113 0.156 C29 YG8 15
YG8 C32 C16 C 0 1 Y N N N N N 8.368 6.018 18.088 -7.276 -1.512 2.455 C32 YG8 16
YG8 C34 C17 C 0 1 Y N N N N N 6.967 7.623 17.973 -7.737 -3.468 3.241 C34 YG8 17
YG8 C35 C18 C 0 1 Y N N N N N 7.533 7.528 16.744 -7.273 -3.651 1.990 C35 YG8 18
YG8 N2 N1 N 0 1 Y N N N N N 14.277 -7.120 20.956 8.478 -3.704 -0.352 N2 YG8 19
YG8 N31 N2 N 0 1 Y N N N N N 8.430 6.494 16.826 -6.984 -2.411 1.490 N31 YG8 20
YG8 N33 N3 N 0 1 Y N N N N N 7.487 6.680 18.816 -7.723 -2.152 3.500 N33 YG8 21
YG8 N40 N4 N 0 1 N N N N N N 13.882 -6.001 22.942 7.959 -3.979 -2.637 N40 YG8 22
YG8 N6 N5 N 0 1 Y N N N N N 12.847 -6.971 19.028 7.362 -2.209 1.012 N6 YG8 23
YG8 N7 N6 N 0 1 Y N N N N N 10.934 -5.537 19.427 5.555 -0.912 -0.119 N7 YG8 24
YG8 N9 N7 N 0 1 Y N N N N N 11.340 -4.945 21.553 5.836 -1.826 -2.080 N9 YG8 25
YG8 O14 O1 O 0 1 N N N N N N 11.208 -4.995 17.197 3.698 0.423 0.588 O14 YG8 26
YG8 O16 O2 O 0 1 N N N N N N 10.260 -2.241 16.871 1.307 2.063 0.370 O16 YG8 27
YG8 O18 O3 O 0 1 N N N N N N 9.517 -0.217 18.004 -0.045 4.184 0.163 O18 YG8 28
YG8 O19 O4 O 0 1 N N N N N N 11.672 -0.171 16.643 0.595 3.010 -1.977 O19 YG8 29
YG8 O20 O5 O 0 1 N N N N N N 9.389 -0.396 15.528 -1.219 2.011 -0.357 O20 YG8 30
YG8 O22 O6 O 0 1 N N N N N N 8.349 0.178 13.441 -2.852 3.096 -1.947 O22 YG8 31
YG8 O23 O7 O 0 1 N N N N N N 10.823 -0.461 13.422 -3.352 3.273 0.521 O23 YG8 32
YG8 O24 O8 O 0 1 N N N N N N 10.098 1.691 14.402 -3.609 0.997 -0.768 O24 YG8 33
YG8 O30 O9 O 0 1 N N N N N N 8.549 4.878 15.194 -5.546 -0.993 0.214 O30 YG8 34
YG8 O36 O10 O 0 1 N N N N N N 11.517 6.591 16.106 -8.041 -2.736 -1.598 O36 YG8 35
YG8 O37 O11 O 0 1 N N N N N N 11.362 5.294 13.773 -6.964 -0.927 -3.031 O37 YG8 36
YG8 O38 O12 O 0 1 N N N N N N 8.568 -6.049 15.774 5.016 2.292 3.120 O38 YG8 37
YG8 O39 O13 O 0 1 N N N N N N 7.938 -5.730 18.452 6.968 1.043 1.939 O39 YG8 38
YG8 P17 P1 P 0 1 N N N N N N 10.291 -0.682 16.822 0.155 2.846 -0.437 P17 YG8 39
YG8 P21 P2 P 0 1 N N N N N N 9.684 0.224 14.081 -2.760 2.360 -0.666 P21 YG8 40
YG8 H11 H1 H 0 1 N N N N N N 9.013 -3.935 18.376 6.174 1.598 0.095 H11 YG8 41
YG8 H10 H2 H 0 1 N N N N N N 10.217 -6.683 17.836 4.985 -0.593 1.889 H10 YG8 42
YG8 H8 H3 H 0 1 N N N N N N 9.633 -4.225 20.544 4.339 -0.354 -1.828 H8 YG8 43
YG8 H1 H4 H 0 1 N N N N N N 14.583 -8.047 19.155 8.895 -3.434 1.656 H1 YG8 44
YG8 H12 H5 H 0 1 N N N N N N 8.328 -3.986 16.094 4.919 3.210 1.257 H12 YG8 45
YG8 H13 H6 H 0 1 N N N N N N 10.705 -5.120 15.176 2.938 1.334 2.294 H13 YG8 46
YG8 H15A H7 H 0 0 N N N N N N 11.801 -2.944 15.653 2.544 3.537 1.122 H15A YG8 47
YG8 H15B H8 H 0 0 N N N N N N 10.198 -2.787 14.858 3.089 2.778 -0.393 H15B YG8 48
YG8 H25B H9 H 0 0 N N N N N N 8.254 2.316 15.144 -5.110 1.390 -2.133 H25B YG8 49
YG8 H25A H10 H 0 0 N N N N N N 9.654 2.566 16.241 -5.570 1.548 -0.421 H25A YG8 50
YG8 H26 H11 H 0 1 N N N N N N 9.381 3.926 13.528 -4.834 -1.106 -1.750 H26 YG8 51
YG8 H27 H12 H 0 1 N N N N N N 11.602 3.770 15.201 -7.444 0.401 -1.504 H27 YG8 52
YG8 H28 H13 H 0 1 N N N N N N 10.606 4.939 17.031 -8.420 -1.239 -0.205 H28 YG8 53
YG8 H29 H14 H 0 1 N N N N N N 9.321 6.775 14.951 -5.954 -2.988 -0.258 H29 YG8 54
YG8 H32 H15 H 0 1 N N N N N N 8.965 5.197 18.457 -7.155 -0.442 2.375 H32 YG8 55
YG8 H34 H16 H 0 1 N N N N N N 6.211 8.343 18.248 -8.059 -4.245 3.919 H34 YG8 56
YG8 H35 H17 H 0 1 N N N N N N 7.321 8.140 15.880 -7.152 -4.596 1.481 H35 YG8 57
YG8 H40B H18 H 0 0 N N N N N N 14.748 -6.458 23.146 7.416 -3.731 -3.401 H40B YG8 58
YG8 H40A H19 H 0 0 N N N N N N 14.000 -5.011 23.022 8.652 -4.652 -2.731 H40A YG8 59
YG8 H2 H20 H 0 1 N N N N N N 11.886 0.421 17.354 0.744 2.171 -2.435 H2 YG8 60
YG8 H3 H21 H 0 1 N N N N N N 10.525 -0.869 12.617 -3.323 2.853 1.392 H3 YG8 61
YG8 H36 H22 H 0 1 N N N N N N 11.316 7.149 16.848 -8.713 -2.487 -2.247 H36 YG8 62
YG8 H37 H23 H 0 1 N N N N N N 12.220 5.658 13.960 -7.853 -0.987 -3.406 H37 YG8 63
YG8 H38 H24 H 0 1 N N N N N N 8.564 -5.933 14.831 5.886 2.620 3.386 H38 YG8 64
YG8 H39 H25 H 0 1 N N N N N N 7.110 -5.281 18.325 7.470 1.849 2.124 H39 YG8 65
#
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
YG8 C1 N2 DOUB Y N 1
YG8 N2 C3 SING Y N 2
YG8 C3 C4 DOUB Y N 3
YG8 C4 C5 SING Y N 4
YG8 C5 N6 DOUB Y N 5
YG8 C5 N7 SING Y N 6
YG8 N7 C8 SING Y N 7
YG8 C8 N9 DOUB Y N 8
YG8 N7 C10 SING N N 9
YG8 C10 C11 SING N N 10
YG8 C11 C12 SING N N 11
YG8 C12 C13 SING N N 12
YG8 C13 O14 SING N N 13
YG8 C13 C15 SING N N 14
YG8 C15 O16 SING N N 15
YG8 O16 P17 SING N N 16
YG8 P17 O18 DOUB N N 17
YG8 P17 O19 SING N N 18
YG8 P17 O20 SING N N 19
YG8 O20 P21 SING N N 20
YG8 P21 O22 DOUB N N 21
YG8 P21 O23 SING N N 22
YG8 P21 O24 SING N N 23
YG8 O24 C25 SING N N 24
YG8 C25 C26 SING N N 25
YG8 C26 C27 SING N N 26
YG8 C27 C28 SING N N 27
YG8 C28 C29 SING N N 28
YG8 C29 O30 SING N N 29
YG8 C29 N31 SING N N 30
YG8 N31 C32 SING Y N 31
YG8 C32 N33 DOUB Y N 32
YG8 N33 C34 SING Y N 33
YG8 C34 C35 DOUB Y N 34
YG8 C28 O36 SING N N 35
YG8 C27 O37 SING N N 36
YG8 C12 O38 SING N N 37
YG8 C11 O39 SING N N 38
YG8 C3 N40 SING N N 39
YG8 N6 C1 SING Y N 40
YG8 N9 C4 SING Y N 41
YG8 O14 C10 SING N N 42
YG8 O30 C26 SING N N 43
YG8 C35 N31 SING Y N 44
YG8 C11 H11 SING N N 45
YG8 C10 H10 SING N N 46
YG8 C8 H8 SING N N 47
YG8 C1 H1 SING N N 48
YG8 C12 H12 SING N N 49
YG8 C13 H13 SING N N 50
YG8 C15 H15A SING N N 51
YG8 C15 H15B SING N N 52
YG8 C25 H25B SING N N 53
YG8 C25 H25A SING N N 54
YG8 C26 H26 SING N N 55
YG8 C27 H27 SING N N 56
YG8 C28 H28 SING N N 57
YG8 C29 H29 SING N N 58
YG8 C32 H32 SING N N 59
YG8 C34 H34 SING N N 60
YG8 C35 H35 SING N N 61
YG8 N40 H40B SING N N 62
YG8 N40 H40A SING N N 63
YG8 O19 H2 SING N N 64
YG8 O23 H3 SING N N 65
YG8 O36 H36 SING N N 66
YG8 O37 H37 SING N N 67
YG8 O38 H38 SING N N 68
YG8 O39 H39 SING N N 69
#
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
YG8 SMILES ACDLabs 12.01 "Nc1ncnc2c1ncn2C1OC(COP(=O)(O)OP(=O)(O)OCC2OC(n3cncc3)C(O)C2O)C(O)C1O"
YG8 InChI InChI 1.06 "InChI=1S/C18H25N7O13P2/c19-15-10-16(22-5-21-15)25(7-23-10)18-14(29)12(27)9(37-18)4-35-40(32,33)38-39(30,31)34-3-8-11(26)13(28)17(36-8)24-2-1-20-6-24/h1-2,5-9,11-14,17-18,26-29H,3-4H2,(H,30,31)(H,32,33)(H2,19,21,22)/t8-,9-,11-,12-,13-,14-,17-,18-/m1/s1"
YG8 InChIKey InChI 1.06 CBBKIMDNCBIDSI-ZZJFPLALSA-N
YG8 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)n5ccnc5)[C@@H](O)[C@H]3O"
YG8 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)n5ccnc5)[CH](O)[CH]3O"
YG8 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1cn(cn1)[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"
YG8 SMILES "OpenEye OEToolkits" 2.0.7 "c1cn(cn1)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)O)O)O)O"
#
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
YG8 "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,5R)-3,4-dihydroxy-5-(1H-imidazol-1-yl)oxolan-2-yl]methyl dihydrogen diphosphate (non-preferred name)"
YG8 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{R})-5-imidazol-1-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
YG8 'Create component' 2023-12-04 RCSB
YG8 'Initial release' 2024-06-12 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
YG8 C11 C 6.604 1.441 1
YG8 C10 C 7.483 0.226 2
YG8 C3 C 4.299 -3.907 3
YG8 C4 C 5.598 -3.157 4
YG8 C8 C 7.893 -2.407 5
YG8 C5 C 5.598 -1.657 6
YG8 C1 C 3.000 -1.657 7
YG8 C12 C 7.487 2.653 8
YG8 C13 C 8.913 2.187 9
YG8 C15 C 10.129 3.067 10
YG8 C25 C 17.881 3.868 11
YG8 C26 C 19.251 3.256 12
YG8 C27 C 20.551 4.003 13
YG8 C28 C 21.664 2.998 14
YG8 C29 C 21.051 1.629 15
YG8 C32 C 23.291 0.169 16
YG8 C34 C 22.300 -2.047 17
YG8 C35 C 21.187 -1.041 18
YG8 N2 N 3.000 -3.157 19
YG8 N31 N 21.799 0.328 20
YG8 N33 N 23.600 -1.299 21
YG8 N40 N 4.299 -5.407 22
YG8 N6 N 4.299 -0.907 23
YG8 N7 N 7.018 -1.200 24
YG8 N9 N 7.018 -3.614 25
YG8 O14 O 8.911 0.687 26
YG8 O16 O 11.498 2.454 27
YG8 O18 O 13.592 2.119 28
YG8 O19 O 11.833 4.549 29
YG8 O20 O 13.928 4.213 30
YG8 O22 O 15.909 4.970 31
YG8 O23 O 14.684 2.232 32
YG8 O24 O 16.666 2.989 33
YG8 O30 O 19.560 1.788 34
YG8 O36 O 23.132 3.307 35
YG8 O37 O 20.710 5.495 36
YG8 O38 O 7.027 4.081 37
YG8 O39 O 5.104 1.444 38
YG8 P17 P 12.713 3.334 39
YG8 P21 P 15.297 3.601 40
#
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
YG8 C1 N2 SINGLE NONE 1
YG8 N2 C3 DOUBLE NONE 2
YG8 C3 C4 SINGLE NONE 3
YG8 C4 C5 DOUBLE NONE 4
YG8 C5 N6 SINGLE NONE 5
YG8 C5 N7 SINGLE NONE 6
YG8 N7 C8 SINGLE NONE 7
YG8 C8 N9 DOUBLE NONE 8
YG8 C10 N7 SINGLE BEGINWEDGE 9
YG8 C10 C11 SINGLE NONE 10
YG8 C11 C12 SINGLE NONE 11
YG8 C12 C13 SINGLE NONE 12
YG8 C13 O14 SINGLE NONE 13
YG8 C13 C15 SINGLE BEGINWEDGE 14
YG8 C15 O16 SINGLE NONE 15
YG8 O16 P17 SINGLE NONE 16
YG8 P17 O18 DOUBLE NONE 17
YG8 P17 O19 SINGLE BEGINDASH 18
YG8 P17 O20 SINGLE NONE 19
YG8 O20 P21 SINGLE NONE 20
YG8 P21 O22 DOUBLE NONE 21
YG8 P21 O23 SINGLE BEGINDASH 22
YG8 P21 O24 SINGLE NONE 23
YG8 O24 C25 SINGLE NONE 24
YG8 C26 C25 SINGLE BEGINDASH 25
YG8 C26 C27 SINGLE NONE 26
YG8 C27 C28 SINGLE NONE 27
YG8 C28 C29 SINGLE NONE 28
YG8 C29 O30 SINGLE NONE 29
YG8 C29 N31 SINGLE BEGINDASH 30
YG8 N31 C32 SINGLE NONE 31
YG8 C32 N33 DOUBLE NONE 32
YG8 N33 C34 SINGLE NONE 33
YG8 C34 C35 DOUBLE NONE 34
YG8 C28 O36 SINGLE BEGINWEDGE 35
YG8 C27 O37 SINGLE BEGINWEDGE 36
YG8 C12 O38 SINGLE BEGINDASH 37
YG8 C11 O39 SINGLE BEGINDASH 38
YG8 C3 N40 SINGLE NONE 39
YG8 N6 C1 DOUBLE NONE 40
YG8 N9 C4 SINGLE NONE 41
YG8 O14 C10 SINGLE NONE 42
YG8 O30 C26 SINGLE NONE 43
YG8 C35 N31 SINGLE NONE 44
#
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
YG8 MurckoScaffold S1 scaffold 'O=[PH](OC[C@@H]1CC[C@H](n2ccnc2)O1)O[PH](=O)OC[C@@H]1CC[C@H](n2cnc3cncnc32)O1' InChI=1S/C18H24N6O7P2/c25-32(27-8-13-1-3-16(29-13)23-6-5-19-11-23)31-33(26)28-9-14-2-4-17(30-14)24-12-22-15-7-20-10-21-18(15)24/h5-7,10-14,16-17,32-33H,1-4,8-9H2/t13-,14-,16+,17+/m0/s1 CHWOKEBVLGCLHI-XJNFMUPTSA-N
YG8 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
YG8 imidazole F2 fragment 'c1c[nH]cn1' InChI=1S/C3H4N2/c1-2-5-3-4-1/h1-3H,(H,4,5) RAXXELZNTBOGNW-UHFFFAOYSA-N
YG8 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
YG8 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
YG8 pyrimidine F5 fragment c1cncnc1 InChI=1S/C4H4N2/c1-2-5-4-6-3-1/h1-4H CZPWVGJYEJSRLH-UHFFFAOYSA-N
YG8 ribose F6 fragment OCC1OCC(O)C1O InChI=1S/C5H10O4/c6-1-4-5(8)3(7)2-9-4/h3-8H,1-2H2 KZVAAIRBJJYZOW-UHFFFAOYSA-N
#
loop_
_pdbe_chem_comp_substructure_mapping.comp_id
_pdbe_chem_comp_substructure_mapping.atom_id
_pdbe_chem_comp_substructure_mapping.substructure_id
_pdbe_chem_comp_substructure_mapping.substructure_ordinal
YG8 C11 S1 1
YG8 C10 S1 1
YG8 C3 S1 1
YG8 C4 S1 1
YG8 C8 S1 1
YG8 C5 S1 1
YG8 C1 S1 1
YG8 C12 S1 1
YG8 C13 S1 1
YG8 C15 S1 1
YG8 C25 S1 1
YG8 C26 S1 1
YG8 C27 S1 1
YG8 C28 S1 1
YG8 C29 S1 1
YG8 C32 S1 1
YG8 C34 S1 1
YG8 C35 S1 1
YG8 N2 S1 1
YG8 N31 S1 1
YG8 N33 S1 1
YG8 N6 S1 1
YG8 N7 S1 1
YG8 N9 S1 1
YG8 O14 S1 1
YG8 O16 S1 1
YG8 O18 S1 1
YG8 O20 S1 1
YG8 O22 S1 1
YG8 O24 S1 1
YG8 O30 S1 1
YG8 P17 S1 1
YG8 P21 S1 1
YG8 N2 F1 1
YG8 C3 F1 1
YG8 C4 F1 1
YG8 C5 F1 1
YG8 N6 F1 1
YG8 C1 F1 1
YG8 N7 F1 1
YG8 C8 F1 1
YG8 N9 F1 1
YG8 N40 F1 1
YG8 C4 F2 1
YG8 C5 F2 1
YG8 N7 F2 1
YG8 C8 F2 1
YG8 N9 F2 1
YG8 C34 F2 2
YG8 C35 F2 2
YG8 N31 F2 2
YG8 C32 F2 2
YG8 N33 F2 2
YG8 O16 F3 1
YG8 P17 F3 1
YG8 O18 F3 1
YG8 O19 F3 1
YG8 O20 F3 1
YG8 O20 F3 2
YG8 P21 F3 2
YG8 O22 F3 2
YG8 O23 F3 2
YG8 O24 F3 2
YG8 N9 F4 1
YG8 C8 F4 1
YG8 N7 F4 1
YG8 C5 F4 1
YG8 C4 F4 1
YG8 C3 F4 1
YG8 N2 F4 1
YG8 C1 F4 1
YG8 N6 F4 1
YG8 C4 F5 1
YG8 C3 F5 1
YG8 N2 F5 1
YG8 C1 F5 1
YG8 N6 F5 1
YG8 C5 F5 1
YG8 C11 F6 1
YG8 C12 F6 1
YG8 C13 F6 1
YG8 O14 F6 1
YG8 C10 F6 1
YG8 C15 F6 1
YG8 O16 F6 1
YG8 O38 F6 1
YG8 O39 F6 1
YG8 C28 F6 2
YG8 C27 F6 2
YG8 C26 F6 2
YG8 O30 F6 2
YG8 C29 F6 2
YG8 C25 F6 2
YG8 O24 F6 2
YG8 O37 F6 2
YG8 O36 F6 2
#
_pdbe_chem_comp_rdkit_properties.comp_id YG8
_pdbe_chem_comp_rdkit_properties.exactmw 609.099
_pdbe_chem_comp_rdkit_properties.amw 609.382
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 20
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 8
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 17
_pdbe_chem_comp_rdkit_properties.NumHBD 7
_pdbe_chem_comp_rdkit_properties.NumHBA 20
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 40
_pdbe_chem_comp_rdkit_properties.NumAtoms 65
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 22
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.556
_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 259.057
_pdbe_chem_comp_rdkit_properties.tpsa 289.110
_pdbe_chem_comp_rdkit_properties.CrippenClogP -3.015
_pdbe_chem_comp_rdkit_properties.CrippenMR 123.419
_pdbe_chem_comp_rdkit_properties.chi0v 20.121
_pdbe_chem_comp_rdkit_properties.chi1v 12.527
_pdbe_chem_comp_rdkit_properties.chi2v 6.524
_pdbe_chem_comp_rdkit_properties.chi3v 6.524
_pdbe_chem_comp_rdkit_properties.chi4v 4.336
_pdbe_chem_comp_rdkit_properties.chi0n 43.332
_pdbe_chem_comp_rdkit_properties.chi1n 21.450
_pdbe_chem_comp_rdkit_properties.chi2n 4.294
_pdbe_chem_comp_rdkit_properties.chi3n 4.294
_pdbe_chem_comp_rdkit_properties.chi4n 2.700
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -2.420
_pdbe_chem_comp_rdkit_properties.kappa1 11.344
_pdbe_chem_comp_rdkit_properties.kappa2 11.103
_pdbe_chem_comp_rdkit_properties.kappa3 5.809
_pdbe_chem_comp_rdkit_properties.Phi 3.149
#
#
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
YG8 C11 -4.405 -0.369 -1.454 ETKDGv3 1
YG8 C10 -5.201 -0.440 -0.155 ETKDGv3 2
YG8 C3 -8.626 2.285 2.024 ETKDGv3 3
YG8 C4 -7.456 2.026 1.176 ETKDGv3 4
YG8 C8 -5.515 2.096 0.257 ETKDGv3 5
YG8 C5 -7.259 0.827 0.699 ETKDGv3 6
YG8 C1 -9.196 -0.031 1.729 ETKDGv3 7
YG8 C12 -3.147 -1.126 -1.109 ETKDGv3 8
YG8 C13 -3.039 -0.934 0.412 ETKDGv3 9
YG8 C15 -2.042 0.171 0.782 ETKDGv3 10
YG8 C25 4.084 -1.161 -1.106 ETKDGv3 11
YG8 C26 5.559 -1.258 -1.507 ETKDGv3 12
YG8 C27 6.297 -2.327 -0.703 ETKDGv3 13
YG8 C28 7.687 -1.748 -0.572 ETKDGv3 14
YG8 C29 7.458 -0.240 -0.733 ETKDGv3 15
YG8 C32 8.027 1.771 0.756 ETKDGv3 16
YG8 C34 6.758 1.321 2.450 ETKDGv3 17
YG8 C35 6.702 0.247 1.684 ETKDGv3 18
YG8 N2 -9.440 1.293 2.268 ETKDGv3 19
YG8 N31 7.542 0.448 0.555 ETKDGv3 20
YG8 N33 7.603 2.304 1.857 ETKDGv3 21
YG8 N40 -8.872 3.578 2.577 ETKDGv3 22
YG8 N6 -8.145 -0.261 0.986 ETKDGv3 23
YG8 N7 -6.008 0.764 0.037 ETKDGv3 24
YG8 N9 -6.339 2.864 0.910 ETKDGv3 25
YG8 O14 -4.310 -0.596 0.929 ETKDGv3 26
YG8 O16 -0.747 -0.220 0.393 ETKDGv3 27
YG8 O18 -0.088 2.302 -0.074 ETKDGv3 28
YG8 O19 0.341 1.420 2.353 ETKDGv3 29
YG8 O20 1.914 0.631 0.244 ETKDGv3 30
YG8 O22 1.161 0.997 -2.267 ETKDGv3 31
YG8 O23 1.030 -1.462 -1.388 ETKDGv3 32
YG8 O24 3.449 -0.201 -1.916 ETKDGv3 33
YG8 O30 6.187 -0.010 -1.302 ETKDGv3 34
YG8 O36 8.563 -2.239 -1.561 ETKDGv3 35
YG8 O37 6.311 -3.562 -1.371 ETKDGv3 36
YG8 O38 -3.240 -2.492 -1.444 ETKDGv3 37
YG8 O39 -5.096 -0.965 -2.521 ETKDGv3 38
YG8 P17 0.332 1.068 0.696 ETKDGv3 39
YG8 P21 1.856 0.018 -1.347 ETKDGv3 40
YG8 H11 -4.133 0.682 -1.710 ETKDGv3 41
YG8 H10 -5.870 -1.329 -0.184 ETKDGv3 42
YG8 H8 -4.536 2.432 -0.058 ETKDGv3 43
YG8 H1 -9.881 -0.837 1.955 ETKDGv3 44
YG8 H12 -2.278 -0.695 -1.654 ETKDGv3 45
YG8 H13 -2.700 -1.878 0.894 ETKDGv3 46
YG8 H15A -2.082 0.317 1.885 ETKDGv3 47
YG8 H15B -2.353 1.113 0.275 ETKDGv3 48
YG8 H25B 4.033 -0.877 -0.029 ETKDGv3 49
YG8 H25A 3.613 -2.159 -1.254 ETKDGv3 50
YG8 H26 5.619 -1.501 -2.592 ETKDGv3 51
YG8 H27 5.859 -2.445 0.316 ETKDGv3 52
YG8 H28 8.116 -1.994 0.425 ETKDGv3 53
YG8 H29 8.232 0.185 -1.411 ETKDGv3 54
YG8 H32 8.671 2.291 0.059 ETKDGv3 55
YG8 H34 6.214 1.460 3.375 ETKDGv3 56
YG8 H35 6.096 -0.630 1.870 ETKDGv3 57
YG8 H40B -8.222 4.372 2.383 ETKDGv3 58
YG8 H40A -9.707 3.744 3.181 ETKDGv3 59
YG8 H2 -0.407 2.055 2.489 ETKDGv3 60
YG8 H3 1.260 -1.909 -0.535 ETKDGv3 61
YG8 H36 8.189 -2.005 -2.451 ETKDGv3 62
YG8 H37 5.406 -3.954 -1.257 ETKDGv3 63
YG8 H38 -4.001 -2.886 -0.941 ETKDGv3 64
YG8 H39 -5.827 -0.339 -2.765 ETKDGv3 65
#