data_V2P # _chem_comp.id V2P _chem_comp.name "(2~{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-2-carboxylic acid" _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 V2P _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 6XHD _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 V2P C C1 C 0 1 N N N 39.040 2.009 12.205 5.404 2.173 0.424 C V2P 1 V2P N N1 N 0 1 N N N 36.704 1.998 11.351 3.711 0.502 -0.122 N V2P 2 V2P O O1 O 0 1 N N N 39.414 2.482 11.100 4.499 2.778 0.948 O V2P 3 V2P C2 C2 C 0 1 Y N N 38.689 2.247 17.308 -6.589 0.266 1.010 C2 V2P 4 V2P C4 C3 C 0 1 Y N N 37.369 4.212 17.472 -4.406 0.450 0.315 C4 V2P 5 V2P C5 C4 C 0 1 Y N N 36.662 3.716 18.503 -4.677 1.743 -0.161 C5 V2P 6 V2P C6 C5 C 0 1 Y N N 36.941 2.511 18.948 -5.979 2.249 -0.003 C6 V2P 7 V2P C8 C6 C 0 1 Y N N 35.901 5.663 18.081 -2.591 1.326 -0.581 C8 V2P 8 V2P N9 N2 N 0 1 Y N N 36.890 5.418 17.220 -3.083 0.214 0.036 N9 V2P 9 V2P CA C7 C 0 1 N N S 37.658 1.309 12.245 5.139 0.849 -0.244 CA V2P 10 V2P CB C8 C 0 1 N N N 37.726 -0.145 11.679 5.458 0.947 -1.751 CB V2P 11 V2P CG C9 C 0 1 N N N 36.385 -0.333 10.941 4.068 1.210 -2.386 CG V2P 12 V2P OXT O2 O 0 1 N N N 39.653 2.132 13.297 6.646 2.684 0.433 OXT V2P 13 V2P CD C10 C 0 1 N N N 36.084 1.060 10.389 3.144 0.359 -1.479 CD V2P 14 V2P PA P1 P 0 1 N N N 36.098 3.441 11.609 3.508 -0.912 0.769 PA V2P 15 V2P O1A O3 O 0 1 N N N 36.688 4.239 10.507 4.211 -2.026 0.093 O1A V2P 16 V2P O2A O4 O 0 1 N N N 34.649 3.224 11.729 4.119 -0.709 2.245 O2A V2P 17 V2P "O5'" O5 O 0 1 N N N 36.609 4.188 12.900 1.939 -1.255 0.879 "O5'" V2P 18 V2P "C5'" C11 C 0 1 N N N 36.182 5.568 12.860 1.181 -1.791 -0.207 "C5'" V2P 19 V2P "C4'" C12 C 0 1 N N R 37.002 6.525 13.745 -0.268 -1.999 0.236 "C4'" V2P 20 V2P "O4'" O6 O 0 1 N N N 36.450 6.646 15.111 -0.922 -0.725 0.428 "O4'" V2P 21 V2P "C3'" C13 C 0 1 N N S 38.444 6.051 13.853 -1.078 -2.693 -0.882 "C3'" V2P 22 V2P "O3'" O7 O 0 1 N N N 39.340 7.192 13.860 -1.180 -4.096 -0.628 "O3'" V2P 23 V2P "C2'" C14 C 0 1 N N R 38.451 5.371 15.202 -2.469 -2.026 -0.807 "C2'" V2P 24 V2P "O2'" O8 O 0 1 N N N 39.791 5.357 15.736 -3.474 -2.997 -0.505 "O2'" V2P 25 V2P "C1'" C15 C 0 1 N N R 37.474 6.235 16.067 -2.336 -1.008 0.346 "C1'" V2P 26 V2P N7 N3 N 0 1 Y N N 35.770 4.605 18.891 -3.528 2.221 -0.696 N7 V2P 27 V2P N3 N4 N 0 1 Y N N 38.365 3.524 16.862 -5.383 -0.246 0.888 N3 V2P 28 V2P N1 N5 N 0 1 Y N N 37.919 1.769 18.374 -6.891 1.477 0.578 N1 V2P 29 V2P N6 N6 N 0 1 N N N 36.189 2.095 19.963 -6.306 3.516 -0.452 N6 V2P 30 V2P H1 H1 H 0 1 N N N 39.481 1.664 16.862 -7.361 -0.327 1.476 H1 V2P 31 V2P H2 H2 H 0 1 N N N 35.306 6.563 18.118 -1.574 1.445 -0.924 H2 V2P 32 V2P H3 H3 H 0 1 N N N 37.280 1.287 13.278 5.750 0.072 0.217 H3 V2P 33 V2P H4 H4 H 0 1 N N N 37.827 -0.876 12.495 6.135 1.779 -1.948 H4 V2P 34 V2P H5 H5 H 0 1 N N N 38.571 -0.253 10.984 5.882 0.012 -2.117 H5 V2P 35 V2P H6 H6 H 0 1 N N N 35.597 -0.660 11.635 3.805 2.267 -2.329 H6 V2P 36 V2P H7 H7 H 0 1 N N N 36.484 -1.066 10.127 4.036 0.858 -3.417 H7 V2P 37 V2P H8 H8 H 0 1 N N N 40.445 2.639 13.161 6.766 3.537 0.873 H8 V2P 38 V2P H9 H9 H 0 1 N N N 36.527 1.183 9.390 3.163 -0.685 -1.791 H9 V2P 39 V2P H10 H10 H 0 1 N N N 34.998 1.227 10.332 2.125 0.745 -1.507 H10 V2P 40 V2P H11 H11 H 0 1 N N N 34.202 3.663 11.015 3.705 0.007 2.747 H11 V2P 41 V2P H12 H12 H 0 1 N N N 36.254 5.918 11.820 1.209 -1.097 -1.047 H12 V2P 42 V2P H13 H13 H 0 1 N N N 35.133 5.611 13.190 1.609 -2.747 -0.511 H13 V2P 43 V2P H14 H14 H 0 1 N N N 36.999 7.517 13.270 -0.304 -2.588 1.152 H14 V2P 44 V2P H15 H15 H 0 1 N N N 38.686 5.340 13.049 -0.618 -2.515 -1.854 H15 V2P 45 V2P H16 H16 H 0 1 N N N 40.238 6.890 13.928 -1.679 -4.582 -1.299 H16 V2P 46 V2P H17 H17 H 0 1 N N N 38.051 4.350 15.112 -2.700 -1.518 -1.744 H17 V2P 47 V2P H18 H18 H 0 1 N N N 39.790 4.929 16.584 -3.559 -3.695 -1.168 H18 V2P 48 V2P H19 H19 H 0 1 N N N 38.013 7.108 16.463 -2.691 -1.443 1.280 H19 V2P 49 V2P H20 H20 H 0 1 N N N 36.461 1.168 20.222 -5.633 4.067 -0.882 H20 V2P 50 V2P H21 H21 H 0 1 N N N 36.312 2.709 20.743 -7.208 3.854 -0.338 H21 V2P 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 V2P CD CG SING N N 1 V2P CD N SING N N 2 V2P O1A PA DOUB N N 3 V2P CG CB SING N N 4 V2P O C DOUB N N 5 V2P N PA SING N N 6 V2P N CA SING N N 7 V2P PA O2A SING N N 8 V2P PA "O5'" SING N N 9 V2P CB CA SING N N 10 V2P C CA SING N N 11 V2P C OXT SING N N 12 V2P "C5'" "O5'" SING N N 13 V2P "C5'" "C4'" SING N N 14 V2P "C4'" "C3'" SING N N 15 V2P "C4'" "O4'" SING N N 16 V2P "C3'" "O3'" SING N N 17 V2P "C3'" "C2'" SING N N 18 V2P "O4'" "C1'" SING N N 19 V2P "C2'" "O2'" SING N N 20 V2P "C2'" "C1'" SING N N 21 V2P "C1'" N9 SING N N 22 V2P N3 C2 DOUB Y N 23 V2P N3 C4 SING Y N 24 V2P N9 C4 SING Y N 25 V2P N9 C8 SING Y N 26 V2P C2 N1 SING Y N 27 V2P C4 C5 DOUB Y N 28 V2P C8 N7 DOUB Y N 29 V2P N1 C6 DOUB Y N 30 V2P C5 N7 SING Y N 31 V2P C5 C6 SING Y N 32 V2P C6 N6 SING N N 33 V2P C2 H1 SING N N 34 V2P C8 H2 SING N N 35 V2P CA H3 SING N N 36 V2P CB H4 SING N N 37 V2P CB H5 SING N N 38 V2P CG H6 SING N N 39 V2P CG H7 SING N N 40 V2P OXT H8 SING N N 41 V2P CD H9 SING N N 42 V2P CD H10 SING N N 43 V2P O2A H11 SING N N 44 V2P "C5'" H12 SING N N 45 V2P "C5'" H13 SING N N 46 V2P "C4'" H14 SING N N 47 V2P "C3'" H15 SING N N 48 V2P "O3'" H16 SING N N 49 V2P "C2'" H17 SING N N 50 V2P "O2'" H18 SING N N 51 V2P "C1'" H19 SING N N 52 V2P N6 H20 SING N N 53 V2P 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 V2P SMILES ACDLabs 12.01 "C(C4N(P(O)(OCC3C(O)C(O)C(n1c2c(nc1)c(N)ncn2)O3)=O)CCC4)(O)=O" V2P InChI InChI 1.03 "InChI=1S/C15H21N6O8P/c16-12-9-13(18-5-17-12)20(6-19-9)14-11(23)10(22)8(29-14)4-28-30(26,27)21-3-1-2-7(21)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" V2P InChIKey InChI 1.03 YHPWCYBNNLQQNG-TWBCTODHSA-N V2P SMILES_CANONICAL CACTVS 3.385 "Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)N4CCC[C@H]4C(O)=O)[C@@H](O)[C@H]3O" V2P SMILES CACTVS 3.385 "Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)N4CCC[CH]4C(O)=O)[CH](O)[CH]3O" V2P SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(N4CCC[C@H]4C(=O)O)O)O)O)N" V2P SMILES "OpenEye OEToolkits" 2.0.7 "c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(N4CCCC4C(=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 V2P "SYSTEMATIC NAME" ACDLabs 12.01 "(2S)-1-[(R)-{[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]pyrrolidine-2-carboxylic acid (non-preferred name)" V2P "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "(2~{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-2-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 V2P "Create component" 2020-06-19 RCSB V2P "Initial release" 2021-03-17 RCSB ##