data_UY4 # _chem_comp.id UY4 _chem_comp.name "(2S,3S)-2-{[(9-{(2R,3R,4S,5R)-3,4-dihydroxy-5-[(phosphonooxy)methyl]tetrahydrofuran-2-yl}-9H-purin-6-yl)carbamoyl]amino}-3-hydroxybutanoic acid" _chem_comp.type "RNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C15 H21 N6 O11 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2020-06-04 _chem_comp.pdbx_modified_date 2020-10-02 _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 492.335 _chem_comp.one_letter_code ? _chem_comp.three_letter_code UY4 _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 6XA1 _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 UY4 C4 C1 C 0 1 Y N N 250.387 294.231 206.137 0.036 -1.085 -0.581 C4 UY4 1 UY4 C6 C2 C 0 1 Y N N 251.964 295.597 204.754 2.346 -0.409 -0.455 C6 UY4 2 UY4 C2 C3 C 0 1 Y N N 252.380 293.316 205.303 1.704 -2.347 -1.530 C2 UY4 3 UY4 C02 C4 C 0 1 N N N 255.516 295.238 201.010 7.588 -0.128 0.739 C02 UY4 4 UY4 C04 C5 C 0 1 N N S 255.623 295.853 202.488 6.997 0.792 -0.298 C04 UY4 5 UY4 C05 C6 C 0 1 N N S 256.712 295.102 203.287 7.784 2.104 -0.324 C05 UY4 6 UY4 C07 C7 C 0 1 N N N 258.090 295.400 202.680 9.215 1.831 -0.793 C07 UY4 7 UY4 C09 C8 C 0 1 N N N 253.545 296.836 203.407 4.630 0.215 -0.357 C09 UY4 8 UY4 "C1'" C9 C 0 1 N N R 248.502 293.368 207.528 -2.482 -1.227 -0.362 "C1'" UY4 9 UY4 "C2'" C10 C 0 1 N N R 249.354 293.089 208.736 -2.793 -2.228 0.773 "C2'" UY4 10 UY4 "C3'" C11 C 0 1 N N S 248.989 294.228 209.656 -4.311 -2.063 1.013 "C3'" UY4 11 UY4 "C4'" C12 C 0 1 N N R 247.535 294.502 209.349 -4.737 -0.983 -0.006 "C4'" UY4 12 UY4 C5 C13 C 0 1 Y N N 250.711 295.515 205.517 1.000 -0.160 -0.145 C5 UY4 13 UY4 "C5'" C14 C 0 1 N N N 247.291 296.000 209.274 -5.804 -0.070 0.601 "C5'" UY4 14 UY4 C8 C15 C 0 1 Y N N 248.825 295.667 206.557 -0.935 0.562 0.518 C8 UY4 15 UY4 N08 N1 N 0 1 N N N 254.368 295.735 203.259 5.597 1.068 0.035 N08 UY4 16 UY4 N1 N2 N 0 1 Y N N 252.761 294.446 204.698 2.645 -1.504 -1.144 N1 UY4 17 UY4 N3 N3 N 0 1 Y N N 251.243 293.197 205.997 0.430 -2.156 -1.261 N3 UY4 18 UY4 N6 N4 N 0 1 N N N 252.326 296.749 204.164 3.343 0.470 -0.051 N6 UY4 19 UY4 N7 N5 N 0 1 Y N N 249.715 296.354 205.809 0.340 0.820 0.519 N7 UY4 20 UY4 N9 N6 N 0 1 Y N N 249.221 294.402 206.751 -1.174 -0.603 -0.148 N9 UY4 21 UY4 O01 O1 O 0 1 N N N 256.363 295.551 200.161 6.910 -0.513 1.662 O01 UY4 22 UY4 O03 O2 O 0 1 N N N 254.591 294.448 200.700 8.868 -0.519 0.638 O03 UY4 23 UY4 O06 O3 O 0 1 N N N 256.441 293.731 203.240 7.812 2.668 0.988 O06 UY4 24 UY4 "O2'" O4 O 0 1 N N N 248.921 291.862 209.320 -2.493 -3.562 0.360 "O2'" UY4 25 UY4 O29 O5 O 0 1 N N N 253.859 297.896 202.886 4.919 -0.783 -0.987 O29 UY4 26 UY4 "O3'" O6 O 0 1 N N N 249.180 293.865 211.019 -4.994 -3.292 0.756 "O3'" UY4 27 UY4 "O4'" O7 O 0 1 N N N 247.300 293.910 208.072 -3.531 -0.237 -0.280 "O4'" UY4 28 UY4 "O5'" O8 O 0 1 N N N 245.936 296.267 209.605 -6.268 0.847 -0.392 "O5'" UY4 29 UY4 OP1 O9 O 0 1 N N N 244.300 298.061 210.242 -7.763 2.721 -1.471 OP1 UY4 30 UY4 OP2 O10 O 0 1 N N N 246.248 298.566 208.579 -8.608 1.301 0.437 OP2 UY4 31 UY4 P P1 P 0 1 N N N 245.215 297.620 209.127 -7.396 1.958 -0.101 P UY4 32 UY4 OP3 O11 O 0 1 N Y N 244.297 297.027 207.975 -6.840 3.020 0.973 OP3 UY4 33 UY4 H1 H1 H 0 1 N N N 253.025 292.453 205.227 1.992 -3.228 -2.085 H1 UY4 34 UY4 H2 H2 H 0 1 N N N 255.910 296.911 202.401 7.051 0.316 -1.278 H2 UY4 35 UY4 H3 H3 H 0 1 N N N 256.698 295.465 204.325 7.304 2.802 -1.010 H3 UY4 36 UY4 H4 H4 H 0 1 N N N 258.865 294.865 203.249 9.193 1.400 -1.794 H4 UY4 37 UY4 H5 H5 H 0 1 N N N 258.109 295.066 201.632 9.775 2.766 -0.812 H5 UY4 38 UY4 H6 H6 H 0 1 N N N 258.284 296.482 202.724 9.695 1.133 -0.107 H6 UY4 39 UY4 H7 H7 H 0 1 N N N 248.329 292.457 206.937 -2.510 -1.730 -1.329 H7 UY4 40 UY4 H8 H8 H 0 1 N N N 250.426 293.093 208.489 -2.232 -1.972 1.672 H8 UY4 41 UY4 H9 H9 H 0 1 N N N 249.591 295.113 209.401 -4.502 -1.727 2.032 H9 UY4 42 UY4 H10 H10 H 0 1 N N N 246.894 294.054 210.123 -5.111 -1.448 -0.918 H10 UY4 43 UY4 H11 H11 H 0 1 N N N 247.953 296.517 209.985 -6.639 -0.674 0.957 H11 UY4 44 UY4 H12 H12 H 0 1 N N N 247.498 296.356 208.254 -5.376 0.485 1.436 H12 UY4 45 UY4 H13 H13 H 0 1 N N N 247.910 296.085 206.949 -1.693 1.179 0.977 H13 UY4 46 UY4 H14 H14 H 0 1 N N N 254.114 294.861 203.673 5.367 1.865 0.537 H14 UY4 47 UY4 H15 H15 H 0 1 N N N 251.741 297.555 204.253 3.112 1.267 0.452 H15 UY4 48 UY4 H16 H16 H 0 1 N N N 254.687 294.189 199.791 9.202 -1.109 1.328 H16 UY4 49 UY4 H17 H17 H 0 1 N N N 257.105 293.259 203.729 8.226 2.101 1.652 H17 UY4 50 UY4 H18 H18 H 0 1 N N N 249.450 291.671 210.086 -2.670 -4.232 1.035 H18 UY4 51 UY4 H19 H19 H 0 1 N N N 248.944 294.596 211.578 -4.720 -4.021 1.328 H19 UY4 52 UY4 H20 H20 H 0 1 N N N 244.503 298.957 210.483 -8.438 3.406 -1.371 H20 UY4 53 UY4 H21 H21 H 0 1 N N N 244.570 297.382 207.137 -6.044 3.489 0.686 H21 UY4 54 # # 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 UY4 O01 C02 DOUB N N 1 UY4 O03 C02 SING N N 2 UY4 C02 C04 SING N N 3 UY4 C04 N08 SING N N 4 UY4 C04 C05 SING N N 5 UY4 C07 C05 SING N N 6 UY4 O29 C09 DOUB N N 7 UY4 O06 C05 SING N N 8 UY4 N08 C09 SING N N 9 UY4 C09 N6 SING N N 10 UY4 N6 C6 SING N N 11 UY4 N1 C6 DOUB Y N 12 UY4 N1 C2 SING Y N 13 UY4 C6 C5 SING Y N 14 UY4 C2 N3 DOUB Y N 15 UY4 C5 N7 SING Y N 16 UY4 C5 C4 DOUB Y N 17 UY4 N7 C8 DOUB Y N 18 UY4 N3 C4 SING Y N 19 UY4 C4 N9 SING Y N 20 UY4 C8 N9 SING Y N 21 UY4 N9 "C1'" SING N N 22 UY4 "C1'" "O4'" SING N N 23 UY4 "C1'" "C2'" SING N N 24 UY4 "O4'" "C4'" SING N N 25 UY4 OP2 P DOUB N N 26 UY4 "C2'" "O2'" SING N N 27 UY4 "C2'" "C3'" SING N N 28 UY4 P "O5'" SING N N 29 UY4 P OP1 SING N N 30 UY4 "C5'" "C4'" SING N N 31 UY4 "C5'" "O5'" SING N N 32 UY4 "C4'" "C3'" SING N N 33 UY4 "C3'" "O3'" SING N N 34 UY4 P OP3 SING N N 35 UY4 C2 H1 SING N N 36 UY4 C04 H2 SING N N 37 UY4 C05 H3 SING N N 38 UY4 C07 H4 SING N N 39 UY4 C07 H5 SING N N 40 UY4 C07 H6 SING N N 41 UY4 "C1'" H7 SING N N 42 UY4 "C2'" H8 SING N N 43 UY4 "C3'" H9 SING N N 44 UY4 "C4'" H10 SING N N 45 UY4 "C5'" H11 SING N N 46 UY4 "C5'" H12 SING N N 47 UY4 C8 H13 SING N N 48 UY4 N08 H14 SING N N 49 UY4 N6 H15 SING N N 50 UY4 O03 H16 SING N N 51 UY4 O06 H17 SING N N 52 UY4 "O2'" H18 SING N N 53 UY4 "O3'" H19 SING N N 54 UY4 OP1 H20 SING N N 55 UY4 OP3 H21 SING N N 56 # # 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 UY4 SMILES ACDLabs 12.01 "c23n(C1OC(C(C1O)O)COP(O)(=O)O)cnc2c(ncn3)NC(NC(C(=O)O)C(C)O)=O" UY4 InChI InChI 1.03 "InChI=1S/C15H21N6O11P/c1-5(22)7(14(25)26)19-15(27)20-11-8-12(17-3-16-11)21(4-18-8)13-10(24)9(23)6(32-13)2-31-33(28,29)30/h3-7,9-10,13,22-24H,2H2,1H3,(H,25,26)(H2,28,29,30)(H2,16,17,19,20,27)/t5-,6+,7-,9+,10+,13+/m0/s1" UY4 InChIKey InChI 1.03 BHFCEFYJTLMMEQ-SDZKHPBCSA-N UY4 SMILES_CANONICAL CACTVS 3.385 "C[C@H](O)[C@H](NC(=O)Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]3O)C(O)=O" UY4 SMILES CACTVS 3.385 "C[CH](O)[CH](NC(=O)Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(O)=O)[CH](O)[CH]3O)C(O)=O" UY4 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C[C@@H]([C@@H](C(=O)O)NC(=O)Nc1c2c(ncn1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)O)O" UY4 SMILES "OpenEye OEToolkits" 2.0.7 "CC(C(C(=O)O)NC(=O)Nc1c2c(ncn1)n(cn2)C3C(C(C(O3)COP(=O)(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 UY4 "SYSTEMATIC NAME" ACDLabs 12.01 "(2S,3S)-2-{[(9-{(2R,3R,4S,5R)-3,4-dihydroxy-5-[(phosphonooxy)methyl]tetrahydrofuran-2-yl}-9H-purin-6-yl)carbamoyl]amino}-3-hydroxybutanoic acid (non-preferred name)" UY4 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "(2~{S},3~{S})-2-[[9-[(2~{R},3~{R},4~{S},5~{R})-3,4-bis(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]purin-6-yl]carbamoylamino]-3-oxidanyl-butanoic 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 UY4 "Create component" 2020-06-04 RCSB UY4 "Initial release" 2020-10-07 RCSB ##