data_AKM # _chem_comp.id AKM _chem_comp.name "[(2R,4S,6R)-4-azanyl-4,6-dimethyl-5,5-bis(oxidanyl)oxan-2-yl] [[(2R,3S,5R)-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] hydrogen phosphate" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C17 H29 N3 O14 P2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "dTDP-3-amino-2,3,6-trideoxy-4-keto-3-methyl-D-glucose (hydrated at C4)" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2013-04-29 _chem_comp.pdbx_modified_date 2021-03-13 _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 561.371 _chem_comp.one_letter_code ? _chem_comp.three_letter_code AKM _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 4KCF _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 AKM O2P O2P O 0 1 N N N 18.197 21.532 -15.712 -0.380 1.543 2.171 O2P AKM 1 AKM P P P 0 1 N N N 19.384 22.392 -16.156 -0.140 2.007 0.648 P AKM 2 AKM O1P O1P O 0 1 N N N 20.763 21.992 -15.719 0.109 3.466 0.610 O1P AKM 3 AKM OPP OPP O 0 1 N N N 19.438 22.426 -17.749 1.133 1.229 0.044 OPP AKM 4 AKM P2 P2 P 0 1 N N N 18.238 22.566 -18.799 2.725 1.368 0.241 P2 AKM 5 AKM O3P O3P O 0 1 N N N 18.939 23.008 -20.077 3.033 1.513 1.681 O3P AKM 6 AKM O1 O1 O 0 1 N N N 17.741 21.066 -19.038 3.453 0.052 -0.334 O1 AKM 7 AKM C1 C1 C 0 1 N N R 16.524 20.523 -18.557 4.863 -0.176 -0.212 C1 AKM 8 AKM C2 C2 C 0 1 N N N 16.577 18.986 -18.599 5.337 -1.019 -1.396 C2 AKM 9 AKM C3 C3 C 0 1 N N S 15.169 18.406 -18.468 6.829 -1.313 -1.270 C3 AKM 10 AKM C3M C3M C 0 1 N N N 14.914 18.506 -16.960 7.643 -0.050 -1.562 C3M AKM 11 AKM N3 N3 N 0 1 N N N 15.139 16.990 -18.862 7.184 -2.323 -2.294 N3 AKM 12 AKM C4 C4 C 0 1 N N N 14.140 19.078 -19.390 7.183 -1.882 0.098 C4 AKM 13 AKM O4A O4A O 0 1 N N N 14.162 18.493 -20.703 6.865 -3.285 0.109 O4A AKM 14 AKM O4B O4B O 0 1 N N N 12.810 18.810 -18.911 8.604 -1.758 0.292 O4B AKM 15 AKM C5 C5 C 0 1 N N R 14.435 20.493 -19.890 6.473 -1.210 1.262 C5 AKM 16 AKM C6 C6 C 0 1 N N N 13.307 21.495 -20.102 7.237 0.027 1.736 C6 AKM 17 AKM O5 O5 O 0 1 N N N 15.604 21.167 -19.429 5.119 -0.893 0.991 O5 AKM 18 AKM O4P O4P O 0 1 N N N 17.045 23.404 -18.368 3.253 2.664 -0.555 O4P AKM 19 AKM "O5'" O5* O 0 1 N N N 19.091 23.883 -15.632 -1.446 1.663 -0.229 O5* AKM 20 AKM "C5'" C5* C 0 1 N N N 20.100 24.857 -15.892 -2.716 2.280 -0.010 C5* AKM 21 AKM "C4'" C4* C 0 1 N N R 19.304 26.139 -16.062 -3.731 1.727 -1.013 C4* AKM 22 AKM "C3'" C3* C 0 1 N N S 20.154 27.339 -16.494 -5.117 2.389 -0.807 C3* AKM 23 AKM "O3'" O3* O 0 1 N N N 19.998 27.496 -17.897 -5.211 3.614 -1.537 O3* AKM 24 AKM "C2'" C2* C 0 1 N N N 19.551 28.542 -15.789 -6.076 1.323 -1.391 C2* AKM 25 AKM "C1'" C1* C 0 1 N N R 18.564 27.963 -14.773 -5.256 0.019 -1.356 C1* AKM 26 AKM "O4'" O4* O 0 1 N N N 18.749 26.532 -14.804 -3.985 0.328 -0.761 O4* AKM 27 AKM N11 N11 N 0 1 N N N 18.688 28.433 -13.387 -5.953 -0.986 -0.550 N11 AKM 28 AKM C21 C21 C 0 1 N N N 17.620 28.957 -12.796 -6.126 -0.780 0.768 C21 AKM 29 AKM O21 O21 O 0 1 N N N 16.473 29.112 -13.502 -5.702 0.241 1.276 O21 AKM 30 AKM N31 N31 N 0 1 N N N 17.628 29.398 -11.527 -6.762 -1.686 1.533 N31 AKM 31 AKM C41 C41 C 0 1 N N N 18.760 29.262 -10.813 -7.239 -2.823 0.986 C41 AKM 32 AKM O41 O41 O 0 1 N N N 18.831 29.666 -9.523 -7.815 -3.643 1.677 O41 AKM 33 AKM C51 C51 C 0 1 N N N 19.957 28.644 -11.411 -7.063 -3.053 -0.400 C51 AKM 34 AKM C5A C5A C 0 1 N N N 21.207 28.485 -10.592 -7.585 -4.315 -1.037 C5A AKM 35 AKM C61 C61 C 0 1 N N N 19.853 28.250 -12.734 -6.426 -2.124 -1.145 C61 AKM 36 AKM H1 H1 H 0 1 N N N 18.510 20.809 -15.182 -0.549 0.596 2.272 H1 AKM 37 AKM H2 H2 H 0 1 N N N 16.349 20.840 -17.518 5.373 0.784 -0.203 H2 AKM 38 AKM H3 H3 H 0 1 N N N 17.015 18.663 -19.555 4.779 -1.957 -1.418 H3 AKM 39 AKM H4 H4 H 0 1 N N N 17.199 18.621 -17.769 5.149 -0.475 -2.325 H4 AKM 40 AKM H5 H5 H 0 1 N N N 15.718 17.988 -16.417 7.371 0.730 -0.851 H5 AKM 41 AKM H6 H6 H 0 1 N N N 14.893 19.564 -16.661 8.706 -0.272 -1.469 H6 AKM 42 AKM H7 H7 H 0 1 N N N 13.948 18.038 -16.720 7.431 0.292 -2.575 H7 AKM 43 AKM H8 H8 H 0 1 N N N 15.789 16.474 -18.303 6.986 -1.982 -3.223 H8 AKM 44 AKM H9 H9 H 0 1 N N N 14.218 16.625 -18.724 8.151 -2.600 -2.210 H9 AKM 45 AKM H11 H11 H 0 1 N N N 13.993 17.561 -20.638 7.099 -3.734 0.933 H11 AKM 46 AKM H12 H12 H 0 1 N N N 12.710 19.168 -18.037 8.916 -2.098 1.142 H12 AKM 47 AKM H13 H13 H 0 1 N N N 14.710 20.281 -20.934 6.476 -1.929 2.109 H13 AKM 48 AKM H14 H14 H 0 1 N N N 12.409 20.968 -20.457 6.778 0.411 2.647 H14 AKM 49 AKM H15 H15 H 0 1 N N N 13.083 22.001 -19.151 8.274 -0.241 1.937 H15 AKM 50 AKM H16 H16 H 0 1 N N N 13.615 22.240 -20.850 7.204 0.794 0.961 H16 AKM 51 AKM H17 H17 H 0 1 N N N 16.911 24.109 -18.990 3.085 2.637 -1.506 H17 AKM 52 AKM H18 H18 H 0 1 N N N 20.657 24.614 -16.809 -3.054 2.066 1.004 H18 AKM 53 AKM H19 H19 H 0 1 N N N 20.800 24.936 -15.047 -2.624 3.358 -0.143 H19 AKM 54 AKM H20 H20 H 0 1 N N N 18.507 25.977 -16.802 -3.380 1.875 -2.034 H20 AKM 55 AKM H21 H21 H 0 1 N N N 21.205 27.198 -16.201 -5.317 2.553 0.252 H21 AKM 56 AKM H22 H22 H 0 1 N N N 20.516 28.235 -18.193 -6.060 4.066 -1.440 H22 AKM 57 AKM H23 H23 H 0 1 N N N 20.334 29.121 -15.278 -6.967 1.230 -0.770 H23 AKM 58 AKM H24 H24 H 0 1 N N N 19.028 29.188 -16.509 -6.348 1.575 -2.416 H24 AKM 59 AKM H25 H25 H 0 1 N N N 17.549 28.195 -15.127 -5.111 -0.355 -2.370 H25 AKM 60 AKM H26 H26 H 0 1 N N N 16.814 29.816 -11.124 -6.879 -1.521 2.482 H26 AKM 61 AKM H27 H27 H 0 1 N N N 21.033 28.873 -9.578 -8.069 -4.931 -0.278 H27 AKM 62 AKM H28 H28 H 0 1 N N N 21.475 27.420 -10.536 -8.308 -4.059 -1.812 H28 AKM 63 AKM H29 H29 H 0 1 N N N 22.028 29.045 -11.063 -6.757 -4.868 -1.480 H29 AKM 64 AKM H30 H30 H 0 1 N N N 20.696 27.801 -13.238 -6.286 -2.280 -2.204 H30 AKM 65 # # 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 AKM O4A C4 SING N N 1 AKM C6 C5 SING N N 2 AKM O3P P2 DOUB N N 3 AKM C5 O5 SING N N 4 AKM C5 C4 SING N N 5 AKM O5 C1 SING N N 6 AKM C4 O4B SING N N 7 AKM C4 C3 SING N N 8 AKM O1 P2 SING N N 9 AKM O1 C1 SING N N 10 AKM N3 C3 SING N N 11 AKM P2 O4P SING N N 12 AKM P2 OPP SING N N 13 AKM C2 C1 SING N N 14 AKM C2 C3 SING N N 15 AKM C3 C3M SING N N 16 AKM "O3'" "C3'" SING N N 17 AKM OPP P SING N N 18 AKM "C3'" "C4'" SING N N 19 AKM "C3'" "C2'" SING N N 20 AKM P O1P DOUB N N 21 AKM P O2P SING N N 22 AKM P "O5'" SING N N 23 AKM "C4'" "C5'" SING N N 24 AKM "C4'" "O4'" SING N N 25 AKM "C5'" "O5'" SING N N 26 AKM "C2'" "C1'" SING N N 27 AKM "O4'" "C1'" SING N N 28 AKM "C1'" N11 SING N N 29 AKM O21 C21 DOUB N N 30 AKM N11 C21 SING N N 31 AKM N11 C61 SING N N 32 AKM C21 N31 SING N N 33 AKM C61 C51 DOUB N N 34 AKM N31 C41 SING N N 35 AKM C51 C41 SING N N 36 AKM C51 C5A SING N N 37 AKM C41 O41 DOUB N N 38 AKM O2P H1 SING N N 39 AKM C1 H2 SING N N 40 AKM C2 H3 SING N N 41 AKM C2 H4 SING N N 42 AKM C3M H5 SING N N 43 AKM C3M H6 SING N N 44 AKM C3M H7 SING N N 45 AKM N3 H8 SING N N 46 AKM N3 H9 SING N N 47 AKM O4A H11 SING N N 48 AKM O4B H12 SING N N 49 AKM C5 H13 SING N N 50 AKM C6 H14 SING N N 51 AKM C6 H15 SING N N 52 AKM C6 H16 SING N N 53 AKM O4P H17 SING N N 54 AKM "C5'" H18 SING N N 55 AKM "C5'" H19 SING N N 56 AKM "C4'" H20 SING N N 57 AKM "C3'" H21 SING N N 58 AKM "O3'" H22 SING N N 59 AKM "C2'" H23 SING N N 60 AKM "C2'" H24 SING N N 61 AKM "C1'" H25 SING N N 62 AKM N31 H26 SING N N 63 AKM C5A H27 SING N N 64 AKM C5A H28 SING N N 65 AKM C5A H29 SING N N 66 AKM C61 H30 SING N N 67 # # 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 AKM SMILES ACDLabs 12.01 "O=C1C(=CN(C(=O)N1)C2OC(C(O)C2)COP(=O)(OP(=O)(OC3OC(C(O)(O)C(N)(C3)C)C)O)O)C" AKM InChI InChI 1.03 "InChI=1S/C17H29N3O14P2/c1-8-6-20(15(23)19-14(8)22)12-4-10(21)11(32-12)7-30-35(26,27)34-36(28,29)33-13-5-16(3,18)17(24,25)9(2)31-13/h6,9-13,21,24-25H,4-5,7,18H2,1-3H3,(H,26,27)(H,28,29)(H,19,22,23)/t9-,10+,11-,12-,13-,16+/m1/s1" AKM InChIKey InChI 1.03 GACNZVKWDHTCBB-HHMBNNFFSA-N AKM SMILES_CANONICAL CACTVS 3.370 "C[C@H]1O[C@@H](C[C@](C)(N)C1(O)O)O[P](O)(=O)O[P](O)(=O)OC[C@H]2O[C@H](C[C@@H]2O)N3C=C(C)C(=O)NC3=O" AKM SMILES CACTVS 3.370 "C[CH]1O[CH](C[C](C)(N)C1(O)O)O[P](O)(=O)O[P](O)(=O)OC[CH]2O[CH](C[CH]2O)N3C=C(C)C(=O)NC3=O" AKM SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "C[C@@H]1C([C@@](C[C@H](O1)OP(=O)(O)OP(=O)(O)OC[C@@H]2[C@H](C[C@@H](O2)N3C=C(C(=O)NC3=O)C)O)(C)N)(O)O" AKM SMILES "OpenEye OEToolkits" 1.7.6 "CC1C(C(CC(O1)OP(=O)(O)OP(=O)(O)OCC2C(CC(O2)N3C=C(C(=O)NC3=O)C)O)(C)N)(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 AKM "SYSTEMATIC NAME" ACDLabs 12.01 "(2R,4S,6R)-4-amino-5,5-dihydroxy-4,6-dimethyltetrahydro-2H-pyran-2-yl [(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)tetrahydrofuran-2-yl]methyl dihydrogen diphosphate (non-preferred name)" AKM "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "[(2R,4S,6R)-4-azanyl-4,6-dimethyl-5,5-bis(oxidanyl)oxan-2-yl] [[(2R,3S,5R)-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] hydrogen 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 AKM "Create component" 2013-04-29 RCSB AKM "Other modification" 2013-05-23 RCSB AKM "Modify synonyms" 2021-03-13 RCSB # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id AKM _pdbx_chem_comp_synonyms.name "dTDP-3-amino-2,3,6-trideoxy-4-keto-3-methyl-D-glucose (hydrated at C4)" _pdbx_chem_comp_synonyms.provenance PDB _pdbx_chem_comp_synonyms.type ? ##