data_L3X # _chem_comp.id L3X _chem_comp.name ;3'-deoxy-3'-(glycylamino)adenosine 5'-(dihydrogen phosphate) ; _chem_comp.type "DNA OH 3 prime terminus" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C12 H18 N7 O7 P" _chem_comp.mon_nstd_parent_comp_id DA _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2022-02-25 _chem_comp.pdbx_modified_date 2022-07-08 _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 403.288 _chem_comp.one_letter_code A _chem_comp.three_letter_code L3X _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 7U2H _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 L3X P P1 P 0 1 N N N 90.972 -48.906 0.024 -4.474 -2.275 0.039 P L3X 1 L3X OP1 O1 O 0 1 N N N 91.582 -49.569 -1.152 -4.182 -2.885 -1.278 OP1 L3X 2 L3X OP2 O2 O 0 1 N N N 90.905 -47.429 0.097 -4.760 -3.436 1.117 OP2 L3X 3 L3X "C1'" C1 C 0 1 N N R 85.980 -48.885 1.025 0.844 0.057 0.505 "C1'" L3X 4 L3X "C2'" C2 C 0 1 N N R 85.285 -49.171 -0.290 0.562 1.119 -0.589 "C2'" L3X 5 L3X "O2'" O3 O 0 1 N N N 84.471 -50.297 -0.027 1.401 2.262 -0.417 "O2'" L3X 6 L3X "C3'" C3 C 0 1 N N S 86.425 -49.560 -1.213 -0.921 1.476 -0.319 "C3'" L3X 7 L3X "N3'" N1 N 0 1 N N N 86.060 -50.460 -2.328 -1.019 2.699 0.481 "N3'" L3X 8 L3X "C4'" C4 C 0 1 N N S 87.351 -50.312 -0.292 -1.462 0.269 0.471 "C4'" L3X 9 L3X "O4'" O4 O 0 1 N N N 87.208 -49.679 1.017 -0.392 -0.686 0.584 "O4'" L3X 10 L3X "C5'" C5 C 0 1 N N N 88.774 -50.100 -0.772 -2.642 -0.356 -0.277 "C5'" L3X 11 L3X "O5'" O5 O 0 1 N N N 89.504 -49.492 0.278 -3.211 -1.399 0.517 "O5'" L3X 12 L3X N9 N2 N 0 1 Y N N 86.295 -47.418 1.184 1.947 -0.819 0.101 N9 L3X 13 L3X C8 C6 C 0 1 Y N N 87.165 -46.696 0.468 1.834 -2.007 -0.557 C8 L3X 14 L3X N7 N3 N 0 1 Y N N 87.144 -45.442 0.900 3.014 -2.518 -0.756 N7 L3X 15 L3X C6 C7 C 0 1 Y N N 85.847 -44.319 2.614 5.359 -1.722 -0.159 C6 L3X 16 L3X N6 N4 N 0 1 N N N 86.372 -43.108 2.409 6.077 -2.781 -0.688 N6 L3X 17 L3X C5 C8 C 0 1 Y N N 86.257 -45.355 1.857 3.956 -1.693 -0.239 C5 L3X 18 L3X C4 C9 C 0 1 Y N N 85.703 -46.555 2.045 3.283 -0.590 0.312 C4 L3X 19 L3X N3 N5 N 0 1 Y N N 84.757 -46.729 2.970 3.991 0.379 0.883 N3 L3X 20 L3X C2 C10 C 0 1 Y N N 84.363 -45.699 3.732 5.304 0.312 0.931 C2 L3X 21 L3X N1 N6 N 0 1 Y N N 84.908 -44.492 3.552 5.981 -0.702 0.424 N1 L3X 22 L3X C C11 C 0 1 N N N 86.865 -50.658 -3.409 -1.091 3.899 -0.128 C L3X 23 L3X O O6 O 0 1 N N N 87.919 -50.046 -3.623 -1.075 3.966 -1.339 O L3X 24 L3X CA C12 C 0 1 N N N 86.374 -51.742 -4.385 -1.192 5.157 0.696 CA L3X 25 L3X N N7 N 0 1 N N N 86.675 -51.469 -5.811 -1.258 6.322 -0.196 N L3X 26 L3X H2 H2 H 0 1 N N N 91.294 -47.055 -0.685 -5.510 -4.005 0.893 H2 L3X 27 L3X H3 H3 H 0 1 N N N 85.332 -49.208 1.853 1.065 0.537 1.458 H3 L3X 28 L3X H4 H4 H 0 1 N N N 84.729 -48.298 -0.664 0.685 0.694 -1.585 H4 L3X 29 L3X H5 H5 H 0 1 N N N 83.760 -50.046 0.551 2.346 2.071 -0.487 H5 L3X 30 L3X H6 H6 H 0 1 N N N 86.923 -48.657 -1.595 -1.460 1.590 -1.259 H6 L3X 31 L3X H7 H7 H 0 1 N N N 85.186 -50.944 -2.287 -1.032 2.645 1.450 H7 L3X 32 L3X H8 H8 H 0 1 N N N 87.099 -51.382 -0.261 -1.777 0.588 1.465 H8 L3X 33 L3X H9 H9 H 0 1 N N N 89.229 -51.068 -1.031 -3.396 0.408 -0.468 H9 L3X 34 L3X H10 H10 H 0 1 N N N 88.776 -49.445 -1.656 -2.295 -0.768 -1.224 H10 L3X 35 L3X H11 H11 H 0 1 N N N 87.784 -47.073 -0.332 0.903 -2.457 -0.868 H11 L3X 36 L3X H12 H12 H 0 1 N N N 85.954 -42.452 3.037 7.045 -2.784 -0.635 H12 L3X 37 L3X H13 H13 H 0 1 N N N 87.358 -43.141 2.570 5.611 -3.519 -1.110 H13 L3X 38 L3X H14 H14 H 0 1 N N N 83.607 -45.844 4.490 5.849 1.117 1.402 H14 L3X 39 L3X H15 H15 H 0 1 N N N 85.283 -51.834 -4.276 -2.093 5.118 1.309 H15 L3X 40 L3X H16 H16 H 0 1 N N N 86.851 -52.694 -4.109 -0.317 5.241 1.340 H16 L3X 41 L3X H17 H17 H 0 1 N N N 86.325 -52.217 -6.375 -1.326 7.179 0.332 H17 L3X 42 L3X H18 H18 H 0 1 N N N 86.239 -50.612 -6.085 -0.465 6.345 -0.820 H18 L3X 43 L3X OP3 OP3 O 0 1 N Y N 90.670 -48.629 1.526 -5.769 -1.326 -0.084 OP3 L3X 44 L3X H1 H1 H 0 1 N N N 91.157 -49.241 2.065 -6.019 -0.893 0.743 H1 L3X 45 # 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 L3X N CA SING N N 1 L3X CA C SING N N 2 L3X O C DOUB N N 3 L3X C "N3'" SING N N 4 L3X "N3'" "C3'" SING N N 5 L3X "C3'" "C4'" SING N N 6 L3X "C3'" "C2'" SING N N 7 L3X OP1 P DOUB N N 8 L3X "C5'" "C4'" SING N N 9 L3X "C5'" "O5'" SING N N 10 L3X "C4'" "O4'" SING N N 11 L3X "C2'" "O2'" SING N N 12 L3X "C2'" "C1'" SING N N 13 L3X P OP2 SING N N 14 L3X P "O5'" SING N N 15 L3X C8 N7 DOUB Y N 16 L3X C8 N9 SING Y N 17 L3X N7 C5 SING Y N 18 L3X "O4'" "C1'" SING N N 19 L3X "C1'" N9 SING N N 20 L3X N9 C4 SING Y N 21 L3X C5 C4 DOUB Y N 22 L3X C5 C6 SING Y N 23 L3X C4 N3 SING Y N 24 L3X N6 C6 SING N N 25 L3X C6 N1 DOUB Y N 26 L3X N3 C2 DOUB Y N 27 L3X N1 C2 SING Y N 28 L3X OP2 H2 SING N N 29 L3X "C1'" H3 SING N N 30 L3X "C2'" H4 SING N N 31 L3X "O2'" H5 SING N N 32 L3X "C3'" H6 SING N N 33 L3X "N3'" H7 SING N N 34 L3X "C4'" H8 SING N N 35 L3X "C5'" H9 SING N N 36 L3X "C5'" H10 SING N N 37 L3X C8 H11 SING N N 38 L3X N6 H12 SING N N 39 L3X N6 H13 SING N N 40 L3X C2 H14 SING N N 41 L3X CA H15 SING N N 42 L3X CA H16 SING N N 43 L3X N H17 SING N N 44 L3X N H18 SING N N 45 L3X P OP3 SING N N 46 L3X OP3 H1 SING N N 47 # 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 L3X SMILES ACDLabs 12.01 "O=P(O)(O)OCC1OC(n2cnc3c(N)ncnc32)C(O)C1NC(=O)CN" L3X InChI InChI 1.03 "InChI=1S/C12H18N7O7P/c13-1-6(20)18-7-5(2-25-27(22,23)24)26-12(9(7)21)19-4-17-8-10(14)15-3-16-11(8)19/h3-5,7,9,12,21H,1-2,13H2,(H,18,20)(H2,14,15,16)(H2,22,23,24)/t5-,7-,9-,12-/m1/s1" L3X InChIKey InChI 1.03 LEUUMALNMKNMGX-MUIQIWNUSA-N L3X SMILES_CANONICAL CACTVS 3.385 "NCC(=O)N[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(O)=O)n2cnc3c(N)ncnc23" L3X SMILES CACTVS 3.385 "NCC(=O)N[CH]1[CH](O)[CH](O[CH]1CO[P](O)(O)=O)n2cnc3c(N)ncnc23" L3X SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)NC(=O)CN)O)N" L3X SMILES "OpenEye OEToolkits" 2.0.7 "c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)O)NC(=O)CN)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 L3X "SYSTEMATIC NAME" ACDLabs 12.01 ;3'-deoxy-3'-(glycylamino)adenosine 5'-(dihydrogen phosphate) ; L3X "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "[(2~{S},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3-(2-azanylethanoylamino)-4-oxidanyl-oxolan-2-yl]methyl dihydrogen 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 L3X "Create component" 2022-02-25 RCSB L3X "Modify parent residue" 2022-02-28 RCSB L3X "Initial release" 2022-07-13 RCSB #