data_V2V # _chem_comp.id V2V _chem_comp.name CDP-ribitol _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C14 H25 N3 O15 P2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "[(2R,3S,4R,5R)-5-(4-amino-2-oxopyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3S,4S)-2,3,4,5-tetrahydroxypentyl dihydrogen diphosphate" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2020-06-19 _chem_comp.pdbx_modified_date 2021-04-16 _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 537.307 _chem_comp.one_letter_code ? _chem_comp.three_letter_code V2V _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 6XHQ _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 V2V C01 C1 C 0 1 N N N -26.254 12.515 20.833 -6.781 3.461 -0.049 C01 V2V 1 V2V C02 C2 C 0 1 N N N -25.617 11.477 19.980 -6.167 2.631 0.826 C02 V2V 2 V2V C04 C3 C 0 1 N N N -27.701 11.488 18.516 -5.698 1.146 -0.933 C04 V2V 3 V2V C07 C4 C 0 1 N N N -27.606 13.037 20.488 -6.842 3.096 -1.410 C07 V2V 4 V2V C09 C5 C 0 1 N N R -25.783 9.955 17.946 -4.955 0.560 1.308 C09 V2V 5 V2V C10 C6 C 0 1 N N R -24.558 10.620 17.210 -5.726 -0.781 1.413 C10 V2V 6 V2V C11 C7 C 0 1 N N S -23.697 9.361 16.814 -4.615 -1.758 1.870 C11 V2V 7 V2V C12 C8 C 0 1 N N R -24.060 8.412 17.618 -3.305 -1.057 1.464 C12 V2V 8 V2V C14 C9 C 0 1 N N N -22.954 8.042 18.540 -2.508 -1.952 0.512 C14 V2V 9 V2V C24 C10 C 0 1 N N N -22.328 5.498 21.675 5.116 -0.387 -0.578 C24 V2V 10 V2V C25 C11 C 0 1 N N R -21.985 4.009 22.069 5.737 0.737 0.255 C25 V2V 11 V2V C26 C12 C 0 1 N N S -22.420 3.031 20.997 7.248 0.772 0.017 C26 V2V 12 V2V C27 C13 C 0 1 N N S -22.000 1.583 21.318 7.869 1.895 0.850 C27 V2V 13 V2V C28 C14 C 0 1 N N N -22.910 0.988 22.373 9.380 1.931 0.613 C28 V2V 14 V2V N03 N1 N 0 1 N N N -26.356 10.976 18.844 -5.624 1.467 0.371 N03 V2V 15 V2V N06 N2 N 0 1 N N N -28.310 12.525 19.362 -6.299 1.953 -1.806 N06 V2V 16 V2V N08 N3 N 0 1 N N N -28.251 14.065 21.288 -7.461 3.921 -2.320 N08 V2V 17 V2V O05 O1 O 0 1 N N N -28.279 11.065 17.544 -5.206 0.100 -1.323 O05 V2V 18 V2V O13 O2 O 0 1 N N N -25.261 8.995 18.637 -3.662 0.167 0.799 O13 V2V 19 V2V O15 O3 O 0 1 N N N -22.716 9.159 19.408 -1.245 -1.346 0.234 O15 V2V 20 V2V O17 O4 O 0 1 N N N -20.163 9.155 18.830 0.159 -3.385 -0.263 O17 V2V 21 V2V O18 O5 O 0 1 N N N -21.046 10.817 20.427 -0.723 -2.081 -2.237 O18 V2V 22 V2V O19 O6 O 0 1 N N N -20.821 8.369 21.161 1.198 -1.129 -0.715 O19 V2V 23 V2V O21 O7 O 0 1 N N N -21.102 8.624 23.709 3.111 -2.770 -0.846 O21 V2V 24 V2V O22 O8 O 0 1 N N N -23.146 8.626 22.312 2.820 -1.178 -2.783 O22 V2V 25 V2V O23 O9 O 0 1 N N N -21.745 6.373 22.667 3.693 -0.346 -0.447 O23 V2V 26 V2V O29 O10 O 0 1 N N N -23.327 -0.326 22.045 9.944 3.050 1.298 O29 V2V 27 V2V O30 O11 O 0 1 N N N -20.644 1.538 21.760 7.610 1.659 2.236 O30 V2V 28 V2V O31 O12 O 0 1 N N N -21.831 3.398 19.763 7.506 1.008 -1.368 O31 V2V 29 V2V O32 O13 O 0 1 N N N -22.527 3.710 23.340 5.478 0.501 1.640 O32 V2V 30 V2V O33 O14 O 0 1 N N N -23.989 9.027 15.392 -4.665 -1.945 3.286 O33 V2V 31 V2V O34 O15 O 0 1 N N N -24.886 11.361 16.160 -6.765 -0.697 2.390 O34 V2V 32 V2V P16 P1 P 0 1 N N N -21.142 9.407 19.947 -0.146 -2.015 -0.735 P16 V2V 33 V2V P20 P2 P 0 1 N N N -21.746 8.027 22.474 2.714 -1.386 -1.190 P20 V2V 34 V2V H1 H1 H 0 1 N N N -25.736 12.891 21.703 -7.222 4.387 0.290 H1 V2V 35 V2V H2 H2 H 0 1 N N N -24.627 11.107 20.204 -6.107 2.889 1.873 H2 V2V 36 V2V H3 H3 H 0 1 N N N -26.524 9.623 17.203 -4.859 1.025 2.289 H3 V2V 37 V2V H4 H4 H 0 1 N N N -23.990 11.200 17.952 -6.128 -1.075 0.444 H4 V2V 38 V2V H5 H5 H 0 1 N N N -22.633 9.620 16.920 -4.712 -2.714 1.354 H5 V2V 39 V2V H6 H6 H 0 1 N N N -24.450 7.521 17.105 -2.711 -0.839 2.351 H6 V2V 40 V2V H8 H8 H 0 1 N N N -23.240 7.161 19.133 -2.350 -2.926 0.976 H8 V2V 41 V2V H9 H9 H 0 1 N N N -22.045 7.816 17.963 -3.063 -2.079 -0.417 H9 V2V 42 V2V H10 H10 H 0 1 N N N -21.909 5.727 20.684 5.388 -0.255 -1.625 H10 V2V 43 V2V H11 H11 H 0 1 N N N -23.419 5.635 21.652 5.486 -1.349 -0.225 H11 V2V 44 V2V H12 H12 H 0 1 N N N -20.889 3.950 22.136 5.300 1.691 -0.039 H12 V2V 45 V2V H13 H13 H 0 1 N N N -23.516 3.063 20.915 7.685 -0.182 0.311 H13 V2V 46 V2V H14 H14 H 0 1 N N N -22.105 0.989 20.398 7.432 2.850 0.557 H14 V2V 47 V2V H15 H15 H 0 1 N N N -22.370 0.959 23.331 9.828 1.011 0.988 H15 V2V 48 V2V H16 H16 H 0 1 N N N -23.800 1.627 22.474 9.578 2.022 -0.456 H16 V2V 49 V2V H17 H17 H 0 1 N N N -29.163 14.392 21.041 -7.857 4.756 -2.027 H17 V2V 50 V2V H18 H18 H 0 1 N N N -27.783 14.445 22.086 -7.501 3.667 -3.256 H18 V2V 51 V2V H20 H20 H 0 1 N N N -20.381 11.277 19.928 -0.946 -1.217 -2.611 H20 V2V 52 V2V H21 H21 H 0 1 N N N -23.311 9.241 23.017 2.574 -0.292 -3.081 H21 V2V 53 V2V H22 H22 H 0 1 N N N -23.894 -0.659 22.731 10.901 3.136 1.192 H22 V2V 54 V2V H23 H23 H 0 1 N N N -20.403 0.640 21.953 7.971 0.825 2.567 H23 V2V 55 V2V H24 H24 H 0 1 N N N -22.102 2.787 19.088 7.146 1.842 -1.699 H24 V2V 56 V2V H25 H25 H 0 1 N N N -22.317 2.813 23.571 5.839 -0.333 1.972 H25 V2V 57 V2V H26 H26 H 0 1 N N N -23.479 8.269 15.133 -5.493 -2.330 3.603 H26 V2V 58 V2V H27 H27 H 0 1 N N N -24.100 11.726 15.771 -7.275 -1.511 2.493 H27 V2V 59 # # 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 V2V C01 C02 DOUB N N 1 V2V C01 C07 SING N N 2 V2V C02 N03 SING N N 3 V2V C04 N03 SING N N 4 V2V C04 N06 SING N N 5 V2V C04 O05 DOUB N N 6 V2V C07 N06 DOUB N N 7 V2V C07 N08 SING N N 8 V2V C09 C10 SING N N 9 V2V C09 N03 SING N N 10 V2V C09 O13 SING N N 11 V2V C10 C11 SING N N 12 V2V C10 O34 SING N N 13 V2V C11 C12 SING N N 14 V2V C11 O33 SING N N 15 V2V C12 C14 SING N N 16 V2V C14 O15 SING N N 17 V2V C24 C25 SING N N 18 V2V C24 O23 SING N N 19 V2V C25 C26 SING N N 20 V2V C25 O32 SING N N 21 V2V C26 C27 SING N N 22 V2V C26 O31 SING N N 23 V2V C27 C28 SING N N 24 V2V C27 O30 SING N N 25 V2V C28 O29 SING N N 26 V2V O15 P16 SING N N 27 V2V O17 P16 DOUB N N 28 V2V O18 P16 SING N N 29 V2V O19 P16 SING N N 30 V2V O19 P20 SING N N 31 V2V O21 P20 DOUB N N 32 V2V O22 P20 SING N N 33 V2V O23 P20 SING N N 34 V2V C01 H1 SING N N 35 V2V C02 H2 SING N N 36 V2V C09 H3 SING N N 37 V2V C10 H4 SING N N 38 V2V C11 H5 SING N N 39 V2V C12 H6 SING N N 40 V2V C14 H8 SING N N 41 V2V C14 H9 SING N N 42 V2V C24 H10 SING N N 43 V2V C24 H11 SING N N 44 V2V C25 H12 SING N N 45 V2V C26 H13 SING N N 46 V2V C27 H14 SING N N 47 V2V C28 H15 SING N N 48 V2V C28 H16 SING N N 49 V2V N08 H17 SING N N 50 V2V N08 H18 SING N N 51 V2V O18 H20 SING N N 52 V2V O22 H21 SING N N 53 V2V O29 H22 SING N N 54 V2V O30 H23 SING N N 55 V2V O31 H24 SING N N 56 V2V O32 H25 SING N N 57 V2V O33 H26 SING N N 58 V2V O34 H27 SING N N 59 V2V C12 O13 SING N N 60 # # 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 V2V SMILES ACDLabs 12.01 "C1=CN(C(N=C1N)=O)C2C(C(C(COP(=O)(O)OP(=O)(O)OCC(C(C(CO)O)O)O)O2)O)O" V2V InChI InChI 1.03 "InChI=1S/C14H25N3O15P2/c15-9-1-2-17(14(24)16-9)13-12(23)11(22)8(31-13)5-30-34(27,28)32-33(25,26)29-4-7(20)10(21)6(19)3-18/h1-2,6-8,10-13,18-23H,3-5H2,(H,25,26)(H,27,28)(H2,15,16,24)/t6-,7+,8+,10-,11+,12+,13+/m0/s1" V2V InChIKey InChI 1.03 DPJKHFICSGCNIR-HRENORGGSA-N V2V SMILES_CANONICAL CACTVS 3.385 "NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO[P](O)(=O)O[P](O)(=O)OC[C@@H](O)[C@@H](O)[C@@H](O)CO)[C@@H](O)[C@H]2O" V2V SMILES CACTVS 3.385 "NC1=NC(=O)N(C=C1)[CH]2O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH](O)[CH](O)[CH](O)CO)[CH](O)[CH]2O" V2V SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H](C(O2)COP(=O)(O)OP(=O)(O)OC[C@H]([C@H]([C@H](CO)O)O)O)O)O" V2V SMILES "OpenEye OEToolkits" 2.0.7 "C1=CN(C(=O)N=C1N)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)OCC(C(C(CO)O)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 V2V "SYSTEMATIC NAME" ACDLabs 12.01 "[(2R,3S,4R,5R)-5-(4-amino-2-oxopyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3S,4S)-2,3,4,5-tetrahydroxypentyl dihydrogen diphosphate (non-preferred name)" V2V "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "[[(3~{S},4~{R},5~{R})-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{S})-2,3,4,5-tetrakis(oxidanyl)pentyl] hydrogen phosphate" # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id V2V _pdbx_chem_comp_synonyms.name "[(2R,3S,4R,5R)-5-(4-amino-2-oxopyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3S,4S)-2,3,4,5-tetrahydroxypentyl dihydrogen diphosphate" _pdbx_chem_comp_synonyms.provenance PDB _pdbx_chem_comp_synonyms.type ? # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site V2V "Create component" 2020-06-19 RCSB V2V "Modify synonyms" 2021-03-13 RCSB V2V "Initial release" 2021-04-21 RCSB ##