data_O8M # _chem_comp.id O8M _chem_comp.name "2-[{[(2R,3S,4R,5R)-5-(6-amino-8-methyl-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl}(methyl)amino]acetamide" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C14 H21 N7 O4" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "5'-[(carboxamidomethyl)methylamino]-5'-deoxy-8-methyladenosine" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2008-07-31 _chem_comp.pdbx_modified_date 2020-06-17 _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 351.361 _chem_comp.one_letter_code ? _chem_comp.three_letter_code O8M _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 3DZ7 _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 O8M O2 O2 O 0 1 N N N -16.845 -9.375 9.377 4.709 -2.169 -1.345 O2 O8M 1 O8M C4 C4 C 0 1 N N N -17.944 -9.302 8.880 5.166 -1.918 -0.250 C4 O8M 2 O8M C5 C5 C 0 1 N N N -18.266 -8.207 7.907 4.652 -0.734 0.528 C5 O8M 3 O8M N2 N2 N 0 1 N N N -17.440 -8.514 6.699 3.608 -0.053 -0.250 N2 O8M 4 O8M C6 C6 C 0 1 N N N -17.524 -9.855 6.213 4.167 0.547 -1.469 C6 O8M 5 O8M "C5'" "C5'" C 0 1 N N N -16.085 -8.060 6.831 2.919 0.956 0.566 "C5'" O8M 6 O8M "C4'" "C4'" C 0 1 N N R -15.511 -7.376 5.562 1.688 1.465 -0.187 "C4'" O8M 7 O8M "O4'" "O4'" O 0 1 N N N -16.395 -6.921 4.486 0.723 0.408 -0.317 "O4'" O8M 8 O8M "C1'" "C1'" C 0 1 N N R -15.987 -5.779 3.971 -0.584 1.018 -0.245 "C1'" O8M 9 O8M N5 N5 N 0 1 Y N N -17.209 -5.049 3.829 -1.594 0.030 0.137 N5 O8M 10 O8M C11 C11 C 0 1 Y N N -18.165 -5.035 4.698 -2.839 -0.117 -0.422 C11 O8M 11 O8M N4 N4 N 0 1 Y N N -18.384 -5.588 5.839 -3.511 0.496 -1.391 N4 O8M 12 O8M C10 C10 C 0 1 Y N N -19.434 -5.440 6.499 -4.729 0.113 -1.708 C10 O8M 13 O8M N3 N3 N 0 1 Y N N -20.355 -4.632 6.104 -5.342 -0.883 -1.095 N3 O8M 14 O8M C9 C9 C 0 1 Y N N -20.223 -4.043 4.955 -4.749 -1.556 -0.113 C9 O8M 15 O8M N7 N7 N 0 1 N N N -21.236 -3.232 4.491 -5.399 -2.598 0.524 N7 O8M 16 O8M C12 C12 C 0 1 Y N N -19.108 -4.272 4.210 -3.447 -1.184 0.262 C12 O8M 17 O8M N6 N6 N 0 1 Y N N -18.726 -3.789 3.073 -2.559 -1.624 1.185 N6 O8M 18 O8M C7 C7 C 0 1 Y N N -17.599 -4.246 2.857 -1.469 -0.917 1.110 C7 O8M 19 O8M "C2'" "C2'" C 0 1 N N R -14.986 -5.218 5.060 -0.422 2.090 0.862 "C2'" O8M 20 O8M "O2'" "O2'" O 0 1 N N N -14.171 -4.459 4.554 -1.372 3.144 0.696 "O2'" O8M 21 O8M "C3'" "C3'" C 0 1 N N S -14.263 -6.405 5.582 1.018 2.601 0.612 "C3'" O8M 22 O8M "O3'" "O3'" O 0 1 N N N -13.415 -6.905 4.804 0.995 3.806 -0.156 "O3'" O8M 23 O8M C8 C8 C 0 1 N N N -17.013 -3.836 1.687 -0.250 -1.114 1.973 C8 O8M 24 O8M N1 N1 N 0 1 N N N -18.863 -10.171 9.183 6.131 -2.700 0.272 N1 O8M 25 O8M H5 H5 H 0 1 N N N -19.338 -8.199 7.661 4.235 -1.076 1.475 H5 O8M 26 O8M H5A H5A H 0 1 N N N -18.043 -7.211 8.317 5.472 -0.042 0.721 H5A O8M 27 O8M H6 H6 H 0 1 N N N -17.546 -9.846 5.113 4.610 -0.234 -2.087 H6 O8M 28 O8M H6A H6A H 0 1 N N N -16.649 -10.425 6.558 3.373 1.045 -2.025 H6A O8M 29 O8M H6B H6B H 0 1 N N N -18.442 -10.326 6.594 4.932 1.275 -1.198 H6B O8M 30 O8M "H5'" "H5'" H 0 1 N N N -16.053 -7.329 7.652 2.609 0.510 1.510 "H5'" O8M 31 O8M "H5'A" "H5'A" H 0 0 N N N -15.469 -8.952 7.016 3.595 1.789 0.761 "H5'A" O8M 32 O8M "H4'" "H4'" H 0 1 N N N -15.126 -8.387 5.361 1.979 1.825 -1.173 "H4'" O8M 33 O8M "H1'" "H1'" H 0 1 N N N -15.463 -5.777 3.004 -0.843 1.482 -1.197 "H1'" O8M 34 O8M H10 H10 H 0 1 N N N -19.571 -5.998 7.414 -5.248 0.633 -2.500 H10 O8M 35 O8M HN7 HN7 H 0 1 N N N -21.874 -3.036 5.236 -6.298 -2.845 0.256 HN7 O8M 36 O8M HN7A HN7A H 0 0 N N N -20.848 -2.376 4.150 -4.956 -3.081 1.239 HN7A O8M 37 O8M "H2'" "H2'" H 0 1 N N N -15.527 -4.663 5.840 -0.509 1.643 1.852 "H2'" O8M 38 O8M "HO2'" "HO2'" H 0 0 N N N -14.432 -4.262 3.662 -1.311 3.839 1.365 "HO2'" O8M 39 O8M "H3'" "H3'" H 0 1 N N N -13.700 -6.205 6.505 1.537 2.759 1.557 "H3'" O8M 40 O8M "HO3'" "HO3'" H 0 0 N N N -13.806 -7.031 3.948 0.584 4.554 0.299 "HO3'" O8M 41 O8M H8 H8 H 0 1 N N N -17.783 -3.726 0.909 -0.338 -0.503 2.871 H8 O8M 42 O8M H8A H8A H 0 1 N N N -16.513 -2.869 1.847 -0.169 -2.164 2.254 H8A O8M 43 O8M H8B H8B H 0 1 N N N -16.273 -4.584 1.366 0.640 -0.817 1.418 H8B O8M 44 O8M HN1 HN1 H 0 1 N N N -18.508 -10.837 9.839 6.460 -3.464 -0.227 HN1 O8M 45 O8M HN1A HN1A H 0 0 N N N -19.792 -10.173 8.813 6.497 -2.499 1.148 HN1A O8M 46 # # 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 O8M O2 C4 DOUB N N 1 O8M C4 C5 SING N N 2 O8M C4 N1 SING N N 3 O8M C5 N2 SING N N 4 O8M N2 C6 SING N N 5 O8M N2 "C5'" SING N N 6 O8M "C5'" "C4'" SING N N 7 O8M "C4'" "O4'" SING N N 8 O8M "C4'" "C3'" SING N N 9 O8M "O4'" "C1'" SING N N 10 O8M "C1'" N5 SING N N 11 O8M "C1'" "C2'" SING N N 12 O8M N5 C11 SING Y N 13 O8M N5 C7 SING Y N 14 O8M C11 N4 DOUB Y N 15 O8M C11 C12 SING Y N 16 O8M N4 C10 SING Y N 17 O8M C10 N3 DOUB Y N 18 O8M N3 C9 SING Y N 19 O8M C9 N7 SING N N 20 O8M C9 C12 DOUB Y N 21 O8M C12 N6 SING Y N 22 O8M N6 C7 DOUB Y N 23 O8M C7 C8 SING N N 24 O8M "C2'" "O2'" SING N N 25 O8M "C2'" "C3'" SING N N 26 O8M "C3'" "O3'" SING N N 27 O8M C5 H5 SING N N 28 O8M C5 H5A SING N N 29 O8M C6 H6 SING N N 30 O8M C6 H6A SING N N 31 O8M C6 H6B SING N N 32 O8M "C5'" "H5'" SING N N 33 O8M "C5'" "H5'A" SING N N 34 O8M "C4'" "H4'" SING N N 35 O8M "C1'" "H1'" SING N N 36 O8M C10 H10 SING N N 37 O8M N7 HN7 SING N N 38 O8M N7 HN7A SING N N 39 O8M "C2'" "H2'" SING N N 40 O8M "O2'" "HO2'" SING N N 41 O8M "C3'" "H3'" SING N N 42 O8M "O3'" "HO3'" SING N N 43 O8M C8 H8 SING N N 44 O8M C8 H8A SING N N 45 O8M C8 H8B SING N N 46 O8M N1 HN1 SING N N 47 O8M N1 HN1A SING N N 48 # # 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 O8M SMILES ACDLabs 10.04 "O=C(N)CN(C)CC3OC(n2c(nc1c(ncnc12)N)C)C(O)C3O" O8M SMILES_CANONICAL CACTVS 3.341 "CN(C[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2c(C)nc3c(N)ncnc23)CC(N)=O" O8M SMILES CACTVS 3.341 "CN(C[CH]1O[CH]([CH](O)[CH]1O)n2c(C)nc3c(N)ncnc23)CC(N)=O" O8M SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "Cc1nc2c(ncnc2n1[C@H]3[C@@H]([C@@H]([C@H](O3)C[N@@](C)CC(=O)N)O)O)N" O8M SMILES "OpenEye OEToolkits" 1.5.0 "Cc1nc2c(ncnc2n1C3C(C(C(O3)CN(C)CC(=O)N)O)O)N" O8M InChI InChI 1.03 "InChI=1S/C14H21N7O4/c1-6-19-9-12(16)17-5-18-13(9)21(6)14-11(24)10(23)7(25-14)3-20(2)4-8(15)22/h5,7,10-11,14,23-24H,3-4H2,1-2H3,(H2,15,22)(H2,16,17,18)/t7-,10-,11-,14-/m1/s1" O8M InChIKey InChI 1.03 IRWBMXVMEDHEJW-FRJWGUMJSA-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 O8M "SYSTEMATIC NAME" ACDLabs 10.04 "2-[{[(2R,3S,4R,5R)-5-(6-amino-8-methyl-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl}(methyl)amino]acetamide" O8M "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "2-[[(2R,3S,4R,5R)-5-(6-amino-8-methyl-purin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl-methyl-amino]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 O8M "Create component" 2008-07-31 RCSB O8M "Modify aromatic_flag" 2011-06-04 RCSB O8M "Modify descriptor" 2011-06-04 RCSB O8M "Modify synonyms" 2020-06-05 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id O8M _pdbx_chem_comp_synonyms.name "5'-[(carboxamidomethyl)methylamino]-5'-deoxy-8-methyladenosine" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##