data_9YM # _chem_comp.id 9YM _chem_comp.name "[4-({[(1R,2S,3S,4R,5S)-5-amino-2,3,4-trihydroxycyclohexyl]amino}methyl)-5-hydroxy-6-methylpyridin-3-yl]methyl dihydrogen phosphate" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C14 H24 N3 O8 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2017-06-26 _chem_comp.pdbx_modified_date 2017-07-07 _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 393.329 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 9YM _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 5W71 _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 9YM O2P O1 O 0 1 N N N -11.966 -3.523 17.845 -5.437 -2.659 -0.348 O2P 9YM 1 9YM P P1 P 0 1 N N N -11.820 -3.125 16.495 -3.948 -2.435 0.222 P 9YM 2 9YM O3P O2 O 0 1 N N N -11.164 -1.872 16.513 -3.908 -2.825 1.784 O3P 9YM 3 9YM O1P O3 O 0 1 N N N -13.015 -3.173 15.716 -3.000 -3.291 -0.525 O1P 9YM 4 9YM O4P O4 O 0 1 N N N -10.959 -4.209 15.816 -3.532 -0.890 0.044 O4P 9YM 5 9YM C5A C1 C 0 1 N N N -9.660 -4.523 16.228 -2.230 -0.394 0.358 C5A 9YM 6 9YM C5 C2 C 0 1 Y N N -8.662 -4.909 15.137 -2.175 1.086 0.078 C5 9YM 7 9YM C4 C3 C 0 1 Y N N -8.211 -4.030 14.172 -1.008 1.799 0.299 C4 9YM 8 9YM C4A C4 C 0 1 N N N -8.651 -2.643 14.086 0.225 1.115 0.830 C4A 9YM 9 9YM C3 C5 C 0 1 Y N N -7.209 -4.429 13.146 -1.003 3.162 0.021 C3 9YM 10 9YM O3 O5 O 0 1 N N N -6.807 -3.645 12.293 0.119 3.902 0.222 O3 9YM 11 9YM C2 C6 C 0 1 Y N N -6.772 -5.839 13.289 -2.158 3.755 -0.466 C2 9YM 12 9YM C2A C7 C 0 1 N N N -5.751 -6.391 12.358 -2.168 5.230 -0.773 C2A 9YM 13 9YM N1 N1 N 0 1 Y N N -7.290 -6.605 14.262 -3.249 3.040 -0.664 N1 9YM 14 9YM C6 C8 C 0 1 Y N N -8.174 -6.202 15.144 -3.287 1.747 -0.410 C6 9YM 15 9YM OD4 O6 O 0 1 N N N -7.378 3.747 15.037 6.267 -1.369 0.349 OD4 9YM 16 9YM CD4 C9 C 0 1 N N R -7.368 2.338 15.010 5.086 -0.713 -0.118 CD4 9YM 17 9YM CD5 C10 C 0 1 N N S -8.782 1.782 15.006 3.991 -1.751 -0.370 CD5 9YM 18 9YM OD5 O7 O 0 1 N N N -9.434 2.219 16.132 4.438 -2.685 -1.355 OD5 9YM 19 9YM CD6 C11 C 0 1 N N S -8.828 0.270 15.002 2.727 -1.049 -0.869 CD6 9YM 20 9YM OD6 O8 O 0 1 N N N -10.151 -0.037 14.668 1.705 -2.019 -1.105 OD6 9YM 21 9YM CD3 C12 C 0 1 N N S -6.713 1.816 13.741 4.608 0.287 0.937 CD3 9YM 22 9YM ND3 N2 N 0 1 N N N -5.383 2.312 13.582 5.659 1.285 1.179 ND3 9YM 23 9YM CD2 C13 C 0 1 N N N -6.620 0.315 13.699 3.344 0.990 0.437 CD2 9YM 24 9YM CD1 C14 C 0 1 N N R -7.935 -0.382 13.938 2.249 -0.049 0.185 CD1 9YM 25 9YM ND1 N3 N 0 1 N N N -7.741 -1.822 14.075 1.035 0.626 -0.294 ND1 9YM 26 9YM H1 H1 H 0 1 N N N -12.870 -3.764 18.009 -5.754 -3.570 -0.273 H1 9YM 27 9YM H2 H2 H 0 1 N N N -11.650 -1.252 15.982 -4.506 -2.303 2.335 H2 9YM 28 9YM H3 H3 H 0 1 N N N -9.729 -5.368 16.929 -2.018 -0.571 1.413 H3 9YM 29 9YM H4 H4 H 0 1 N N N -9.256 -3.644 16.752 -1.488 -0.907 -0.253 H4 9YM 30 9YM H5 H5 H 0 1 N N N -9.294 -2.432 14.953 0.809 1.822 1.417 H5 9YM 31 9YM H6 H6 H 0 1 N N N -9.233 -2.524 13.160 -0.068 0.274 1.459 H6 9YM 32 9YM H8 H8 H 0 1 N N N -5.545 -7.440 12.619 -1.866 5.388 -1.809 H8 9YM 33 9YM H9 H9 H 0 1 N N N -6.129 -6.337 11.326 -3.172 5.626 -0.623 H9 9YM 34 9YM H10 H10 H 0 1 N N N -4.824 -5.804 12.440 -1.472 5.743 -0.110 H10 9YM 35 9YM H11 H11 H 0 1 N N N -8.528 -6.896 15.892 -4.199 1.196 -0.589 H11 9YM 36 9YM H12 H12 H 0 1 N N N -7.792 4.046 15.838 6.627 -2.018 -0.270 H12 9YM 37 9YM H13 H13 H 0 1 N N N -6.829 1.939 15.882 5.307 -0.185 -1.045 H13 9YM 38 9YM H14 H14 H 0 1 N N N -9.293 2.147 14.103 3.771 -2.279 0.558 H14 9YM 39 9YM H15 H15 H 0 1 N N N -9.419 3.169 16.159 5.238 -3.168 -1.104 H15 9YM 40 9YM H16 H16 H 0 1 N N N -8.560 -0.116 15.997 2.948 -0.521 -1.797 H16 9YM 41 9YM H17 H17 H 0 1 N N N -10.738 0.351 15.307 1.940 -2.686 -1.764 H17 9YM 42 9YM H18 H18 H 0 1 N N N -7.323 2.144 12.887 4.387 -0.241 1.865 H18 9YM 43 9YM H19 H19 H 0 1 N N N -5.395 3.312 13.604 6.505 0.845 1.510 H19 9YM 44 9YM H20 H20 H 0 1 N N N -4.809 1.969 14.325 5.836 1.832 0.350 H20 9YM 45 9YM H22 H22 H 0 1 N N N -6.245 0.018 12.708 3.003 1.702 1.189 H22 9YM 46 9YM H23 H23 H 0 1 N N N -5.909 -0.010 14.473 3.564 1.518 -0.491 H23 9YM 47 9YM H24 H24 H 0 1 N N N -8.492 -0.255 12.998 2.029 -0.577 1.113 H24 9YM 48 9YM H25 H25 H 0 1 N N N -7.147 -2.088 13.316 1.265 1.377 -0.928 H25 9YM 49 9YM H27 H27 H 0 1 N N N -7.235 -2.804 12.408 0.183 4.287 1.107 H27 9YM 50 # 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 9YM O3 C3 SING N N 1 9YM C2A C2 SING N N 2 9YM C3 C2 DOUB Y N 3 9YM C3 C4 SING Y N 4 9YM C2 N1 SING Y N 5 9YM ND3 CD3 SING N N 6 9YM CD2 CD3 SING N N 7 9YM CD2 CD1 SING N N 8 9YM CD3 CD4 SING N N 9 9YM CD1 ND1 SING N N 10 9YM CD1 CD6 SING N N 11 9YM ND1 C4A SING N N 12 9YM C4A C4 SING N N 13 9YM C4 C5 DOUB Y N 14 9YM N1 C6 DOUB Y N 15 9YM OD6 CD6 SING N N 16 9YM CD6 CD5 SING N N 17 9YM CD5 CD4 SING N N 18 9YM CD5 OD5 SING N N 19 9YM CD4 OD4 SING N N 20 9YM C5 C6 SING Y N 21 9YM C5 C5A SING N N 22 9YM O1P P DOUB N N 23 9YM O4P C5A SING N N 24 9YM O4P P SING N N 25 9YM P O3P SING N N 26 9YM P O2P SING N N 27 9YM O2P H1 SING N N 28 9YM O3P H2 SING N N 29 9YM C5A H3 SING N N 30 9YM C5A H4 SING N N 31 9YM C4A H5 SING N N 32 9YM C4A H6 SING N N 33 9YM C2A H8 SING N N 34 9YM C2A H9 SING N N 35 9YM C2A H10 SING N N 36 9YM C6 H11 SING N N 37 9YM OD4 H12 SING N N 38 9YM CD4 H13 SING N N 39 9YM CD5 H14 SING N N 40 9YM OD5 H15 SING N N 41 9YM CD6 H16 SING N N 42 9YM OD6 H17 SING N N 43 9YM CD3 H18 SING N N 44 9YM ND3 H19 SING N N 45 9YM ND3 H20 SING N N 46 9YM CD2 H22 SING N N 47 9YM CD2 H23 SING N N 48 9YM CD1 H24 SING N N 49 9YM ND1 H25 SING N N 50 9YM O3 H27 SING N N 51 # 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 9YM SMILES ACDLabs 12.01 "OP(O)(=O)OCc1cnc(c(c1CNC2C(C(C(O)C(N)C2)O)O)O)C" 9YM InChI InChI 1.03 "InChI=1S/C14H24N3O8P/c1-6-11(18)8(7(3-16-6)5-25-26(22,23)24)4-17-10-2-9(15)12(19)14(21)13(10)20/h3,9-10,12-14,17-21H,2,4-5,15H2,1H3,(H2,22,23,24)/t9-,10+,12+,13-,14-/m0/s1" 9YM InChIKey InChI 1.03 QHLVFXGQUJCQEL-MYALOSSISA-N 9YM SMILES_CANONICAL CACTVS 3.385 "Cc1ncc(CO[P](O)(O)=O)c(CN[C@@H]2C[C@H](N)[C@@H](O)[C@H](O)[C@H]2O)c1O" 9YM SMILES CACTVS 3.385 "Cc1ncc(CO[P](O)(O)=O)c(CN[CH]2C[CH](N)[CH](O)[CH](O)[CH]2O)c1O" 9YM SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "Cc1c(c(c(cn1)COP(=O)(O)O)CN[C@@H]2C[C@@H]([C@H]([C@@H]([C@H]2O)O)O)N)O" 9YM SMILES "OpenEye OEToolkits" 2.0.6 "Cc1c(c(c(cn1)COP(=O)(O)O)CNC2CC(C(C(C2O)O)O)N)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 9YM "SYSTEMATIC NAME" ACDLabs 12.01 "[4-({[(1R,2S,3S,4R,5S)-5-amino-2,3,4-trihydroxycyclohexyl]amino}methyl)-5-hydroxy-6-methylpyridin-3-yl]methyl dihydrogen phosphate" 9YM "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "[4-[[[(1~{R},2~{S},3~{S},4~{R},5~{S})-5-azanyl-2,3,4-tris(oxidanyl)cyclohexyl]amino]methyl]-6-methyl-5-oxidanyl-pyridin-3-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 9YM "Create component" 2017-06-26 RCSB 9YM "Other modification" 2017-06-27 RCSB 9YM "Initial release" 2017-07-12 RCSB #