data_6CX # _chem_comp.id 6CX _chem_comp.name "5'-{[(3S)-3-amino-3-carboxypropyl][(1H-imidazol-4-yl)methyl]amino}-5'-deoxyadenosine" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C18 H25 N9 O5" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2016-03-15 _chem_comp.pdbx_modified_date 2017-03-24 _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 447.448 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 6CX _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 5ISB _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site EBI # 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 6CX C2 C1 C 0 1 Y N N 50.244 42.012 127.250 6.207 0.674 0.830 C2 6CX 1 6CX C4 C2 C 0 1 Y N N 50.048 39.696 127.279 4.088 -0.111 0.409 C4 6CX 2 6CX C5 C3 C 0 1 Y N N 50.246 39.649 125.907 4.460 -1.361 0.931 C5 6CX 3 6CX C6 C4 C 0 1 Y N N 50.429 40.854 125.234 5.778 -1.523 1.390 C6 6CX 4 6CX C8 C5 C 0 1 Y N N 49.986 37.604 126.579 2.385 -1.508 0.319 C8 6CX 5 6CX N9 N1 N 0 1 Y N N 49.882 38.415 127.656 2.775 -0.234 0.031 N9 6CX 6 6CX C10 C6 C 0 1 N N N 52.212 33.176 131.239 -2.661 2.334 -0.327 C10 6CX 7 6CX ND N2 N 0 1 N N N 51.209 34.188 131.518 -2.395 0.902 -0.520 ND 6CX 8 6CX CG C7 C 0 1 N N N 51.519 34.740 132.850 -3.647 0.146 -0.646 CG 6CX 9 6CX CB C8 C 0 1 N N N 52.909 35.267 133.108 -3.364 -1.346 -0.457 CB 6CX 10 6CX CA C9 C 0 1 N N S 53.235 35.908 134.496 -4.683 -2.121 -0.463 CA 6CX 11 6CX C C10 C 0 1 N N N 53.727 34.811 135.387 -4.397 -3.599 -0.400 C 6CX 12 6CX O O1 O 0 1 N N N 54.907 34.415 135.188 -4.489 -4.188 0.651 O 6CX 13 6CX OXT O2 O 0 1 N N N 52.974 34.211 136.223 -4.041 -4.262 -1.512 OXT 6CX 14 6CX N N3 N 0 1 N N N 54.303 36.843 134.258 -5.488 -1.727 0.701 N 6CX 15 6CX "C5'" C11 C 0 1 N N N 51.266 35.225 130.467 -1.526 0.680 -1.683 "C5'" 6CX 16 6CX "C4'" C12 C 0 1 N N R 50.561 36.557 130.590 -0.143 1.274 -1.408 "C4'" 6CX 17 6CX "C3'" C13 C 0 1 N N S 49.094 36.399 130.610 0.750 1.164 -2.664 "C3'" 6CX 18 6CX "C2'" C14 C 0 1 N N R 48.644 37.027 129.382 2.154 0.853 -2.100 "C2'" 6CX 19 6CX "O2'" O3 O 0 1 N N N 47.363 37.625 129.505 3.075 1.887 -2.451 "O2'" 6CX 20 6CX "C1'" C15 C 0 1 N N R 49.700 38.031 129.067 1.944 0.812 -0.570 "C1'" 6CX 21 6CX N3 N4 N 0 1 Y N N 50.047 40.887 127.914 4.985 0.869 0.378 N3 6CX 22 6CX N1 N5 N 0 1 Y N N 50.428 42.011 125.936 6.604 -0.484 1.324 N1 6CX 23 6CX N6 N6 N 0 1 N N N 50.653 40.878 123.862 6.201 -2.732 1.915 N6 6CX 24 6CX N7 N7 N 0 1 Y N N 50.190 38.354 125.511 3.375 -2.168 0.846 N7 6CX 25 6CX "O4'" O4 O 0 1 N N N 50.861 37.314 129.471 0.544 0.503 -0.398 "O4'" 6CX 26 6CX "O3'" O5 O 0 1 N N N 48.605 37.012 131.780 0.760 2.400 -3.381 "O3'" 6CX 27 6CX C51 C16 C 0 1 Y N N 52.085 32.378 129.979 -3.123 2.574 1.087 C51 6CX 28 6CX C52 C17 C 0 1 Y N N 50.907 31.985 129.463 -2.344 2.937 2.123 C52 6CX 29 6CX N53 N8 N 0 1 Y N N 51.098 31.262 128.298 -3.162 3.045 3.215 N53 6CX 30 6CX C54 C18 C 0 1 Y N N 52.500 31.289 128.224 -4.414 2.744 2.808 C54 6CX 31 6CX N55 N9 N 0 1 Y N N 53.050 31.968 129.241 -4.384 2.468 1.533 N55 6CX 32 6CX H21 H1 H 0 1 N N N 50.255 42.949 127.786 6.912 1.491 0.790 H21 6CX 33 6CX H81 H2 H 0 1 N N N 49.914 36.526 126.590 1.399 -1.911 0.136 H81 6CX 34 6CX H102 H3 H 0 0 N N N 52.198 32.464 132.078 -1.750 2.902 -0.513 H102 6CX 35 6CX H101 H4 H 0 0 N N N 53.187 33.685 131.205 -3.437 2.656 -1.023 H101 6CX 36 6CX HG2 H6 H 0 1 N N N 50.819 35.570 133.028 -4.353 0.481 0.115 HG2 6CX 37 6CX HG3 H7 H 0 1 N N N 51.334 33.941 133.583 -4.074 0.312 -1.635 HG3 6CX 38 6CX HB2 H8 H 0 1 N N N 53.603 34.424 132.972 -2.730 -1.701 -1.269 HB2 6CX 39 6CX HB3 H9 H 0 1 N N N 53.109 36.034 132.345 -2.856 -1.501 0.495 HB3 6CX 40 6CX HA H10 H 0 1 N N N 52.341 36.394 134.914 -5.232 -1.895 -1.377 HA 6CX 41 6CX H3 H11 H 0 1 N N N 53.448 33.486 136.613 -3.868 -5.209 -1.422 H3 6CX 42 6CX H2 H12 H 0 1 N N N 54.556 37.287 135.118 -6.391 -2.177 0.685 H2 6CX 43 6CX H H13 H 0 1 N N N 55.095 36.357 133.889 -5.000 -1.926 1.562 H 6CX 44 6CX "H5'2" H15 H 0 0 N N N 50.870 34.755 129.555 -1.431 -0.390 -1.867 "H5'2" 6CX 45 6CX "H5'1" H16 H 0 0 N N N 52.332 35.457 130.327 -1.961 1.162 -2.559 "H5'1" 6CX 46 6CX "H4'1" H17 H 0 0 N N N 50.894 37.060 131.510 -0.233 2.315 -1.097 "H4'1" 6CX 47 6CX "H3'1" H18 H 0 0 N N N 48.839 35.329 130.599 0.406 0.354 -3.306 "H3'1" 6CX 48 6CX "H2'1" H19 H 0 0 N N N 48.624 36.275 128.579 2.507 -0.112 -2.465 "H2'1" 6CX 49 6CX "H2'2" H20 H 0 0 N N N 46.719 36.956 129.705 3.199 1.997 -3.404 "H2'2" 6CX 50 6CX "H1'1" H21 H 0 0 N N N 49.559 38.928 129.687 2.177 1.781 -0.129 "H1'1" 6CX 51 6CX H61 H22 H 0 1 N N N 50.793 41.822 123.563 5.586 -3.480 1.969 H61 6CX 52 6CX H62 H23 H 0 1 N N N 51.466 40.337 123.648 7.114 -2.831 2.228 H62 6CX 53 6CX "H3'2" H24 H 0 0 N N N 48.938 36.552 132.542 1.306 2.387 -4.179 "H3'2" 6CX 54 6CX H521 H25 H 0 0 N N N 49.943 32.204 129.898 -1.278 3.109 2.098 H521 6CX 55 6CX H531 H26 H 0 0 N N N 50.429 30.841 127.685 -2.893 3.292 4.114 H531 6CX 56 6CX H541 H27 H 0 0 N N N 53.070 30.817 127.438 -5.295 2.737 3.433 H541 6CX 57 # 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 6CX N6 C6 SING N N 1 6CX C6 C5 DOUB Y N 2 6CX C6 N1 SING Y N 3 6CX N7 C5 SING Y N 4 6CX N7 C8 DOUB Y N 5 6CX C5 C4 SING Y N 6 6CX N1 C2 DOUB Y N 7 6CX C8 N9 SING Y N 8 6CX C2 N3 SING Y N 9 6CX C4 N9 SING Y N 10 6CX C4 N3 DOUB Y N 11 6CX N9 "C1'" SING N N 12 6CX C54 N53 SING Y N 13 6CX C54 N55 DOUB Y N 14 6CX N53 C52 SING Y N 15 6CX "C1'" "C2'" SING N N 16 6CX "C1'" "O4'" SING N N 17 6CX N55 C51 SING Y N 18 6CX "C2'" "O2'" SING N N 19 6CX "C2'" "C3'" SING N N 20 6CX C52 C51 DOUB Y N 21 6CX "O4'" "C4'" SING N N 22 6CX C51 C10 SING N N 23 6CX "C5'" "C4'" SING N N 24 6CX "C5'" ND SING N N 25 6CX "C4'" "C3'" SING N N 26 6CX "C3'" "O3'" SING N N 27 6CX C10 ND SING N N 28 6CX ND CG SING N N 29 6CX CG CB SING N N 30 6CX CB CA SING N N 31 6CX N CA SING N N 32 6CX CA C SING N N 33 6CX O C DOUB N N 34 6CX C OXT SING N N 35 6CX C2 H21 SING N N 36 6CX C8 H81 SING N N 37 6CX C10 H102 SING N N 38 6CX C10 H101 SING N N 39 6CX CG HG2 SING N N 40 6CX CG HG3 SING N N 41 6CX CB HB2 SING N N 42 6CX CB HB3 SING N N 43 6CX CA HA SING N N 44 6CX OXT H3 SING N N 45 6CX N H2 SING N N 46 6CX N H SING N N 47 6CX "C5'" "H5'2" SING N N 48 6CX "C5'" "H5'1" SING N N 49 6CX "C4'" "H4'1" SING N N 50 6CX "C3'" "H3'1" SING N N 51 6CX "C2'" "H2'1" SING N N 52 6CX "O2'" "H2'2" SING N N 53 6CX "C1'" "H1'1" SING N N 54 6CX N6 H61 SING N N 55 6CX N6 H62 SING N N 56 6CX "O3'" "H3'2" SING N N 57 6CX C52 H521 SING N N 58 6CX N53 H531 SING N N 59 6CX C54 H541 SING N N 60 # 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 6CX SMILES ACDLabs 12.01 "c2nc1n(cnc1c(n2)N)C4C(C(C(CN(Cc3cncn3)CCC(C(O)=O)N)O4)O)O" 6CX InChI InChI 1.03 "InChI=1S/C18H25N9O5/c19-10(18(30)31)1-2-26(4-9-3-21-6-22-9)5-11-13(28)14(29)17(32-11)27-8-25-12-15(20)23-7-24-16(12)27/h3,6-8,10-11,13-14,17,28-29H,1-2,4-5,19H2,(H,21,22)(H,30,31)(H2,20,23,24)/t10-,11+,13+,14+,17+/m0/s1" 6CX InChIKey InChI 1.03 PWEFHAQFFKNLPL-YRGUDCOPSA-N 6CX SMILES_CANONICAL CACTVS 3.385 "N[C@@H](CCN(C[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23)Cc4c[nH]cn4)C(O)=O" 6CX SMILES CACTVS 3.385 "N[CH](CCN(C[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23)Cc4c[nH]cn4)C(O)=O" 6CX SMILES_CANONICAL "OpenEye OEToolkits" 2.0.4 "c1c(nc[nH]1)CN(CC[C@@H](C(=O)O)N)C[C@@H]2[C@H]([C@H]([C@@H](O2)n3cnc4c3ncnc4N)O)O" 6CX SMILES "OpenEye OEToolkits" 2.0.4 "c1c(nc[nH]1)CN(CCC(C(=O)O)N)CC2C(C(C(O2)n3cnc4c3ncnc4N)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 6CX "SYSTEMATIC NAME" ACDLabs 12.01 "5'-{[(3S)-3-amino-3-carboxypropyl][(1H-imidazol-4-yl)methyl]amino}-5'-deoxyadenosine" 6CX "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.4 "(2~{S})-4-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl-(1~{H}-imidazol-4-ylmethyl)amino]-2-azanyl-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 6CX "Create component" 2016-03-15 EBI 6CX "Initial release" 2017-03-29 RCSB #