data_ZJ3
#
_chem_comp.id ZJ3
_chem_comp.name "[(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-{[2-oxo-4-(trifluoromethyl)-2H-1-benzopyran-7-yl]oxy}oxolan-2-yl]methyl dihydrogen diphosphate"
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C25 H26 F3 N5 O16 P2"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2023-03-14
_chem_comp.pdbx_modified_date 2023-05-12
_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 771.441
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code ZJ3
_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 8GIA
_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.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
ZJ3 C02 C1 C 0 1 N N R -26.276 -5.076 30.949 6.523 -1.031 1.532 C02 ZJ3 1
ZJ3 C03 C2 C 0 1 N N R -25.383 -4.241 31.711 5.700 -0.866 0.236 C03 ZJ3 2
ZJ3 C05 C3 C 0 1 N N R -25.892 -3.005 29.760 4.272 -0.175 1.895 C05 ZJ3 3
ZJ3 C06 C4 C 0 1 N N S -26.050 -4.518 29.546 5.562 -0.565 2.649 C06 ZJ3 4
ZJ3 C08 C5 C 0 1 N N N -27.213 -2.235 29.562 3.625 1.053 2.541 C08 ZJ3 5
ZJ3 C14 C6 C 0 1 N N N -32.611 0.234 28.831 -3.326 3.823 -0.189 C14 ZJ3 6
ZJ3 C15 C7 C 0 1 N N R -33.756 -0.213 29.751 -3.778 3.498 -1.614 C15 ZJ3 7
ZJ3 C17 C8 C 0 1 N N R -33.906 -0.802 31.994 -5.502 1.959 -1.467 C17 ZJ3 8
ZJ3 C18 C9 C 0 1 N N R -34.054 0.719 31.988 -6.123 3.177 -2.196 C18 ZJ3 9
ZJ3 C19 C10 C 0 1 N N S -34.383 0.965 30.516 -5.064 4.278 -1.947 C19 ZJ3 10
ZJ3 C23 C11 C 0 1 Y N N -35.291 -2.752 32.300 -5.662 -0.410 -1.372 C23 ZJ3 11
ZJ3 C24 C12 C 0 1 Y N N -36.552 -3.349 32.515 -4.879 -0.352 -0.221 C24 ZJ3 12
ZJ3 C25 C13 C 0 1 Y N N -36.638 -4.735 32.749 -4.542 -1.496 0.443 C25 ZJ3 13
ZJ3 C26 C14 C 0 1 Y N N -35.471 -5.524 32.769 -4.985 -2.734 -0.034 C26 ZJ3 14
ZJ3 C27 C15 C 0 1 N N N -35.536 -6.911 33.007 -4.639 -3.977 0.658 C27 ZJ3 15
ZJ3 C28 C16 C 0 1 N N N -36.880 -7.633 33.223 -3.794 -3.958 1.906 C28 ZJ3 16
ZJ3 C32 C17 C 0 1 N N N -34.325 -7.623 33.008 -5.100 -5.148 0.146 C32 ZJ3 17
ZJ3 C33 C18 C 0 1 N N N -33.130 -6.907 32.793 -5.889 -5.139 -1.023 C33 ZJ3 18
ZJ3 C36 C19 C 0 1 Y N N -34.211 -4.929 32.556 -5.777 -2.799 -1.196 C36 ZJ3 19
ZJ3 C37 C20 C 0 1 Y N N -34.123 -3.540 32.319 -6.110 -1.628 -1.859 C37 ZJ3 20
ZJ3 C43 C21 C 0 1 Y N N -24.825 -3.744 34.069 7.327 -1.193 -1.676 C43 ZJ3 21
ZJ3 C45 C22 C 0 1 Y N N -22.887 -2.997 35.139 8.366 -2.969 -2.700 C45 ZJ3 22
ZJ3 C47 C23 C 0 1 Y N N -24.826 -3.415 36.425 8.832 -0.866 -3.531 C47 ZJ3 23
ZJ3 C49 C24 C 0 1 Y N N -25.502 -3.782 35.311 7.969 -0.317 -2.567 C49 ZJ3 24
ZJ3 C51 C25 C 0 1 Y N N -26.868 -4.424 33.721 6.739 0.889 -1.251 C51 ZJ3 25
ZJ3 F29 F1 F 0 1 N N N -37.643 -7.457 32.125 -2.550 -3.387 1.619 F29 ZJ3 26
ZJ3 F30 F2 F 0 1 N N N -37.513 -7.146 34.305 -4.437 -3.203 2.893 F30 ZJ3 27
ZJ3 F31 F3 F 0 1 N N N -36.688 -8.962 33.343 -3.612 -5.267 2.366 F31 ZJ3 28
ZJ3 N42 N1 N 0 1 Y N N -25.696 -4.147 33.110 6.558 -0.404 -0.858 N42 ZJ3 29
ZJ3 N44 N2 N 0 1 Y N N -23.537 -3.345 34.013 7.553 -2.499 -1.778 N44 ZJ3 30
ZJ3 N46 N3 N 0 1 Y N N -23.533 -3.033 36.321 8.992 -2.185 -3.559 N46 ZJ3 31
ZJ3 N48 N4 N 0 1 N N N -25.455 -3.440 37.707 9.492 -0.054 -4.436 N48 ZJ3 32
ZJ3 N50 N5 N 0 1 Y N N -26.754 -4.206 35.049 7.567 0.938 -2.253 N50 ZJ3 33
ZJ3 O01 O1 O 0 1 N N N -25.845 -6.445 31.009 6.888 -2.399 1.724 O01 ZJ3 34
ZJ3 O04 O2 O 0 1 N N N -25.405 -2.912 31.122 4.708 0.134 0.553 O04 ZJ3 35
ZJ3 O07 O3 O 0 1 N N N -24.805 -4.987 28.984 5.304 -1.632 3.564 O07 ZJ3 36
ZJ3 O09 O4 O 0 1 N N N -28.284 -3.073 29.999 2.412 1.368 1.855 O09 ZJ3 37
ZJ3 O11 O5 O 0 1 N N N -29.889 -1.090 29.534 0.131 2.583 1.370 O11 ZJ3 38
ZJ3 O13 O6 O 0 1 N N N -32.076 -0.942 28.200 -2.073 3.187 0.070 O13 ZJ3 39
ZJ3 O16 O7 O 0 1 N N N -33.254 -1.130 30.749 -4.087 2.098 -1.722 O16 ZJ3 40
ZJ3 O20 O8 O 0 1 N N N -35.807 0.859 30.257 -4.879 5.069 -3.123 O20 ZJ3 41
ZJ3 O21 O9 O 0 1 N N N -35.158 1.211 32.757 -6.267 2.915 -3.594 O21 ZJ3 42
ZJ3 O22 O10 O 0 1 N N N -35.237 -1.338 32.054 -5.994 0.736 -2.019 O22 ZJ3 43
ZJ3 O34 O11 O 0 1 N N N -33.143 -5.640 32.577 -6.203 -3.996 -1.653 O34 ZJ3 44
ZJ3 O35 O12 O 0 1 N N N -32.046 -7.490 32.838 -6.295 -6.195 -1.472 O35 ZJ3 45
ZJ3 O38 O13 O 0 1 N N N -30.011 0.203 27.389 -2.174 2.614 2.634 O38 ZJ3 46
ZJ3 O39 O14 O 0 1 N N N -30.177 -2.292 27.240 -1.101 4.743 1.804 O39 ZJ3 47
ZJ3 O40 O15 O 0 1 N N N -29.562 -2.009 31.865 2.256 3.988 2.022 O40 ZJ3 48
ZJ3 O41 O16 O 0 1 N N N -30.757 -3.406 30.106 1.104 2.493 3.697 O41 ZJ3 49
ZJ3 P10 P1 P 0 1 N N N -29.659 -2.394 30.399 1.468 2.605 2.267 P10 ZJ3 50
ZJ3 P12 P2 P 0 1 N N N -30.501 -1.056 28.065 -1.300 3.313 1.477 P12 ZJ3 51
ZJ3 H021 H1 H 0 0 N N N -27.325 -4.954 31.257 7.412 -0.400 1.503 H021 ZJ3 52
ZJ3 H031 H2 H 0 0 N N N -24.364 -4.643 31.610 5.220 -1.808 -0.031 H031 ZJ3 53
ZJ3 H051 H3 H 0 0 N N N -25.140 -2.617 29.057 3.571 -1.010 1.883 H051 ZJ3 54
ZJ3 H061 H4 H 0 0 N N N -26.909 -4.733 28.893 5.974 0.297 3.173 H061 ZJ3 55
ZJ3 H081 H5 H 0 0 N N N -27.198 -1.309 30.156 3.406 0.840 3.587 H081 ZJ3 56
ZJ3 H082 H6 H 0 0 N N N -27.344 -1.986 28.499 4.309 1.899 2.478 H082 ZJ3 57
ZJ3 H141 H7 H 0 0 N N N -31.828 0.732 29.422 -3.216 4.902 -0.080 H141 ZJ3 58
ZJ3 H142 H8 H 0 0 N N N -32.992 0.929 28.068 -4.071 3.460 0.520 H142 ZJ3 59
ZJ3 H151 H9 H 0 0 N N N -34.534 -0.700 29.144 -2.991 3.761 -2.321 H151 ZJ3 60
ZJ3 H171 H10 H 0 0 N N N -33.304 -1.120 32.858 -5.707 2.006 -0.397 H171 ZJ3 61
ZJ3 H181 H11 H 0 0 N N N -33.106 1.205 32.263 -7.080 3.449 -1.752 H181 ZJ3 62
ZJ3 H191 H12 H 0 0 N N N -33.967 1.923 30.172 -5.357 4.906 -1.106 H191 ZJ3 63
ZJ3 H241 H13 H 0 0 N N N -37.447 -2.745 32.500 -4.537 0.603 0.148 H241 ZJ3 64
ZJ3 H251 H14 H 0 0 N N N -37.601 -5.194 32.914 -3.934 -1.445 1.335 H251 ZJ3 65
ZJ3 H321 H15 H 0 0 N N N -34.310 -8.691 33.169 -4.862 -6.082 0.632 H321 ZJ3 66
ZJ3 H371 H16 H 0 0 N N N -33.160 -3.081 32.152 -6.717 -1.664 -2.751 H371 ZJ3 67
ZJ3 H451 H17 H 0 0 N N N -21.852 -2.690 35.095 8.525 -4.036 -2.758 H451 ZJ3 68
ZJ3 H511 H18 H 0 0 N N N -27.762 -4.768 33.223 6.264 1.747 -0.797 H511 ZJ3 69
ZJ3 H481 H19 H 0 0 N N N -24.801 -3.149 38.405 9.361 0.907 -4.410 H481 ZJ3 70
ZJ3 H482 H20 H 0 0 N N N -26.239 -2.820 37.705 10.085 -0.445 -5.096 H482 ZJ3 71
ZJ3 H011 H21 H 0 0 N N N -25.989 -6.785 31.884 7.407 -2.559 2.524 H011 ZJ3 72
ZJ3 H071 H22 H 0 0 N N N -24.858 -5.924 28.834 6.080 -1.918 4.065 H071 ZJ3 73
ZJ3 H201 H23 H 0 0 N N N -36.264 1.562 30.703 -5.658 5.582 -3.379 H201 ZJ3 74
ZJ3 H211 H24 H 0 0 N N N -34.987 1.074 33.681 -6.852 2.172 -3.796 H211 ZJ3 75
ZJ3 H1 H25 H 0 1 N N N -29.589 -0.022 26.568 -2.343 1.674 2.485 H1 ZJ3 76
ZJ3 H2 H26 H 0 1 N N N -30.222 -2.479 32.361 2.526 4.129 1.104 H2 ZJ3 77
#
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
ZJ3 O39 P12 DOUB N N 1
ZJ3 O38 P12 SING N N 2
ZJ3 P12 O13 SING N N 3
ZJ3 P12 O11 SING N N 4
ZJ3 O13 C14 SING N N 5
ZJ3 C14 C15 SING N N 6
ZJ3 O07 C06 SING N N 7
ZJ3 O11 P10 SING N N 8
ZJ3 C06 C05 SING N N 9
ZJ3 C06 C02 SING N N 10
ZJ3 C08 C05 SING N N 11
ZJ3 C08 O09 SING N N 12
ZJ3 C15 C19 SING N N 13
ZJ3 C15 O16 SING N N 14
ZJ3 C05 O04 SING N N 15
ZJ3 O09 P10 SING N N 16
ZJ3 O41 P10 DOUB N N 17
ZJ3 O20 C19 SING N N 18
ZJ3 P10 O40 SING N N 19
ZJ3 C19 C18 SING N N 20
ZJ3 O16 C17 SING N N 21
ZJ3 C02 O01 SING N N 22
ZJ3 C02 C03 SING N N 23
ZJ3 O04 C03 SING N N 24
ZJ3 C03 N42 SING N N 25
ZJ3 C18 C17 SING N N 26
ZJ3 C18 O21 SING N N 27
ZJ3 C17 O22 SING N N 28
ZJ3 O22 C23 SING N N 29
ZJ3 F29 C28 SING N N 30
ZJ3 C23 C37 DOUB Y N 31
ZJ3 C23 C24 SING Y N 32
ZJ3 C37 C36 SING Y N 33
ZJ3 C24 C25 DOUB Y N 34
ZJ3 C36 O34 SING N N 35
ZJ3 C36 C26 DOUB Y N 36
ZJ3 O34 C33 SING N N 37
ZJ3 C25 C26 SING Y N 38
ZJ3 C26 C27 SING N N 39
ZJ3 C33 O35 DOUB N N 40
ZJ3 C33 C32 SING N N 41
ZJ3 C27 C32 DOUB N N 42
ZJ3 C27 C28 SING N N 43
ZJ3 N42 C51 SING Y N 44
ZJ3 N42 C43 SING Y N 45
ZJ3 C28 F31 SING N N 46
ZJ3 C28 F30 SING N N 47
ZJ3 C51 N50 DOUB Y N 48
ZJ3 N44 C43 DOUB Y N 49
ZJ3 N44 C45 SING Y N 50
ZJ3 C43 C49 SING Y N 51
ZJ3 N50 C49 SING Y N 52
ZJ3 C45 N46 DOUB Y N 53
ZJ3 C49 C47 DOUB Y N 54
ZJ3 N46 C47 SING Y N 55
ZJ3 C47 N48 SING N N 56
ZJ3 C02 H021 SING N N 57
ZJ3 C03 H031 SING N N 58
ZJ3 C05 H051 SING N N 59
ZJ3 C06 H061 SING N N 60
ZJ3 C08 H081 SING N N 61
ZJ3 C08 H082 SING N N 62
ZJ3 C14 H141 SING N N 63
ZJ3 C14 H142 SING N N 64
ZJ3 C15 H151 SING N N 65
ZJ3 C17 H171 SING N N 66
ZJ3 C18 H181 SING N N 67
ZJ3 C19 H191 SING N N 68
ZJ3 C24 H241 SING N N 69
ZJ3 C25 H251 SING N N 70
ZJ3 C32 H321 SING N N 71
ZJ3 C37 H371 SING N N 72
ZJ3 C45 H451 SING N N 73
ZJ3 C51 H511 SING N N 74
ZJ3 N48 H481 SING N N 75
ZJ3 N48 H482 SING N N 76
ZJ3 O01 H011 SING N N 77
ZJ3 O07 H071 SING N N 78
ZJ3 O20 H201 SING N N 79
ZJ3 O21 H211 SING N N 80
ZJ3 O38 H1 SING N N 81
ZJ3 O40 H2 SING N N 82
#
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
ZJ3 SMILES ACDLabs 12.01 "Nc1ncnc2c1ncn2C1OC(COP(=O)(O)OP(=O)(O)OCC2OC(Oc3cc4OC(=O)C=C(c4cc3)C(F)(F)F)C(O)C2O)C(O)C1O"
ZJ3 InChI InChI 1.06 "InChI=1S/C25H26F3N5O16P2/c26-25(27,28)11-4-15(34)46-12-3-9(1-2-10(11)12)45-24-20(38)18(36)14(48-24)6-44-51(41,42)49-50(39,40)43-5-13-17(35)19(37)23(47-13)33-8-32-16-21(29)30-7-31-22(16)33/h1-4,7-8,13-14,17-20,23-24,35-38H,5-6H2,(H,39,40)(H,41,42)(H2,29,30,31)/t13-,14-,17-,18-,19-,20-,23-,24+/m1/s1"
ZJ3 InChIKey InChI 1.06 JNMHMJORTGCLAH-IPSZZCKZSA-N
ZJ3 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](Oc5ccc6c(OC(=O)C=C6C(F)(F)F)c5)[C@H](O)[C@@H]4O)[C@@H](O)[C@H]3O"
ZJ3 SMILES CACTVS 3.385 "Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]4O[CH](Oc5ccc6c(OC(=O)C=C6C(F)(F)F)c5)[CH](O)[CH]4O)[CH](O)[CH]3O"
ZJ3 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1cc2c(cc1O[C@@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)OP(=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)n5cnc6c5ncnc6N)O)O)O)O)OC(=O)C=C2C(F)(F)F"
ZJ3 SMILES "OpenEye OEToolkits" 2.0.7 "c1cc2c(cc1OC3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)n5cnc6c5ncnc6N)O)O)O)O)OC(=O)C=C2C(F)(F)F"
#
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
ZJ3 "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-{[2-oxo-4-(trifluoromethyl)-2H-1-benzopyran-7-yl]oxy}oxolan-2-yl]methyl dihydrogen diphosphate (non-preferred name)"
ZJ3 "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})-3,4-bis(oxidanyl)-5-[2-oxidanylidene-4-(trifluoromethyl)chromen-7-yl]oxy-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
ZJ3 "Create component" 2023-03-14 RCSB
ZJ3 "Initial release" 2023-05-17 RCSB
#