data_V2J # _chem_comp.id V2J _chem_comp.name "5'-O-[(S)-[(3S)-3-carboxypyrrolidin-1-yl](hydroxy)phosphoryl]adenosine" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C15 H21 N6 O8 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2020-06-19 _chem_comp.pdbx_modified_date 2021-03-12 _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 444.336 _chem_comp.one_letter_code ? _chem_comp.three_letter_code V2J _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 6XHE _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 V2J C4 C1 C 0 1 Y N N 37.543 -20.450 -21.326 5.018 -0.089 0.425 C4 V2J 1 V2J C5 C2 C 0 1 Y N N 36.813 -20.001 -22.526 5.699 -1.212 -0.074 C5 V2J 2 V2J C6 C3 C 0 1 Y N N 37.002 -18.635 -23.004 7.070 -1.336 0.206 C6 V2J 3 V2J C8 C4 C 0 1 Y N N 36.292 -22.044 -22.134 3.630 -1.378 -0.703 C8 V2J 4 V2J N1 N1 N 0 1 Y N N 37.831 -17.796 -22.335 7.657 -0.387 0.929 N1 V2J 5 V2J C2 C5 C 0 1 Y N N 38.611 -18.191 -21.141 6.975 0.651 1.377 C2 V2J 6 V2J O2A O1 O 0 1 N N N 38.064 -19.297 -15.378 -2.780 -1.715 -1.546 O2A V2J 7 V2J PA P1 P 0 1 N N N 39.202 -20.277 -15.566 -2.937 -1.030 -0.243 PA V2J 8 V2J O1A O2 O 0 1 N N N 39.599 -21.116 -14.356 -3.294 -2.113 0.893 O1A V2J 9 V2J N N2 N 0 1 N N N 40.587 -19.503 -15.991 -4.178 0.101 -0.350 N V2J 10 V2J CA C6 C 0 1 N N N 41.624 -20.358 -16.636 -5.465 -0.553 -0.703 CA V2J 11 V2J CD C7 C 0 1 N N N 40.437 -18.292 -16.839 -4.439 0.732 0.969 CD V2J 12 V2J CG C8 C 0 1 N N N 41.656 -18.215 -17.754 -5.873 1.293 0.856 CG V2J 13 V2J CB C9 C 0 1 N N S 42.098 -19.662 -17.911 -6.548 0.447 -0.244 CB V2J 14 V2J C C10 C 0 1 N N N 41.431 -20.315 -19.086 -7.737 -0.289 0.317 C V2J 15 V2J OX O3 O 0 1 N N N 41.898 -21.375 -19.575 -7.759 -1.497 0.307 OX V2J 16 V2J O O4 O 0 1 N N N 40.391 -19.778 -19.505 -8.771 0.396 0.829 O V2J 17 V2J "O5'" O5 O 0 1 N N N 38.640 -21.271 -16.727 -1.562 -0.284 0.140 "O5'" V2J 18 V2J "C5'" C11 C 0 1 N N N 38.631 -22.700 -16.636 -0.869 0.581 -0.762 "C5'" V2J 19 V2J "C4'" C12 C 0 1 N N R 38.218 -23.330 -17.975 0.392 1.120 -0.084 "C4'" V2J 20 V2J "C3'" C13 C 0 1 N N S 39.409 -23.650 -18.895 1.113 2.125 -1.009 "C3'" V2J 21 V2J "O3'" O6 O 0 1 N N N 39.599 -25.067 -19.002 0.779 3.467 -0.647 "O3'" V2J 22 V2J "C2'" C14 C 0 1 N N R 39.078 -23.000 -20.237 2.614 1.853 -0.763 "C2'" V2J 23 V2J "O2'" O7 O 0 1 N N N 39.394 -23.777 -21.408 3.256 3.017 -0.241 "O2'" V2J 24 V2J "C1'" C15 C 0 1 N N R 37.565 -22.732 -20.119 2.622 0.715 0.282 "C1'" V2J 25 V2J "O4'" O8 O 0 1 N N N 37.336 -22.462 -18.723 1.346 0.055 0.123 "O4'" V2J 26 V2J N9 N3 N 0 1 Y N N 37.139 -21.712 -21.147 3.717 -0.219 0.009 N9 V2J 27 V2J N3 N4 N 0 1 Y N N 38.372 -19.583 -20.679 5.690 0.811 1.135 N3 V2J 28 V2J N6 N5 N 0 1 N N N 36.320 -18.263 -24.113 7.793 -2.420 -0.259 N6 V2J 29 V2J N7 N6 N 0 1 Y N N 36.066 -21.026 -22.976 4.795 -1.956 -0.756 N7 V2J 30 V2J H1 H1 H 0 1 N N N 35.843 -23.021 -22.238 2.729 -1.757 -1.163 H1 V2J 31 V2J H2 H2 H 0 1 N N N 39.298 -17.522 -20.645 7.490 1.399 1.961 H2 V2J 32 V2J H3 H3 H 0 1 N N N 39.045 -20.891 -13.618 -3.411 -1.734 1.775 H3 V2J 33 V2J H4 H4 H 0 1 N N N 41.194 -21.339 -16.886 -5.527 -0.713 -1.779 H4 V2J 34 V2J H5 H5 H 0 1 N N N 42.473 -20.494 -15.950 -5.569 -1.499 -0.172 H5 V2J 35 V2J H6 H6 H 0 1 N N N 40.386 -17.394 -16.205 -4.383 -0.012 1.764 H6 V2J 36 V2J H7 H7 H 0 1 N N N 39.520 -18.367 -17.442 -3.727 1.537 1.153 H7 V2J 37 V2J H8 H8 H 0 1 N N N 42.452 -17.612 -17.293 -6.401 1.174 1.802 H8 V2J 38 V2J H9 H9 H 0 1 N N N 41.385 -17.782 -18.728 -5.847 2.343 0.566 H9 V2J 39 V2J H10 H10 H 0 1 N N N 43.193 -19.724 -17.998 -6.853 1.083 -1.076 H10 V2J 40 V2J H11 H11 H 0 1 N N N 40.037 -20.290 -20.222 -9.511 -0.120 1.177 H11 V2J 41 V2J H12 H12 H 0 1 N N N 37.917 -23.007 -15.858 -0.590 0.025 -1.657 H12 V2J 42 V2J H13 H13 H 0 1 N N N 39.639 -23.051 -16.368 -1.517 1.413 -1.038 H13 V2J 43 V2J H14 H14 H 0 1 N N N 37.695 -24.273 -17.758 0.139 1.592 0.866 H14 V2J 44 V2J H15 H15 H 0 1 N N N 40.312 -23.176 -18.483 0.856 1.937 -2.051 H15 V2J 45 V2J H16 H16 H 0 1 N N N 39.802 -25.425 -18.146 1.204 4.140 -1.196 H16 V2J 46 V2J H17 H17 H 0 1 N N N 39.595 -22.031 -20.289 3.098 1.529 -1.684 H17 V2J 47 V2J H18 H18 H 0 1 N N N 40.332 -23.923 -21.448 3.280 3.763 -0.855 H18 V2J 48 V2J H19 H19 H 0 1 N N N 37.056 -23.675 -20.369 2.713 1.124 1.288 H19 V2J 49 V2J H20 H20 H 0 1 N N N 36.531 -17.310 -24.331 7.354 -3.106 -0.785 H20 V2J 50 V2J H21 H21 H 0 1 N N N 36.586 -18.847 -24.880 8.739 -2.494 -0.058 H21 V2J 51 # # 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 V2J N6 C6 SING N N 1 V2J C6 C5 DOUB Y N 2 V2J C6 N1 SING Y N 3 V2J N7 C5 SING Y N 4 V2J N7 C8 DOUB Y N 5 V2J C5 C4 SING Y N 6 V2J N1 C2 DOUB Y N 7 V2J C8 N9 SING Y N 8 V2J "O2'" "C2'" SING N N 9 V2J C4 N9 SING Y N 10 V2J C4 N3 DOUB Y N 11 V2J N9 "C1'" SING N N 12 V2J C2 N3 SING Y N 13 V2J "C2'" "C1'" SING N N 14 V2J "C2'" "C3'" SING N N 15 V2J "C1'" "O4'" SING N N 16 V2J OX C DOUB N N 17 V2J O C SING N N 18 V2J C CB SING N N 19 V2J "O3'" "C3'" SING N N 20 V2J "C3'" "C4'" SING N N 21 V2J "O4'" "C4'" SING N N 22 V2J "C4'" "C5'" SING N N 23 V2J CB CG SING N N 24 V2J CB CA SING N N 25 V2J CG CD SING N N 26 V2J CD N SING N N 27 V2J "O5'" "C5'" SING N N 28 V2J "O5'" PA SING N N 29 V2J CA N SING N N 30 V2J N PA SING N N 31 V2J PA O2A DOUB N N 32 V2J PA O1A SING N N 33 V2J C8 H1 SING N N 34 V2J C2 H2 SING N N 35 V2J O1A H3 SING N N 36 V2J CA H4 SING N N 37 V2J CA H5 SING N N 38 V2J CD H6 SING N N 39 V2J CD H7 SING N N 40 V2J CG H8 SING N N 41 V2J CG H9 SING N N 42 V2J CB H10 SING N N 43 V2J O H11 SING N N 44 V2J "C5'" H12 SING N N 45 V2J "C5'" H13 SING N N 46 V2J "C4'" H14 SING N N 47 V2J "C3'" H15 SING N N 48 V2J "O3'" H16 SING N N 49 V2J "C2'" H17 SING N N 50 V2J "O2'" H18 SING N N 51 V2J "C1'" H19 SING N N 52 V2J N6 H20 SING N N 53 V2J N6 H21 SING N N 54 # # 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 V2J SMILES ACDLabs 12.01 "c21n(cnc1c(ncn2)N)C4C(C(C(COP(=O)(O)N3CC(CC3)C(=O)O)O4)O)O" V2J InChI InChI 1.03 "InChI=1S/C15H21N6O8P/c16-12-9-13(18-5-17-12)21(6-19-9)14-11(23)10(22)8(29-14)4-28-30(26,27)20-2-1-7(3-20)15(24)25/h5-8,10-11,14,22-23H,1-4H2,(H,24,25)(H,26,27)(H2,16,17,18)/t7-,8+,10+,11+,14+/m0/s1" V2J InChIKey InChI 1.03 XUGWBNVYRBVAFE-TWBCTODHSA-N V2J SMILES_CANONICAL CACTVS 3.385 "Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)N4CC[C@@H](C4)C(O)=O)[C@@H](O)[C@H]3O" V2J SMILES CACTVS 3.385 "Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)N4CC[CH](C4)C(O)=O)[CH](O)[CH]3O" V2J SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(N4CC[C@@H](C4)C(=O)O)O)O)O)N" V2J SMILES "OpenEye OEToolkits" 2.0.7 "c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(N4CCC(C4)C(=O)O)O)O)O)N" # # 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 V2J "SYSTEMATIC NAME" ACDLabs 12.01 "5'-O-[(S)-[(3S)-3-carboxypyrrolidin-1-yl](hydroxy)phosphoryl]adenosine" V2J "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "(3~{S})-1-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]pyrrolidine-3-carboxylic acid" # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site V2J "Create component" 2020-06-19 RCSB V2J "Initial release" 2021-03-17 RCSB ##