data_A1D8A
#
_chem_comp.id A1D8A
_chem_comp.name "[(2R,3R,4R,5R)-5-(6-aminopurin-9-yl)-4-[(2S,3R,4S,5R)-3,4-bis(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]oxy-3-oxidanyl-oxolan-2-yl]methyl phosphono hydrogen phosphate"
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C15 H24 N5 O17 P3"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2024-05-15
_chem_comp.pdbx_modified_date 2024-11-01
_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 639.296
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code A1D8A
_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 8ZF0
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site PDBC
_chem_comp.pdbx_pcm ?
#
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
A1D8A "C1'" C1 C 0 1 N N R N N N 105.625 123.142 113.416 0.253 -0.124 1.486 "C1'" A1D8A 1
A1D8A "C2'" C2 C 0 1 N N R N N N 106.854 124.197 113.790 -0.273 -1.260 0.572 "C2'" A1D8A 2
A1D8A "C3'" C3 C 0 1 N N R N N N 107.586 123.629 114.626 0.960 -2.192 0.472 "C3'" A1D8A 3
A1D8A "C4'" C4 C 0 1 N N R N N N 106.782 122.379 115.162 2.150 -1.285 0.842 "C4'" A1D8A 4
A1D8A "C5'" C5 C 0 1 N N N N N N 106.606 122.462 116.571 3.156 -1.252 -0.311 "C5'" A1D8A 5
A1D8A "O2'" O1 O 0 1 N N N N N N 107.646 124.501 112.570 -1.375 -1.936 1.181 "O2'" A1D8A 6
A1D8A "O5'" O2 O 0 1 N N N N N N 107.743 123.028 117.119 4.308 -0.504 0.084 "O5'" A1D8A 7
A1D8A C2 C6 C 0 1 Y N N N N N 102.248 122.249 110.710 -3.614 1.482 3.104 C2 A1D8A 8
A1D8A C26 C7 C 0 1 N N S N N N 107.066 125.648 111.873 -2.313 -2.476 0.248 C26 A1D8A 9
A1D8A C28 C8 C 0 1 N N R N N N 106.706 125.174 109.445 -4.241 -1.984 -0.936 C28 A1D8A 10
A1D8A C29 C9 C 0 1 N N N N N N 106.568 123.786 108.761 -5.360 -0.941 -0.887 C29 A1D8A 11
A1D8A C35 C10 C 0 1 N N S N N N 107.959 125.439 109.698 -4.600 -3.182 -0.030 C35 A1D8A 12
A1D8A C37 C11 C 0 1 N N R N N N 107.971 126.238 111.154 -3.434 -3.249 0.987 C37 A1D8A 13
A1D8A C4 C12 C 0 1 Y N N N N N 103.459 123.471 112.242 -1.691 1.457 1.845 C4 A1D8A 14
A1D8A C5 C13 C 0 1 Y N N N N N 102.492 124.441 112.232 -2.028 2.718 1.326 C5 A1D8A 15
A1D8A C6 C14 C 0 1 Y N N N N N 101.363 124.263 111.404 -3.215 3.324 1.771 C6 A1D8A 16
A1D8A C8 C15 C 0 1 Y N N N N N 104.056 125.021 113.589 -0.146 2.130 0.423 C8 A1D8A 17
A1D8A N1 N1 N 0 1 Y N N N N N 101.284 123.176 110.675 -3.969 2.670 2.648 N1 A1D8A 18
A1D8A N3 N2 N 0 1 Y N N N N N 103.317 122.383 111.473 -2.506 0.882 2.723 N3 A1D8A 19
A1D8A N6 N3 N 0 1 N N N N N N 100.283 125.286 111.354 -3.598 4.566 1.296 N6 A1D8A 20
A1D8A N7 N4 N 0 1 Y N N N N N 102.893 125.386 113.077 -1.043 3.071 0.465 N7 A1D8A 21
A1D8A N9 N5 N 0 1 Y N N N N N 104.415 123.867 113.094 -0.501 1.112 1.258 N9 A1D8A 22
A1D8A O1A O3 O 0 1 N N N N N N 108.083 123.575 119.599 5.120 0.628 -2.145 O1A A1D8A 23
A1D8A O1B O4 O 0 1 N N N N N N 108.554 120.386 121.200 8.476 1.977 -1.375 O1B A1D8A 24
A1D8A O27 O5 O 0 1 N N N N N N 105.985 125.159 110.837 -3.021 -1.416 -0.430 O27 A1D8A 25
A1D8A O2A O6 O 0 1 N N N N N N 109.686 122.118 118.487 6.082 -1.569 -1.361 O2A A1D8A 26
A1D8A O2B O7 O 0 1 N N N N N N 106.613 121.810 121.401 9.024 1.128 1.053 O2B A1D8A 27
A1D8A "O3'" O8 O 0 1 N N N N N N 108.891 123.162 113.953 0.847 -3.272 1.401 "O3'" A1D8A 28
A1D8A O30 O9 O 0 1 N N N N N N 107.842 123.393 108.258 -5.075 0.107 -1.815 O30 A1D8A 29
A1D8A O32 O10 O 0 1 N N N N N N 109.432 121.357 108.565 -5.351 2.414 -3.047 O32 A1D8A 30
A1D8A O33 O11 O 0 1 N N N N N N 106.991 120.923 108.565 -7.449 0.882 -2.639 O33 A1D8A 31
A1D8A O34 O12 O 0 1 N N N N N N 108.167 121.530 106.434 -6.277 2.043 -0.728 O34 A1D8A 32
A1D8A O36 O13 O 0 1 N N N N N N 108.499 126.286 108.670 -4.666 -4.386 -0.795 O36 A1D8A 33
A1D8A O38 O14 O 0 1 N N N N N N 107.622 127.634 110.957 -3.046 -4.603 1.229 O38 A1D8A 34
A1D8A O3A O15 O 0 1 N N N N N N 107.401 121.198 119.025 6.732 0.501 -0.072 O3A A1D8A 35
A1D8A O3B O16 O 0 1 N N N N N N 106.328 119.493 120.694 8.911 -0.465 -0.902 O3B A1D8A 36
A1D8A "O4'" O17 O 0 1 N N N N N N 105.430 122.441 114.466 1.627 0.034 1.072 "O4'" A1D8A 37
A1D8A P31 P1 P 0 1 N N N N N N 108.119 121.761 107.953 -6.043 1.376 -2.029 P31 A1D8A 38
A1D8A PA P2 P 0 1 N N N N N N 108.258 122.487 118.579 5.572 -0.265 -0.884 PA A1D8A 39
A1D8A PB P3 P 0 1 N N N N N N 107.220 120.719 120.628 8.299 0.758 -0.337 PB A1D8A 40
A1D8A H1 H1 H 0 1 N N N N N N 105.952 122.544 112.553 0.200 -0.419 2.534 H1 A1D8A 41
A1D8A H2 H2 H 0 1 N N N N N N 106.391 125.121 114.168 -0.549 -0.874 -0.409 H2 A1D8A 42
A1D8A H3 H3 H 0 1 N N N N N N 107.841 124.267 115.485 1.070 -2.571 -0.544 H3 A1D8A 43
A1D8A H4 H4 H 0 1 N N N N N N 107.311 121.458 114.876 2.633 -1.657 1.745 H4 A1D8A 44
A1D8A H5 H5 H 0 1 N N N N N N 105.731 123.089 116.800 3.452 -2.270 -0.563 H5 A1D8A 45
A1D8A H6 H6 H 0 1 N N N N N N 106.455 121.455 116.987 2.697 -0.781 -1.180 H6 A1D8A 46
A1D8A H7 H7 H 0 1 N N N N N N 102.149 121.366 110.096 -4.254 0.988 3.820 H7 A1D8A 47
A1D8A H8 H8 H 0 1 N N N N N N 106.583 126.325 112.593 -1.810 -3.122 -0.470 H8 A1D8A 48
A1D8A H9 H9 H 0 1 N N N N N N 106.231 125.935 108.808 -4.095 -2.325 -1.961 H9 A1D8A 49
A1D8A H10 H10 H 0 1 N N N N N N 105.848 123.852 107.932 -6.307 -1.412 -1.150 H10 A1D8A 50
A1D8A H11 H11 H 0 1 N N N N N N 106.216 123.046 109.495 -5.427 -0.527 0.119 H11 A1D8A 51
A1D8A H12 H12 H 0 1 N N N N N N 108.570 124.532 109.810 -5.544 -3.003 0.484 H12 A1D8A 52
A1D8A H13 H13 H 0 1 N N N N N N 108.982 126.150 111.578 -3.702 -2.751 1.919 H13 A1D8A 53
A1D8A H14 H14 H 0 1 N N N N N N 104.624 125.592 114.309 0.748 2.152 -0.182 H14 A1D8A 54
A1D8A H15 H15 H 0 1 N N N N N N 99.572 124.990 110.716 -3.045 5.029 0.647 H15 A1D8A 55
A1D8A H16 H16 H 0 1 N N N N N N 99.887 125.397 112.266 -4.420 4.974 1.611 H16 A1D8A 56
A1D8A H17 H17 H 0 1 N N N N N N 108.928 123.799 119.972 4.774 1.499 -1.906 H17 A1D8A 57
A1D8A H18 H18 H 0 1 N N N N N N 108.560 119.479 121.483 8.097 2.812 -1.069 H18 A1D8A 58
A1D8A H19 H19 H 0 1 N N N N N N 105.792 121.514 121.777 9.973 1.296 0.969 H19 A1D8A 59
A1D8A H20 H20 H 0 1 N N N N N N 109.442 122.731 114.595 1.593 -3.887 1.382 H20 A1D8A 60
A1D8A H21 H21 H 0 1 N N N N N N 110.016 121.044 107.884 -5.879 3.204 -3.222 H21 A1D8A 61
A1D8A H22 H22 H 0 1 N N N N N N 106.553 120.432 107.880 -7.372 0.436 -3.493 H22 A1D8A 62
A1D8A H23 H23 H 0 1 N N N N N N 109.410 126.474 108.861 -4.887 -5.171 -0.276 H23 A1D8A 63
A1D8A H24 H24 H 0 1 N N N N N N 107.631 128.084 111.794 -2.319 -4.698 1.859 H24 A1D8A 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
A1D8A O34 P31 DOUB N N 1
A1D8A P31 O30 SING N N 2
A1D8A P31 O33 SING N N 3
A1D8A P31 O32 SING N N 4
A1D8A O30 C29 SING N N 5
A1D8A O36 C35 SING N N 6
A1D8A C29 C28 SING N N 7
A1D8A C28 C35 SING N N 8
A1D8A C28 O27 SING N N 9
A1D8A C35 C37 SING N N 10
A1D8A N1 C2 DOUB Y N 11
A1D8A N1 C6 SING Y N 12
A1D8A C2 N3 SING Y N 13
A1D8A O27 C26 SING N N 14
A1D8A O38 C37 SING N N 15
A1D8A C37 C26 SING N N 16
A1D8A N6 C6 SING N N 17
A1D8A C6 C5 DOUB Y N 18
A1D8A N3 C4 DOUB Y N 19
A1D8A C26 "O2'" SING N N 20
A1D8A C5 C4 SING Y N 21
A1D8A C5 N7 SING Y N 22
A1D8A C4 N9 SING Y N 23
A1D8A "O2'" "C2'" SING N N 24
A1D8A N7 C8 DOUB Y N 25
A1D8A N9 "C1'" SING N N 26
A1D8A N9 C8 SING Y N 27
A1D8A "C1'" "C2'" SING N N 28
A1D8A "C1'" "O4'" SING N N 29
A1D8A "C2'" "C3'" SING N N 30
A1D8A "O3'" "C3'" SING N N 31
A1D8A "O4'" "C4'" SING N N 32
A1D8A "C3'" "C4'" SING N N 33
A1D8A "C4'" "C5'" SING N N 34
A1D8A "C5'" "O5'" SING N N 35
A1D8A "O5'" PA SING N N 36
A1D8A O2A PA DOUB N N 37
A1D8A PA O3A SING N N 38
A1D8A PA O1A SING N N 39
A1D8A O3A PB SING N N 40
A1D8A PB O3B DOUB N N 41
A1D8A PB O1B SING N N 42
A1D8A PB O2B SING N N 43
A1D8A "C1'" H1 SING N N 44
A1D8A "C2'" H2 SING N N 45
A1D8A "C3'" H3 SING N N 46
A1D8A "C4'" H4 SING N N 47
A1D8A "C5'" H5 SING N N 48
A1D8A "C5'" H6 SING N N 49
A1D8A C2 H7 SING N N 50
A1D8A C26 H8 SING N N 51
A1D8A C28 H9 SING N N 52
A1D8A C29 H10 SING N N 53
A1D8A C29 H11 SING N N 54
A1D8A C35 H12 SING N N 55
A1D8A C37 H13 SING N N 56
A1D8A C8 H14 SING N N 57
A1D8A N6 H15 SING N N 58
A1D8A N6 H16 SING N N 59
A1D8A O1A H17 SING N N 60
A1D8A O1B H18 SING N N 61
A1D8A O2B H19 SING N N 62
A1D8A "O3'" H20 SING N N 63
A1D8A O32 H21 SING N N 64
A1D8A O33 H22 SING N N 65
A1D8A O36 H23 SING N N 66
A1D8A O38 H24 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
A1D8A InChI InChI 1.06 "InChI=1S/C15H24N5O17P3/c16-12-7-13(18-3-17-12)20(4-19-7)14-11(9(22)6(34-14)2-33-40(30,31)37-39(27,28)29)36-15-10(23)8(21)5(35-15)1-32-38(24,25)26/h3-6,8-11,14-15,21-23H,1-2H2,(H,30,31)(H2,16,17,18)(H2,24,25,26)(H2,27,28,29)/t5-,6-,8-,9-,10-,11-,14-,15+/m1/s1"
A1D8A InChIKey InChI 1.06 GOABUQLPPRUQSR-ZQSHOCFMSA-N
A1D8A SMILES_CANONICAL CACTVS 3.385 "Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O[C@@H]4O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]4O"
A1D8A SMILES CACTVS 3.385 "Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O[CH]4O[CH](CO[P](O)(O)=O)[CH](O)[CH]4O"
A1D8A SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)OP(=O)(O)O)O)O[C@H]4[C@@H]([C@@H]([C@H](O4)COP(=O)(O)O)O)O)N"
A1D8A SMILES "OpenEye OEToolkits" 2.0.7 "c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)OC4C(C(C(O4)COP(=O)(O)O)O)O)N"
#
_pdbx_chem_comp_identifier.comp_id A1D8A
_pdbx_chem_comp_identifier.type "SYSTEMATIC NAME"
_pdbx_chem_comp_identifier.program "OpenEye OEToolkits"
_pdbx_chem_comp_identifier.program_version 2.0.7
_pdbx_chem_comp_identifier.identifier "[(2~{R},3~{R},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-[(2~{S},3~{R},4~{S},5~{R})-3,4-bis(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]oxy-3-oxidanyl-oxolan-2-yl]methyl phosphono 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
A1D8A "Create component" 2024-05-15 PDBC
A1D8A "Initial release" 2024-11-06 RCSB
#