data_5AL # _chem_comp.id 5AL _chem_comp.name "5'-O-[(R)-{[(2S)-2-aminopropanoyl]oxy}(hydroxy)phosphoryl]adenosine" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C13 H19 N6 O8 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "Alanyl Adenylate" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2009-06-25 _chem_comp.pdbx_modified_date 2021-03-01 _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 418.299 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 5AL _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 3HXY _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 5AL C C C 0 1 N N N 12.336 4.408 -3.702 5.637 -0.783 -0.244 C 5AL 1 5AL N N N 0 1 N N N 10.404 3.191 -4.788 7.895 -1.448 -0.849 N 5AL 2 5AL O O O 0 1 N N N 11.805 4.479 -2.608 6.102 -0.386 0.798 O 5AL 3 5AL P P P 0 1 N N N 14.731 5.113 -2.626 3.546 0.433 0.464 P 5AL 4 5AL N1 N1 N 0 1 Y N N 16.344 10.511 4.387 -6.809 -1.482 -0.551 N1 5AL 5 5AL C2 C2 C 0 1 Y N N 16.103 11.438 3.448 -6.448 -0.361 -1.147 C2 5AL 6 5AL N3 N3 N 0 1 Y N N 15.864 11.126 2.167 -5.231 0.130 -1.052 N3 5AL 7 5AL C4 C4 C 0 1 Y N N 15.859 9.834 1.763 -4.302 -0.497 -0.338 C4 5AL 8 5AL C5 C5 C 0 1 Y N N 16.113 8.808 2.723 -4.636 -1.695 0.317 C5 5AL 9 5AL C6 C6 C 0 1 Y N N 16.359 9.196 4.086 -5.949 -2.178 0.185 C6 5AL 10 5AL N6 N6 N 0 1 N N N 16.606 8.277 5.047 -6.337 -3.352 0.807 N6 5AL 11 5AL N7 N7 N 0 1 Y N N 16.044 7.640 2.061 -3.524 -2.121 0.963 N7 5AL 12 5AL C8 C8 C 0 1 Y N N 15.768 7.917 0.765 -2.553 -1.281 0.752 C8 5AL 13 5AL N9 N9 N 0 1 Y N N 15.657 9.243 0.583 -2.982 -0.262 -0.045 N9 5AL 14 5AL CA CA C 0 1 N N S 11.523 4.119 -4.911 6.473 -1.632 -1.167 CA 5AL 15 5AL CB CB C 0 1 N N N 11.396 5.231 -5.955 6.096 -3.104 -0.986 CB 5AL 16 5AL "C1'" C1* C 0 1 N N R 15.352 9.967 -0.689 -2.181 0.875 -0.505 C1* 5AL 17 5AL O1A O1A O 0 1 N N N 14.652 4.117 -1.501 3.331 -0.384 1.834 O1A 5AL 18 5AL "C2'" C2* C 0 1 N N R 16.463 9.901 -1.687 -2.334 2.077 0.463 C2* 5AL 19 5AL "O2'" O2* O 0 1 N N N 16.990 11.151 -2.188 -3.474 2.866 0.119 O2* 5AL 20 5AL O2A O2A O 0 1 N N N 16.055 5.412 -3.282 4.298 1.677 0.744 O2A 5AL 21 5AL "C3'" C3* C 0 1 N N S 16.128 8.865 -2.661 -1.023 2.861 0.215 C3* 5AL 22 5AL "O3'" O3* O 0 1 N N N 16.748 8.830 -3.964 -1.247 3.935 -0.702 O3* 5AL 23 5AL O3A O3A O 0 1 N N N 13.773 4.612 -3.824 4.375 -0.472 -0.578 O3A 5AL 24 5AL "C4'" C4* C 0 1 N N R 14.665 8.752 -2.559 -0.069 1.818 -0.400 C4* 5AL 25 5AL "O4'" O4* O 0 1 N N N 14.212 9.391 -1.354 -0.773 0.564 -0.441 O4* 5AL 26 5AL "C5'" C5* C 0 1 N N N 13.910 7.564 -3.085 1.185 1.685 0.467 C5* 5AL 27 5AL "O5'" O5* O 0 1 N N N 14.072 6.501 -2.154 2.113 0.804 -0.170 O5* 5AL 28 5AL HN HN H 0 1 N N N 9.952 3.094 -5.675 8.090 -1.717 0.104 HN 5AL 29 5AL H2 H2 H 0 1 N N N 16.102 12.479 3.736 -7.179 0.174 -1.736 H2 5AL 30 5AL HN6 HN6 H 0 1 N N N 16.756 8.740 5.921 -5.700 -3.851 1.341 HN6 5AL 31 5AL HN6A HN6A H 0 0 N N N 15.823 7.660 5.127 -7.246 -3.676 0.708 HN6A 5AL 32 5AL H8 H8 H 0 1 N N N 15.653 7.176 -0.013 -1.553 -1.378 1.150 H8 5AL 33 5AL HB HB H 0 1 N N N 10.771 4.881 -6.790 5.041 -3.241 -1.222 HB 5AL 34 5AL HBA HBA H 0 1 N N N 10.931 6.115 -5.494 6.701 -3.719 -1.653 HBA 5AL 35 5AL HBB HBB H 0 1 N N N 12.395 5.496 -6.331 6.280 -3.401 0.047 HBB 5AL 36 5AL "H1'" H1* H 0 1 N N N 15.178 11.007 -0.377 -2.466 1.160 -1.518 H1* 5AL 37 5AL HO1A HO1A H 0 0 N N N 15.518 3.768 -1.325 2.844 -1.213 1.725 HO1A 5AL 38 5AL "H2'" H2* H 0 1 N N N 17.383 9.599 -1.164 -2.395 1.738 1.497 H2* 5AL 39 5AL "HO2'" HO2* H 0 0 N N N 17.686 10.975 -2.810 -3.612 3.630 0.696 HO2* 5AL 40 5AL "H3'" H3* H 0 1 N N N 16.645 7.929 -2.404 -0.620 3.239 1.155 H3* 5AL 41 5AL "HO3'" HO3* H 0 0 N N N 16.409 8.092 -4.457 -1.885 4.591 -0.390 HO3* 5AL 42 5AL "H4'" H4* H 0 1 N N N 14.297 9.312 -3.431 0.207 2.119 -1.411 H4* 5AL 43 5AL "H5'" H5* H 0 1 N N N 12.844 7.812 -3.193 1.644 2.665 0.596 H5* 5AL 44 5AL "H5'A" H5*A H 0 0 N N N 14.308 7.269 -4.067 0.911 1.281 1.442 H5*A 5AL 45 5AL H18 H18 H 0 1 N N N 10.742 2.299 -4.487 8.479 -1.957 -1.495 H18 5AL 46 5AL H19 H19 H 0 1 N N N 12.233 3.450 -5.418 6.290 -1.335 -2.200 H19 5AL 47 # # 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 5AL C O DOUB N N 1 5AL N HN SING N N 2 5AL P "O5'" SING N N 3 5AL P O1A SING N N 4 5AL C2 N1 DOUB Y N 5 5AL C2 H2 SING N N 6 5AL N3 C2 SING Y N 7 5AL C4 N3 DOUB Y N 8 5AL C4 C5 SING Y N 9 5AL C5 C6 DOUB Y N 10 5AL C6 N1 SING Y N 11 5AL C6 N6 SING N N 12 5AL N6 HN6 SING N N 13 5AL N6 HN6A SING N N 14 5AL N7 C5 SING Y N 15 5AL C8 N7 DOUB Y N 16 5AL C8 H8 SING N N 17 5AL N9 C4 SING Y N 18 5AL N9 C8 SING Y N 19 5AL CA C SING N N 20 5AL CA N SING N N 21 5AL CB CA SING N N 22 5AL CB HB SING N N 23 5AL CB HBA SING N N 24 5AL CB HBB SING N N 25 5AL "C1'" N9 SING N N 26 5AL "C1'" "H1'" SING N N 27 5AL O1A HO1A SING N N 28 5AL "C2'" "C1'" SING N N 29 5AL "C2'" "H2'" SING N N 30 5AL "O2'" "C2'" SING N N 31 5AL "O2'" "HO2'" SING N N 32 5AL O2A P DOUB N N 33 5AL "C3'" "C2'" SING N N 34 5AL "C3'" "C4'" SING N N 35 5AL "C3'" "H3'" SING N N 36 5AL "O3'" "C3'" SING N N 37 5AL "O3'" "HO3'" SING N N 38 5AL O3A C SING N N 39 5AL O3A P SING N N 40 5AL "C4'" "O4'" SING N N 41 5AL "C4'" "H4'" SING N N 42 5AL "O4'" "C1'" SING N N 43 5AL "C5'" "C4'" SING N N 44 5AL "C5'" "O5'" SING N N 45 5AL "C5'" "H5'" SING N N 46 5AL "C5'" "H5'A" SING N N 47 5AL N H18 SING N N 48 5AL CA H19 SING N N 49 # # 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 5AL SMILES ACDLabs 11.02 "O=P(OC(=O)C(N)C)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O" 5AL SMILES_CANONICAL CACTVS 3.352 "C[C@H](N)C(=O)O[P](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23" 5AL SMILES CACTVS 3.352 "C[CH](N)C(=O)O[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23" 5AL SMILES_CANONICAL "OpenEye OEToolkits" 1.7.0 "C[C@@H](C(=O)O[P@](=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O)N" 5AL SMILES "OpenEye OEToolkits" 1.7.0 "CC(C(=O)OP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)O)N" 5AL InChI InChI 1.03 "InChI=1S/C13H19N6O8P/c1-5(14)13(22)27-28(23,24)25-2-6-8(20)9(21)12(26-6)19-4-18-7-10(15)16-3-17-11(7)19/h3-6,8-9,12,20-21H,2,14H2,1H3,(H,23,24)(H2,15,16,17)/t5-,6+,8+,9+,12+/m0/s1" 5AL InChIKey InChI 1.03 ISYFCRWDMNBLTM-MACXSXHHSA-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 5AL "SYSTEMATIC NAME" ACDLabs 11.02 "5'-O-[(R)-{[(2S)-2-aminopropanoyl]oxy}(hydroxy)phosphoryl]adenosine" 5AL "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.6.1 "[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl] (2S)-2-azanylpropanoate" # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site 5AL "Create component" 2009-06-25 RCSB 5AL "Modify aromatic_flag" 2011-06-04 RCSB 5AL "Modify descriptor" 2011-06-04 RCSB 5AL "Modify synonyms" 2021-03-01 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id 5AL _pdbx_chem_comp_synonyms.name "Alanyl Adenylate" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##