data_LR7 # _chem_comp.id LR7 _chem_comp.name "[[(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{R},4~{R},5~{R},6~{R})-3-(hex-5-ynoylamino)-6-(hydroxymethyl)-4,5-bis(oxidanyl)oxan-2-yl] hydrogen phosphate" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C21 H31 N3 O17 P2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2019-03-12 _chem_comp.pdbx_modified_date 2020-01-24 _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 659.428 _chem_comp.one_letter_code ? _chem_comp.three_letter_code LR7 _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 6NQT _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 LR7 O4 O1 O 0 1 N N N -7.953 39.752 -54.656 8.655 -3.147 -1.497 O4 LR7 1 LR7 C4 C1 C 0 1 N N N -8.501 40.771 -54.215 8.040 -2.245 -0.956 C4 LR7 2 LR7 N3 N1 N 0 1 N N N -8.228 42.065 -54.788 8.173 -2.029 0.368 N3 LR7 3 LR7 C2 C2 C 0 1 N N N -8.898 43.197 -54.217 7.493 -1.033 0.965 C2 LR7 4 LR7 O2 O2 O 0 1 N N N -8.684 44.304 -54.710 7.623 -0.850 2.160 O2 LR7 5 LR7 C5 C3 C 0 1 N N N -9.410 40.625 -53.114 7.183 -1.411 -1.714 C5 LR7 6 LR7 C6 C4 C 0 1 N N N -10.004 41.690 -52.602 6.513 -0.418 -1.090 C6 LR7 7 LR7 N1 N2 N 0 1 N N N -9.785 43.015 -53.136 6.672 -0.235 0.257 N1 LR7 8 LR7 C1B C5 C 0 1 N N R -10.467 44.164 -52.528 5.945 0.842 0.934 C1B LR7 9 LR7 C2B C6 C 0 1 N N R -11.986 44.044 -52.403 6.417 2.226 0.420 C2B LR7 10 LR7 "O2'" O3 O 0 1 N N N -12.694 44.597 -53.528 7.562 2.676 1.146 "O2'" LR7 11 LR7 C3B C7 C 0 1 N N S -12.254 44.780 -51.107 5.187 3.118 0.717 C3B LR7 12 LR7 O3B O4 O 0 1 N N N -12.500 46.163 -51.365 5.370 3.828 1.944 O3B LR7 13 LR7 O4B O5 O 0 1 N N N -9.943 44.329 -51.205 4.545 0.810 0.581 O4B LR7 14 LR7 C4B C8 C 0 1 N N R -10.988 44.605 -50.273 4.018 2.122 0.840 C4B LR7 15 LR7 C5B C9 C 0 1 N N N -11.041 43.494 -49.211 2.937 2.460 -0.189 C5B LR7 16 LR7 O5B O6 O 0 1 N N N -11.820 42.356 -49.588 1.808 1.606 0.008 O5B LR7 17 LR7 PA P1 P 0 1 N N N -13.233 42.010 -48.904 0.481 1.684 -0.899 PA LR7 18 LR7 O1A O7 O 0 1 N N N -13.865 43.268 -48.339 -0.243 3.104 -0.672 O1A LR7 19 LR7 O2A O8 O 0 1 N N N -14.069 41.389 -49.988 0.849 1.541 -2.326 O2A LR7 20 LR7 O3A O9 O 0 1 N N N -13.082 40.888 -47.769 -0.524 0.497 -0.483 O3A LR7 21 LR7 PB P2 P 0 1 N N N -13.514 41.115 -46.243 -1.764 -0.226 -1.213 PB LR7 22 LR7 O1B O10 O 0 1 N N N -14.773 41.946 -46.161 -2.573 0.786 -1.929 O1B LR7 23 LR7 O2B O11 O 0 1 N N N -13.803 39.720 -45.776 -1.210 -1.312 -2.264 O2B LR7 24 LR7 "O1'" O12 O 0 1 N N N -12.211 41.798 -45.511 -2.679 -0.963 -0.112 "O1'" LR7 25 LR7 "C1'" C10 C 0 1 N N R -11.594 41.616 -44.184 -3.914 -1.607 -0.431 "C1'" LR7 26 LR7 "O5'" O13 O 0 1 N N N -10.367 40.863 -44.060 -3.666 -2.976 -0.761 "O5'" LR7 27 LR7 "C5'" C11 C 0 1 N N R -9.420 41.094 -45.112 -3.034 -3.722 0.281 "C5'" LR7 28 LR7 "C6'" C12 C 0 1 N N N -8.287 40.106 -44.913 -2.794 -5.157 -0.193 "C6'" LR7 29 LR7 "O6'" O14 O 0 1 N N N -7.180 40.461 -45.728 -1.859 -5.151 -1.274 "O6'" LR7 30 LR7 "C4'" C13 C 0 1 N N R -8.981 42.549 -45.196 -3.938 -3.737 1.517 "C4'" LR7 31 LR7 "O4'" O15 O 0 1 N N N -7.785 42.738 -44.444 -5.168 -4.392 1.201 "O4'" LR7 32 LR7 "C3'" C14 C 0 1 N N R -10.064 43.513 -44.717 -4.223 -2.295 1.949 "C3'" LR7 33 LR7 "O3'" O16 O 0 1 N N N -9.327 44.514 -44.078 -5.125 -2.297 3.057 "O3'" LR7 34 LR7 "C2'" C15 C 0 1 N N R -11.093 42.964 -43.717 -4.853 -1.537 0.776 "C2'" LR7 35 LR7 "N2'" N3 N 0 1 N N N -12.264 43.822 -43.754 -5.062 -0.137 1.153 "N2'" LR7 36 LR7 "C7'" C16 C 0 1 N N N -12.624 44.588 -42.664 -6.011 0.593 0.536 "C7'" LR7 37 LR7 "O7'" O17 O 0 1 N N N -11.989 44.612 -41.625 -6.694 0.091 -0.332 "O7'" LR7 38 LR7 "C8'" C17 C 0 1 N N N -13.867 45.414 -42.846 -6.226 2.033 0.924 "C8'" LR7 39 LR7 C40 C18 C 0 1 N N N -13.729 46.738 -42.106 -7.354 2.627 0.078 C40 LR7 40 LR7 C41 C19 C 0 1 N N N -14.212 47.900 -42.964 -7.572 4.089 0.472 C41 LR7 41 LR7 C42 C20 C 0 1 N N N -14.666 48.983 -42.089 -8.657 4.661 -0.343 C42 LR7 42 LR7 C43 C21 C 0 1 N N N -15.074 49.817 -41.227 -9.522 5.116 -0.992 C43 LR7 43 LR7 H1 H1 H 0 1 N N N -7.595 42.170 -55.555 8.761 -2.595 0.893 H1 LR7 44 LR7 H2 H2 H 0 1 N N N -9.609 39.646 -52.704 7.068 -1.565 -2.776 H2 LR7 45 LR7 H3 H3 H 0 1 N N N -10.671 41.566 -51.762 5.855 0.229 -1.651 H3 LR7 46 LR7 H4 H4 H 0 1 N N N -10.244 45.063 -53.122 6.073 0.770 2.014 H4 LR7 47 LR7 H5 H5 H 0 1 N N N -12.250 42.984 -52.275 6.624 2.193 -0.650 H5 LR7 48 LR7 H6 H6 H 0 1 N N N -13.629 44.495 -53.396 7.894 3.538 0.860 H6 LR7 49 LR7 H7 H7 H 0 1 N N N -13.106 44.318 -50.586 5.012 3.813 -0.104 H7 LR7 50 LR7 H8 H8 H 0 1 N N N -12.667 46.614 -50.545 6.129 4.427 1.943 H8 LR7 51 LR7 H9 H9 H 0 1 N N N -10.781 45.556 -49.761 3.601 2.162 1.846 H9 LR7 52 LR7 H10 H10 H 0 1 N N N -10.013 43.157 -49.013 2.632 3.499 -0.067 H10 LR7 53 LR7 H11 H11 H 0 1 N N N -11.472 43.917 -48.291 3.333 2.313 -1.194 H11 LR7 54 LR7 H12 H12 H 0 1 N N N -14.688 43.436 -48.782 -0.512 3.266 0.243 H12 LR7 55 LR7 H13 H13 H 0 1 N N N -14.717 39.652 -45.527 -0.670 -2.007 -1.863 H13 LR7 56 LR7 H14 H14 H 0 1 N N N -12.344 41.241 -43.472 -4.376 -1.106 -1.281 H14 LR7 57 LR7 H15 H15 H 0 1 N N N -9.903 40.846 -46.069 -2.081 -3.258 0.534 H15 LR7 58 LR7 H16 H16 H 0 1 N N N -8.631 39.098 -45.187 -2.394 -5.749 0.630 H16 LR7 59 LR7 H17 H17 H 0 1 N N N -7.979 40.114 -43.857 -3.736 -5.591 -0.529 H17 LR7 60 LR7 H18 H18 H 0 1 N N N -6.476 39.837 -45.596 -1.659 -6.030 -1.625 H18 LR7 61 LR7 H19 H19 H 0 1 N N N -8.777 42.776 -46.253 -3.439 -4.268 2.327 H19 LR7 62 LR7 H20 H20 H 0 1 N N N -7.516 43.647 -44.500 -5.062 -5.310 0.914 H20 LR7 63 LR7 H21 H21 H 0 1 N N N -10.597 43.916 -45.591 -3.291 -1.810 2.239 H21 LR7 64 LR7 H22 H22 H 0 1 N N N -9.918 45.175 -43.738 -4.793 -2.767 3.834 H22 LR7 65 LR7 H23 H23 H 0 1 N N N -10.660 42.899 -42.708 -5.810 -1.993 0.520 H23 LR7 66 LR7 H24 H24 H 0 1 N N N -12.820 43.858 -44.585 -4.516 0.264 1.848 H24 LR7 67 LR7 H25 H25 H 0 1 N N N -14.020 45.610 -43.918 -6.495 2.089 1.979 H25 LR7 68 LR7 H26 H26 H 0 1 N N N -14.732 44.863 -42.447 -5.308 2.596 0.753 H26 LR7 69 LR7 H27 H27 H 0 1 N N N -12.671 46.897 -41.849 -7.084 2.571 -0.977 H27 LR7 70 LR7 H28 H28 H 0 1 N N N -14.329 46.699 -41.185 -8.271 2.064 0.249 H28 LR7 71 LR7 H29 H29 H 0 1 N N N -13.387 48.259 -43.597 -7.841 4.145 1.527 H29 LR7 72 LR7 H30 H30 H 0 1 N N N -15.045 47.567 -43.601 -6.654 4.652 0.301 H30 LR7 73 LR7 H31 H31 H 0 1 N N N -15.415 50.515 -40.506 -10.296 5.524 -1.573 H31 LR7 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 LR7 N3 C2 SING N N 1 LR7 N3 C4 SING N N 2 LR7 O2 C2 DOUB N N 3 LR7 O4 C4 DOUB N N 4 LR7 C2 N1 SING N N 5 LR7 C4 C5 SING N N 6 LR7 "O2'" C2B SING N N 7 LR7 N1 C6 SING N N 8 LR7 N1 C1B SING N N 9 LR7 C5 C6 DOUB N N 10 LR7 C1B C2B SING N N 11 LR7 C1B O4B SING N N 12 LR7 C2B C3B SING N N 13 LR7 O3B C3B SING N N 14 LR7 O4B C4B SING N N 15 LR7 C3B C4B SING N N 16 LR7 C4B C5B SING N N 17 LR7 O2A PA DOUB N N 18 LR7 O5B C5B SING N N 19 LR7 O5B PA SING N N 20 LR7 PA O1A SING N N 21 LR7 PA O3A SING N N 22 LR7 O3A PB SING N N 23 LR7 PB O1B DOUB N N 24 LR7 PB O2B SING N N 25 LR7 PB "O1'" SING N N 26 LR7 "O6'" "C6'" SING N N 27 LR7 "O1'" "C1'" SING N N 28 LR7 "C4'" "C5'" SING N N 29 LR7 "C4'" "C3'" SING N N 30 LR7 "C4'" "O4'" SING N N 31 LR7 "C5'" "C6'" SING N N 32 LR7 "C5'" "O5'" SING N N 33 LR7 "C3'" "O3'" SING N N 34 LR7 "C3'" "C2'" SING N N 35 LR7 "C1'" "O5'" SING N N 36 LR7 "C1'" "C2'" SING N N 37 LR7 "N2'" "C2'" SING N N 38 LR7 "N2'" "C7'" SING N N 39 LR7 C41 C40 SING N N 40 LR7 C41 C42 SING N N 41 LR7 "C8'" "C7'" SING N N 42 LR7 "C8'" C40 SING N N 43 LR7 "C7'" "O7'" DOUB N N 44 LR7 C42 C43 TRIP N N 45 LR7 N3 H1 SING N N 46 LR7 C5 H2 SING N N 47 LR7 C6 H3 SING N N 48 LR7 C1B H4 SING N N 49 LR7 C2B H5 SING N N 50 LR7 "O2'" H6 SING N N 51 LR7 C3B H7 SING N N 52 LR7 O3B H8 SING N N 53 LR7 C4B H9 SING N N 54 LR7 C5B H10 SING N N 55 LR7 C5B H11 SING N N 56 LR7 O1A H12 SING N N 57 LR7 O2B H13 SING N N 58 LR7 "C1'" H14 SING N N 59 LR7 "C5'" H15 SING N N 60 LR7 "C6'" H16 SING N N 61 LR7 "C6'" H17 SING N N 62 LR7 "O6'" H18 SING N N 63 LR7 "C4'" H19 SING N N 64 LR7 "O4'" H20 SING N N 65 LR7 "C3'" H21 SING N N 66 LR7 "O3'" H22 SING N N 67 LR7 "C2'" H23 SING N N 68 LR7 "N2'" H24 SING N N 69 LR7 "C8'" H25 SING N N 70 LR7 "C8'" H26 SING N N 71 LR7 C40 H27 SING N N 72 LR7 C40 H28 SING N N 73 LR7 C41 H29 SING N N 74 LR7 C41 H30 SING N N 75 LR7 C43 H31 SING N N 76 # # 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 LR7 SMILES ACDLabs 12.01 "O=C1C=CN(C(N1)=O)C2C(C(C(O2)COP(O)(OP(=O)(O)OC3OC(CO)C(C(O)C3NC(=O)CCCC#C)O)=O)O)O" LR7 InChI InChI 1.03 "InChI=1S/C21H31N3O17P2/c1-2-3-4-5-12(26)22-14-17(30)15(28)10(8-25)39-20(14)40-43(35,36)41-42(33,34)37-9-11-16(29)18(31)19(38-11)24-7-6-13(27)23-21(24)32/h1,6-7,10-11,14-20,25,28-31H,3-5,8-9H2,(H,22,26)(H,33,34)(H,35,36)(H,23,27,32)/t10-,11-,14-,15+,16-,17-,18-,19-,20-/m1/s1" LR7 InChIKey InChI 1.03 SPUYDPWWABYYLH-SSBRDYMUSA-N LR7 SMILES_CANONICAL CACTVS 3.385 "OC[C@H]1O[C@H](O[P](O)(=O)O[P](O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)N3C=CC(=O)NC3=O)[C@H](NC(=O)CCCC#C)[C@@H](O)[C@H]1O" LR7 SMILES CACTVS 3.385 "OC[CH]1O[CH](O[P](O)(=O)O[P](O)(=O)OC[CH]2O[CH]([CH](O)[CH]2O)N3C=CC(=O)NC3=O)[CH](NC(=O)CCCC#C)[CH](O)[CH]1O" LR7 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C#CCCCC(=O)N[C@@H]1[C@H]([C@H]([C@H](O[C@@H]1OP(=O)(O)OP(=O)(O)OC[C@@H]2[C@H]([C@H]([C@@H](O2)N3C=CC(=O)NC3=O)O)O)CO)O)O" LR7 SMILES "OpenEye OEToolkits" 2.0.7 "C#CCCCC(=O)NC1C(C(C(OC1OP(=O)(O)OP(=O)(O)OCC2C(C(C(O2)N3C=CC(=O)NC3=O)O)O)CO)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 LR7 "SYSTEMATIC NAME" ACDLabs 12.01 "[(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3R,4R,5R,6R)-3-(hex-5-ynoylamino)-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl dihydrogen diphosphate (non-preferred name)" LR7 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "[[(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{R},4~{R},5~{R},6~{R})-3-(hex-5-ynoylamino)-6-(hydroxymethyl)-4,5-bis(oxidanyl)oxan-2-yl] 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 LR7 "Create component" 2019-03-12 RCSB LR7 "Initial release" 2020-01-29 RCSB ##