data_2QR # _chem_comp.id 2QR _chem_comp.name ;(2R,3R,4S,5S)-3,4-dihydroxy-5-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)amino]tetrahydro-2H-pyr an-2-yl [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate ; _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C22 H33 N4 O20 P3" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms PLP-UDP-Ara4N _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2014-01-09 _chem_comp.pdbx_modified_date 2020-06-17 _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 766.434 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 2QR _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 4OCA _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 2QR O01 O01 O 0 1 N N N -16.027 -2.325 16.510 -10.431 -1.511 -1.841 O01 2QR 1 2QR C02 C02 C 0 1 N N R -16.255 -2.949 15.285 -9.393 -0.743 -1.229 C02 2QR 2 2QR C03 C03 C 0 1 N N S -17.552 -3.556 15.281 -8.447 -0.141 -2.297 C03 2QR 3 2QR O04 O04 O 0 1 N N N -18.432 -2.805 16.088 -8.556 -0.864 -3.525 O04 2QR 4 2QR C05 C05 C 0 1 N N R -17.305 -4.871 15.869 -7.039 -0.312 -1.694 C05 2QR 5 2QR C06 C06 C 0 1 N N N -18.237 -5.927 15.371 -6.359 1.052 -1.567 C06 2QR 6 2QR O07 O07 O 0 1 N N N -18.134 -7.160 16.078 -5.014 0.874 -1.117 O07 2QR 7 2QR P08 P08 P 0 1 N N N -19.370 -8.162 16.173 -4.001 2.102 -0.873 P08 2QR 8 2QR O09 O09 O 0 1 N N N -20.404 -7.575 17.112 -4.546 3.014 0.337 O09 2QR 9 2QR O10 O10 O 0 1 N N N -19.989 -8.285 14.695 -2.544 1.529 -0.498 O10 2QR 10 2QR P11 P11 P 0 1 N N N -19.528 -9.285 13.630 -1.070 2.173 -0.440 P11 2QR 11 2QR O12 O12 O 0 1 N N N -20.700 -9.559 12.703 -0.886 3.088 -1.590 O12 2QR 12 2QR O13 O13 O 0 1 N N N -19.001 -10.600 14.231 0.032 1.000 -0.506 O13 2QR 13 2QR C14 C14 C 0 1 N N R -19.711 -11.726 14.207 1.436 1.255 -0.580 C14 2QR 14 2QR C15 C15 C 0 1 N N R -19.525 -12.458 15.503 2.121 0.120 -1.345 C15 2QR 15 2QR O16 O16 O 0 1 N N N -20.040 -11.703 16.565 1.851 -1.125 -0.697 O16 2QR 16 2QR O17 O17 O 0 1 N N N -19.252 -12.561 13.097 1.976 1.330 0.741 O17 2QR 17 2QR C18 C18 C 0 1 N N N -17.880 -13.035 13.258 3.377 1.609 0.784 C18 2QR 18 2QR C19 C19 C 0 1 N N S -17.533 -13.503 14.651 4.140 0.488 0.072 C19 2QR 19 2QR C20 C20 C 0 1 N N S -18.106 -12.704 15.735 3.632 0.369 -1.368 C20 2QR 20 2QR O21 O21 O 0 1 N N N -17.952 -13.401 16.963 3.906 1.581 -2.073 O21 2QR 21 2QR N22 N22 N 0 1 N N N -18.016 -14.863 14.789 5.575 0.801 0.062 N22 2QR 22 2QR C23 C23 C 0 1 N N N -17.218 -15.777 14.312 6.219 0.362 1.308 C23 2QR 23 2QR C24 C24 C 0 1 Y N N -17.434 -17.268 14.538 7.687 0.699 1.261 C24 2QR 24 2QR C25 C25 C 0 1 Y N N -17.450 -17.734 15.834 8.152 1.922 1.732 C25 2QR 25 2QR O26 O26 O 0 1 N N N -17.307 -16.851 16.857 7.288 2.838 2.244 O26 2QR 26 2QR C27 C27 C 0 1 Y N N -17.626 -19.085 16.054 9.511 2.194 1.671 C27 2QR 27 2QR C28 C28 C 0 1 N N N -17.654 -19.569 17.449 10.031 3.515 2.178 C28 2QR 28 2QR N29 N29 N 0 1 Y N N -17.765 -19.935 14.993 10.353 1.309 1.176 N29 2QR 29 2QR C30 C30 C 0 1 Y N N -17.739 -19.502 13.697 9.944 0.141 0.722 C30 2QR 30 2QR C31 C31 C 0 1 Y N N -17.573 -18.158 13.460 8.607 -0.204 0.753 C31 2QR 31 2QR C32 C32 C 0 1 N N N -17.536 -17.603 12.034 8.152 -1.543 0.231 C32 2QR 32 2QR O33 O33 O 0 1 N N N -16.264 -17.492 11.477 9.282 -2.278 -0.243 O33 2QR 33 2QR P34 P34 P 0 1 N N N -16.127 -16.582 10.221 9.166 -3.756 -0.872 P34 2QR 34 2QR O35 O35 O 0 1 N N N -16.687 -15.247 10.565 10.608 -4.222 -1.416 O35 2QR 35 2QR O36 O36 O 0 1 N N N -14.648 -16.465 9.848 8.663 -4.783 0.262 O36 2QR 36 2QR O37 O37 O 0 1 N N N -16.930 -17.232 9.058 8.197 -3.741 -1.990 O37 2QR 37 2QR O38 O38 O 0 1 N N N -18.430 -8.656 12.836 -0.897 2.995 0.933 O38 2QR 38 2QR O39 O39 O 0 1 N N N -18.914 -9.542 16.761 -3.909 2.918 -2.104 O39 2QR 39 2QR O40 O40 O 0 1 N N N -15.958 -5.221 15.545 -7.200 -0.904 -0.394 O40 2QR 40 2QR C41 C41 C 0 1 N N R -15.281 -4.068 15.107 -8.434 -1.654 -0.421 C41 2QR 41 2QR N42 N42 N 0 1 N N N -14.875 -4.138 13.757 -8.942 -1.863 0.937 N42 2QR 42 2QR C43 C43 C 0 1 N N N -15.656 -4.972 12.842 -9.321 -3.116 1.334 C43 2QR 43 2QR C44 C44 C 0 1 N N N -15.252 -5.066 11.411 -9.790 -3.308 2.586 C44 2QR 44 2QR C45 C45 C 0 1 N N N -13.694 -3.381 13.310 -9.026 -0.821 1.784 C45 2QR 45 2QR N46 N46 N 0 1 N N N -13.331 -3.504 11.889 -9.489 -0.984 3.037 N46 2QR 46 2QR C47 C47 C 0 1 N N N -14.061 -4.313 10.926 -9.878 -2.202 3.465 C47 2QR 47 2QR O48 O48 O 0 1 N N N -13.706 -4.378 9.729 -10.298 -2.351 4.598 O48 2QR 48 2QR O49 O49 O 0 1 N N N -13.012 -2.664 14.070 -8.678 0.283 1.413 O49 2QR 49 2QR H011 H011 H 0 0 N N N -16.646 -1.613 16.624 -11.030 -0.992 -2.394 H011 2QR 50 2QR H021 H021 H 0 0 N N N -16.158 -2.237 14.452 -9.812 0.039 -0.596 H021 2QR 51 2QR H031 H031 H 0 0 N N N -17.937 -3.657 14.256 -8.670 0.914 -2.453 H031 2QR 52 2QR H041 H041 H 0 0 N N N -19.291 -3.211 16.083 -9.439 -0.839 -3.919 H041 2QR 53 2QR H051 H051 H 0 0 N N N -17.411 -4.799 16.962 -6.441 -0.967 -2.328 H051 2QR 54 2QR H061 H061 H 0 0 N N N -19.268 -5.555 15.469 -6.354 1.548 -2.538 H061 2QR 55 2QR H062 H062 H 0 0 N N N -18.014 -6.115 14.310 -6.904 1.665 -0.849 H062 2QR 56 2QR H1 H1 H 0 1 N N N -20.544 -8.168 17.841 -4.632 2.544 1.177 H1 2QR 57 2QR H141 H141 H 0 0 N N N -20.782 -11.513 14.076 1.608 2.198 -1.097 H141 2QR 58 2QR H151 H151 H 0 0 N N N -20.051 -13.422 15.439 1.742 0.089 -2.367 H151 2QR 59 2QR H161 H161 H 0 0 N N N -19.583 -10.872 16.614 0.911 -1.344 -0.642 H161 2QR 60 2QR H182 H182 H 0 0 N N N -17.724 -13.875 12.566 3.575 2.557 0.284 H182 2QR 61 2QR H181 H181 H 0 0 N N N -17.200 -12.212 12.994 3.704 1.669 1.821 H181 2QR 62 2QR H191 H191 H 0 0 N N N -16.438 -13.501 14.751 3.976 -0.454 0.596 H191 2QR 63 2QR H201 H201 H 0 0 N N N -17.578 -11.741 15.788 4.131 -0.464 -1.863 H201 2QR 64 2QR H211 H211 H 0 0 N N N -18.323 -12.885 17.669 3.605 1.578 -2.992 H211 2QR 65 2QR H2 H2 H 0 1 N N N -18.891 -14.933 14.310 5.730 1.785 -0.097 H2 2QR 66 2QR H231 H231 H 0 0 N N N -16.221 -15.550 14.718 5.756 0.870 2.154 H231 2QR 67 2QR H4 H4 H 0 1 N N N -17.211 -15.634 13.221 6.097 -0.715 1.420 H4 2QR 68 2QR H261 H261 H 0 0 N N N -17.338 -17.317 17.684 7.144 2.753 3.196 H261 2QR 69 2QR H282 H282 H 0 0 N N N -17.797 -20.660 17.456 10.279 3.427 3.236 H282 2QR 70 2QR H281 H281 H 0 0 N N N -16.703 -19.321 17.942 10.923 3.794 1.617 H281 2QR 71 2QR H283 H283 H 0 0 N N N -18.483 -19.087 17.988 9.266 4.281 2.047 H283 2QR 72 2QR H301 H301 H 0 0 N N N -17.846 -20.199 12.879 10.665 -0.558 0.323 H301 2QR 73 2QR H322 H322 H 0 0 N N N -17.992 -16.602 12.046 7.667 -2.100 1.033 H322 2QR 74 2QR H321 H321 H 0 0 N N N -18.132 -18.269 11.393 7.446 -1.394 -0.586 H321 2QR 75 2QR H5 H5 H 0 1 N N N -17.428 -15.059 10.001 10.612 -5.105 -1.810 H5 2QR 76 2QR H6 H6 H 0 1 N N N -14.512 -16.815 8.975 9.251 -4.844 1.027 H6 2QR 77 2QR H7 H7 H 0 1 N N N -18.704 -8.566 11.931 -1.005 2.458 1.729 H7 2QR 78 2QR H411 H411 H 0 0 N N N -14.408 -3.880 15.749 -8.291 -2.608 -0.929 H411 2QR 79 2QR H431 H431 H 0 0 N N N -16.518 -5.515 13.201 -9.247 -3.948 0.649 H431 2QR 80 2QR H441 H441 H 0 0 N N N -15.821 -5.678 10.727 -10.093 -4.292 2.911 H441 2QR 81 2QR H461 H461 H 0 0 N N N -12.531 -2.999 11.565 -9.543 -0.222 3.635 H461 2QR 82 # # 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 2QR O37 P34 DOUB N N 1 2QR O48 C47 DOUB N N 2 2QR O36 P34 SING N N 3 2QR P34 O35 SING N N 4 2QR P34 O33 SING N N 5 2QR C47 C44 SING N N 6 2QR C47 N46 SING N N 7 2QR C44 C43 DOUB N N 8 2QR O33 C32 SING N N 9 2QR N46 C45 SING N N 10 2QR C32 C31 SING N N 11 2QR O12 P11 DOUB N N 12 2QR O38 P11 SING N N 13 2QR C43 N42 SING N N 14 2QR O17 C18 SING N N 15 2QR O17 C14 SING N N 16 2QR C18 C19 SING N N 17 2QR C45 N42 SING N N 18 2QR C45 O49 DOUB N N 19 2QR C31 C30 DOUB Y N 20 2QR C31 C24 SING Y N 21 2QR P11 O13 SING N N 22 2QR P11 O10 SING N N 23 2QR C30 N29 SING Y N 24 2QR N42 C41 SING N N 25 2QR C14 O13 SING N N 26 2QR C14 C15 SING N N 27 2QR C23 C24 SING N N 28 2QR C23 N22 SING N N 29 2QR C24 C25 DOUB Y N 30 2QR C19 N22 SING N N 31 2QR C19 C20 SING N N 32 2QR O10 P08 SING N N 33 2QR N29 C27 DOUB Y N 34 2QR C41 C02 SING N N 35 2QR C41 O40 SING N N 36 2QR C03 C02 SING N N 37 2QR C03 C05 SING N N 38 2QR C03 O04 SING N N 39 2QR C02 O01 SING N N 40 2QR C06 C05 SING N N 41 2QR C06 O07 SING N N 42 2QR C15 C20 SING N N 43 2QR C15 O16 SING N N 44 2QR O40 C05 SING N N 45 2QR C20 O21 SING N N 46 2QR C25 C27 SING Y N 47 2QR C25 O26 SING N N 48 2QR C27 C28 SING N N 49 2QR O07 P08 SING N N 50 2QR P08 O39 DOUB N N 51 2QR P08 O09 SING N N 52 2QR O01 H011 SING N N 53 2QR C02 H021 SING N N 54 2QR C03 H031 SING N N 55 2QR O04 H041 SING N N 56 2QR C05 H051 SING N N 57 2QR C06 H061 SING N N 58 2QR C06 H062 SING N N 59 2QR O09 H1 SING N N 60 2QR C14 H141 SING N N 61 2QR C15 H151 SING N N 62 2QR O16 H161 SING N N 63 2QR C18 H182 SING N N 64 2QR C18 H181 SING N N 65 2QR C19 H191 SING N N 66 2QR C20 H201 SING N N 67 2QR O21 H211 SING N N 68 2QR N22 H2 SING N N 69 2QR C23 H231 SING N N 70 2QR C23 H4 SING N N 71 2QR O26 H261 SING N N 72 2QR C28 H282 SING N N 73 2QR C28 H281 SING N N 74 2QR C28 H283 SING N N 75 2QR C30 H301 SING N N 76 2QR C32 H322 SING N N 77 2QR C32 H321 SING N N 78 2QR O35 H5 SING N N 79 2QR O36 H6 SING N N 80 2QR O38 H7 SING N N 81 2QR C41 H411 SING N N 82 2QR C43 H431 SING N N 83 2QR C44 H441 SING N N 84 2QR N46 H461 SING N N 85 # # 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 2QR SMILES ACDLabs 12.01 "O=C1C=CN(C(=O)N1)C2OC(C(O)C2O)COP(=O)(OP(=O)(OC4OCC(NCc3c(cnc(c3O)C)COP(=O)(O)O)C(O)C4O)O)O" 2QR InChI InChI 1.03 "InChI=1S/C22H33N4O20P3/c1-9-15(28)11(10(4-23-9)6-42-47(34,35)36)5-24-12-7-41-21(19(32)16(12)29)45-49(39,40)46-48(37,38)43-8-13-17(30)18(31)20(44-13)26-3-2-14(27)25-22(26)33/h2-4,12-13,16-21,24,28-32H,5-8H2,1H3,(H,37,38)(H,39,40)(H,25,27,33)(H2,34,35,36)/t12-,13+,16-,17+,18+,19+,20+,21+/m0/s1" 2QR InChIKey InChI 1.03 SNDXWZNPMTZYQI-LLAQWDROSA-N 2QR SMILES_CANONICAL CACTVS 3.385 "Cc1ncc(CO[P](O)(O)=O)c(CN[C@H]2CO[C@H](O[P](O)(=O)O[P](O)(=O)OC[C@H]3O[C@H]([C@H](O)[C@@H]3O)N4C=CC(=O)NC4=O)[C@H](O)[C@H]2O)c1O" 2QR SMILES CACTVS 3.385 "Cc1ncc(CO[P](O)(O)=O)c(CN[CH]2CO[CH](O[P](O)(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O)[CH]3O)N4C=CC(=O)NC4=O)[CH](O)[CH]2O)c1O" 2QR SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "Cc1c(c(c(cn1)COP(=O)(O)O)CN[C@H]2CO[C@@H]([C@@H]([C@H]2O)O)OP(=O)(O)OP(=O)(O)OC[C@@H]3[C@H]([C@H]([C@@H](O3)N4C=CC(=O)NC4=O)O)O)O" 2QR SMILES "OpenEye OEToolkits" 1.7.6 "Cc1c(c(c(cn1)COP(=O)(O)O)CNC2COC(C(C2O)O)OP(=O)(O)OP(=O)(O)OCC3C(C(C(O3)N4C=CC(=O)NC4=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 2QR "SYSTEMATIC NAME" ACDLabs 12.01 "(2R,3R,4S,5S)-3,4-dihydroxy-5-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)amino]tetrahydro-2H-pyran-2-yl [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate (non-preferred name)" 2QR "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "[[(2R,3S,4R,5R)-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2R,3R,4S,5S)-5-[[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylamino]-3,4-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 2QR "Create component" 2014-01-09 RCSB 2QR "Initial release" 2014-03-12 RCSB 2QR "Modify synonyms" 2020-06-05 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id 2QR _pdbx_chem_comp_synonyms.name PLP-UDP-Ara4N _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##