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
#