data_D8M # _chem_comp.id D8M _chem_comp.name "2-[(2S,3R,4S,5R)-5-(aminomethyl)-3,4-dihydroxytetrahydrofuran-2-yl]-N-(pyridin-2-ylmethyl)acetamide" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C13 H19 N3 O4" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2017-10-23 _chem_comp.pdbx_modified_date 2020-04-17 _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 281.308 _chem_comp.one_letter_code ? _chem_comp.three_letter_code D8M _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 5QBH _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 D8M O3 O1 O 0 1 N N N 3.202 6.490 8.994 3.348 -2.683 0.079 O3 D8M 1 D8M C4 C1 C 0 1 Y N N -2.995 2.830 10.254 -4.915 -0.720 0.831 C4 D8M 2 D8M C5 C2 C 0 1 N N N -2.185 4.123 8.239 -2.744 0.516 0.868 C5 D8M 3 D8M C6 C3 C 0 1 N N N -0.902 6.124 8.790 -0.447 -0.154 0.409 C6 D8M 4 D8M N1 N1 N 0 1 N N N -1.151 5.110 7.965 -1.753 -0.221 0.081 N1 D8M 5 D8M C7 C4 C 0 1 N N N 0.112 7.133 8.296 0.573 -0.912 -0.400 C7 D8M 6 D8M C8 C5 C 0 1 N N S 1.077 7.585 9.391 1.968 -0.668 0.179 C8 D8M 7 D8M N2 N2 N 0 1 N N N 0.714 11.708 9.904 4.011 3.161 0.264 N2 D8M 8 D8M C9 C6 C 0 1 N N R 2.532 7.743 8.986 3.026 -1.472 -0.608 C9 D8M 9 D8M C10 C7 C 0 1 N N S 3.066 8.659 10.083 4.252 -0.534 -0.656 C10 D8M 10 D8M C11 C8 C 0 1 N N R 1.885 9.591 10.344 3.790 0.727 0.109 C11 D8M 11 D8M C12 C9 C 0 1 N N N 1.971 10.961 9.640 4.363 1.986 -0.545 C12 D8M 12 D8M O O2 O 0 1 N N N -1.455 6.249 9.880 -0.094 0.515 1.357 O D8M 13 D8M C3 C10 C 0 1 Y N N -1.942 3.308 9.488 -4.118 0.275 0.297 C3 D8M 14 D8M N N3 N 0 1 Y N N -0.660 3.042 9.781 -4.546 1.016 -0.706 N D8M 15 D8M C2 C11 C 0 1 Y N N -0.418 2.265 10.848 -5.740 0.841 -1.237 C2 D8M 16 D8M C1 C12 C 0 1 Y N N -1.407 1.739 11.652 -6.592 -0.134 -0.756 C1 D8M 17 D8M C C13 C 0 1 Y N N -2.712 2.032 11.347 -6.177 -0.934 0.298 C D8M 18 D8M O1 O3 O 0 1 N N N 0.706 8.889 9.885 2.350 0.714 0.004 O1 D8M 19 D8M O2 O4 O 0 1 N N N 3.412 7.924 11.252 5.370 -1.136 0.001 O2 D8M 20 D8M H1 H1 H 0 1 N N N 4.108 6.613 8.738 4.008 -3.227 -0.371 H1 D8M 21 D8M H2 H2 H 0 1 N N N -4.016 3.076 10.002 -4.557 -1.327 1.650 H2 D8M 22 D8M H3 H3 H 0 1 N N N -3.144 4.649 8.351 -2.715 0.172 1.902 H3 D8M 23 D8M H4 H4 H 0 1 N N N -2.242 3.435 7.383 -2.518 1.581 0.833 H4 D8M 24 D8M H5 H5 H 0 1 N N N -0.610 5.023 7.129 -2.035 -0.756 -0.677 H5 D8M 25 D8M H6 H6 H 0 1 N N N 0.693 6.677 7.481 0.347 -1.978 -0.365 H6 D8M 26 D8M H7 H7 H 0 1 N N N -0.425 8.014 7.915 0.544 -0.569 -1.434 H7 D8M 27 D8M H8 H8 H 0 1 N N N 1.026 6.857 10.214 1.992 -0.938 1.235 H8 D8M 28 D8M H9 H9 H 0 1 N N N 0.755 12.600 9.453 4.331 3.053 1.215 H9 D8M 29 D8M H10 H10 H 0 1 N N N -0.063 11.189 9.547 4.379 4.006 -0.147 H10 D8M 30 D8M H12 H12 H 0 1 N N N 2.605 8.239 8.007 2.669 -1.689 -1.615 H12 D8M 31 D8M H13 H13 H 0 1 N N N 3.922 9.237 9.704 4.503 -0.285 -1.687 H13 D8M 32 D8M H14 H14 H 0 1 N N N 1.811 9.764 11.428 4.096 0.670 1.153 H14 D8M 33 D8M H15 H15 H 0 1 N N N 2.095 10.814 8.557 3.947 2.096 -1.546 H15 D8M 34 D8M H16 H16 H 0 1 N N N 2.828 11.527 10.033 5.448 1.901 -0.610 H16 D8M 35 D8M H17 H17 H 0 1 N N N 0.610 2.039 11.091 -6.056 1.468 -2.058 H17 D8M 36 D8M H18 H18 H 0 1 N N N -1.161 1.114 12.498 -7.569 -0.273 -1.196 H18 D8M 37 D8M H19 H19 H 0 1 N N N -3.513 1.642 11.957 -6.820 -1.707 0.692 H19 D8M 38 D8M H20 H20 H 0 1 N N N 3.740 8.519 11.915 5.663 -1.964 -0.402 H20 D8M 39 # # 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 D8M N1 C5 SING N N 1 D8M N1 C6 SING N N 2 D8M C5 C3 SING N N 3 D8M C7 C6 SING N N 4 D8M C7 C8 SING N N 5 D8M C6 O DOUB N N 6 D8M C9 O3 SING N N 7 D8M C9 C8 SING N N 8 D8M C9 C10 SING N N 9 D8M C8 O1 SING N N 10 D8M C3 N DOUB Y N 11 D8M C3 C4 SING Y N 12 D8M C12 N2 SING N N 13 D8M C12 C11 SING N N 14 D8M N C2 SING Y N 15 D8M O1 C11 SING N N 16 D8M C10 C11 SING N N 17 D8M C10 O2 SING N N 18 D8M C4 C DOUB Y N 19 D8M C2 C1 DOUB Y N 20 D8M C C1 SING Y N 21 D8M O3 H1 SING N N 22 D8M C4 H2 SING N N 23 D8M C5 H3 SING N N 24 D8M C5 H4 SING N N 25 D8M N1 H5 SING N N 26 D8M C7 H6 SING N N 27 D8M C7 H7 SING N N 28 D8M C8 H8 SING N N 29 D8M N2 H9 SING N N 30 D8M N2 H10 SING N N 31 D8M C9 H12 SING N N 32 D8M C10 H13 SING N N 33 D8M C11 H14 SING N N 34 D8M C12 H15 SING N N 35 D8M C12 H16 SING N N 36 D8M C2 H17 SING N N 37 D8M C1 H18 SING N N 38 D8M C H19 SING N N 39 D8M O2 H20 SING N N 40 # # 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 D8M SMILES ACDLabs 12.01 "OC2C(CC(=O)NCc1ccccn1)OC(C2O)CN" D8M InChI InChI 1.03 "InChI=1S/C13H19N3O4/c14-6-10-13(19)12(18)9(20-10)5-11(17)16-7-8-3-1-2-4-15-8/h1-4,9-10,12-13,18-19H,5-7,14H2,(H,16,17)/t9-,10+,12-,13+/m0/s1" D8M InChIKey InChI 1.03 BIGFPMOCLWRIMB-JULQROHOSA-N D8M SMILES_CANONICAL CACTVS 3.385 "NC[C@H]1O[C@@H](CC(=O)NCc2ccccn2)[C@H](O)[C@@H]1O" D8M SMILES CACTVS 3.385 "NC[CH]1O[CH](CC(=O)NCc2ccccn2)[CH](O)[CH]1O" D8M SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "c1ccnc(c1)CNC(=O)C[C@H]2[C@@H]([C@@H]([C@H](O2)CN)O)O" D8M SMILES "OpenEye OEToolkits" 2.0.6 "c1ccnc(c1)CNC(=O)CC2C(C(C(O2)CN)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 D8M "SYSTEMATIC NAME" ACDLabs 12.01 "2-[(2S,3R,4S,5R)-5-(aminomethyl)-3,4-dihydroxytetrahydrofuran-2-yl]-N-(pyridin-2-ylmethyl)acetamide (non-preferred name)" D8M "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "2-[(2~{S},3~{R},4~{S},5~{R})-5-(aminomethyl)-3,4-bis(oxidanyl)oxolan-2-yl]-~{N}-(pyridin-2-ylmethyl)ethanamide" # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site D8M "Create component" 2017-10-23 RCSB D8M "Initial release" 2020-04-22 RCSB ##