data_MDJ # _chem_comp.id MDJ _chem_comp.name "4-amino-1-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-3-(hydroxymethyl)pyridin-2(1H)-one" _chem_comp.type "DNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C11 H17 N2 O8 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2010-07-23 _chem_comp.pdbx_modified_date 2011-06-04 _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 336.235 _chem_comp.one_letter_code ? _chem_comp.three_letter_code MDJ _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 3O1V _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 MDJ P P P 0 1 N N N 0.777 0.578 -1.169 -4.546 1.144 -0.038 P MDJ 1 MDJ N1 N1 N 0 1 N N N 0.141 -1.543 3.492 1.968 -0.435 0.039 N1 MDJ 2 MDJ C2 C2 C 0 1 N N N -0.539 -2.289 4.435 3.088 -0.153 -0.653 C2 MDJ 3 MDJ O2 O2 O 0 1 N N N 0.103 -2.977 5.267 3.167 -0.456 -1.833 O2 MDJ 4 MDJ C3 C3 C 0 1 N N N -1.961 -2.309 4.490 4.161 0.484 -0.023 C3 MDJ 5 MDJ C4 C4 C 0 1 N N N -2.669 -1.512 3.558 4.053 0.820 1.317 C4 MDJ 6 MDJ N4 N4 N 0 1 N N N -4.072 -1.506 3.508 5.096 1.452 1.969 N4 MDJ 7 MDJ C5 C5 C 0 1 N N N -1.970 -0.713 2.642 2.861 0.506 2.006 C5 MDJ 8 MDJ C6 C6 C 0 1 N N N -0.568 -0.739 2.639 1.853 -0.109 1.354 C6 MDJ 9 MDJ "C1'" C1* C 0 1 N N R 1.597 -1.631 3.383 0.851 -1.098 -0.639 C1* MDJ 10 MDJ O1P O1P O 0 1 N N N 1.434 1.689 -1.955 -5.805 0.153 0.124 O1P MDJ 11 MDJ "C2'" C2* C 0 1 N N N 2.060 -3.024 2.883 0.626 -2.497 -0.033 C2* MDJ 12 MDJ C20 C20 C 0 1 N N N -2.717 -3.147 5.466 5.418 0.802 -0.791 C20 MDJ 13 MDJ O21 O21 O 0 1 N N N -3.496 -2.324 6.329 5.097 1.638 -1.905 O21 MDJ 14 MDJ O2P O2P O 0 1 N N N -0.399 1.109 -0.450 -4.281 1.819 1.252 O2P MDJ 15 MDJ "C3'" C3* C 0 1 N N S 3.217 -2.723 1.924 -0.837 -2.461 0.472 C3* MDJ 16 MDJ "O3'" O3* O 0 1 N N N 4.466 -2.771 2.611 -1.505 -3.691 0.188 O3* MDJ 17 MDJ "C4'" C4* C 0 1 N N R 2.899 -1.293 1.442 -1.439 -1.299 -0.360 C4* MDJ 18 MDJ "O4'" O4* O 0 1 N N N 2.225 -0.648 2.532 -0.358 -0.346 -0.439 O4* MDJ 19 MDJ "C5'" C5* C 0 1 N N N 2.027 -1.240 0.158 -2.644 -0.689 0.360 C5* MDJ 20 MDJ "O5'" O5* O 0 1 N N N 1.789 0.036 -0.169 -3.249 0.298 -0.477 O5* MDJ 21 MDJ HN4 HN4 H 0 1 N N N -4.378 -0.883 2.788 5.872 1.750 1.469 HN4 MDJ 22 MDJ HN4A HN4A H 0 0 N N N -4.402 -2.429 3.313 5.052 1.597 2.927 HN4A MDJ 23 MDJ H5 H5 H 0 1 N N N -2.506 -0.084 1.946 2.757 0.759 3.050 H5 MDJ 24 MDJ H6 H6 H 0 1 N N N -0.032 -0.108 1.945 0.943 -0.347 1.884 H6 MDJ 25 MDJ "H1'" H1* H 0 1 N N N 1.920 -1.437 4.416 1.063 -1.185 -1.705 H1* MDJ 26 MDJ "H2'" H2* H 0 1 N N N 2.392 -3.656 3.720 0.748 -3.266 -0.795 H2* MDJ 27 MDJ "H2'A" H2*A H 0 0 N N N 1.244 -3.552 2.368 1.312 -2.668 0.797 H2*A MDJ 28 MDJ H20 H20 H 0 1 N N N -3.384 -3.827 4.917 6.121 1.320 -0.139 H20 MDJ 29 MDJ H20A H20A H 0 0 N N N -2.005 -3.730 6.069 5.868 -0.123 -1.150 H20A MDJ 30 MDJ HO21 HO21 H 0 0 N N N -3.971 -2.870 6.944 5.860 1.883 -2.445 HO21 MDJ 31 MDJ "H3'" H3* H 0 1 N N N 3.306 -3.446 1.100 -0.875 -2.237 1.538 H3* MDJ 32 MDJ "HO3'" HO3* H 0 0 N N N 5.170 -2.582 2.002 -1.108 -4.463 0.615 HO3* MDJ 33 MDJ "H4'" H4* H 0 1 N N N 3.836 -0.789 1.163 -1.720 -1.645 -1.355 H4* MDJ 34 MDJ "H5'" H5* H 0 1 N N N 2.559 -1.736 -0.667 -3.369 -1.472 0.582 H5* MDJ 35 MDJ "H5'A" H5*A H 0 0 N N N 1.073 -1.755 0.342 -2.315 -0.225 1.290 H5*A MDJ 36 MDJ O8 O8 O 0 1 N N N 0.340 -0.506 -2.126 -4.873 2.248 -1.163 O8 MDJ 37 MDJ H16 H16 H 0 1 N N N 0.954 2.498 -1.823 -6.036 -0.324 -0.685 H16 MDJ 38 MDJ H17 H17 H 0 1 N N N -0.601 -0.621 -2.067 -5.644 2.796 -0.964 H17 MDJ 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 MDJ P O1P SING N N 1 MDJ P O2P DOUB N N 2 MDJ P "O5'" SING N N 3 MDJ N1 C2 SING N N 4 MDJ N1 C6 SING N N 5 MDJ N1 "C1'" SING N N 6 MDJ C2 O2 DOUB N N 7 MDJ C2 C3 SING N N 8 MDJ C3 C4 DOUB N N 9 MDJ C3 C20 SING N N 10 MDJ C4 N4 SING N N 11 MDJ C4 C5 SING N N 12 MDJ N4 HN4 SING N N 13 MDJ N4 HN4A SING N N 14 MDJ C5 C6 DOUB N N 15 MDJ C5 H5 SING N N 16 MDJ C6 H6 SING N N 17 MDJ "C1'" "C2'" SING N N 18 MDJ "C1'" "O4'" SING N N 19 MDJ "C1'" "H1'" SING N N 20 MDJ "C2'" "C3'" SING N N 21 MDJ "C2'" "H2'" SING N N 22 MDJ "C2'" "H2'A" SING N N 23 MDJ C20 O21 SING N N 24 MDJ C20 H20 SING N N 25 MDJ C20 H20A SING N N 26 MDJ O21 HO21 SING N N 27 MDJ "C3'" "O3'" SING N N 28 MDJ "C3'" "C4'" SING N N 29 MDJ "C3'" "H3'" SING N N 30 MDJ "O3'" "HO3'" SING N N 31 MDJ "C4'" "O4'" SING N N 32 MDJ "C4'" "C5'" SING N N 33 MDJ "C4'" "H4'" SING N N 34 MDJ "C5'" "O5'" SING N N 35 MDJ "C5'" "H5'" SING N N 36 MDJ "C5'" "H5'A" SING N N 37 MDJ O8 P SING N N 38 MDJ O1P H16 SING N N 39 MDJ O8 H17 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 MDJ SMILES ACDLabs 12.01 "O=P(O)(O)OCC2OC(N1C(=O)C(=C(N)C=C1)CO)CC2O" MDJ SMILES_CANONICAL CACTVS 3.370 "NC1=C(CO)C(=O)N(C=C1)[C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=O)O2" MDJ SMILES CACTVS 3.370 "NC1=C(CO)C(=O)N(C=C1)[CH]2C[CH](O)[CH](CO[P](O)(O)=O)O2" MDJ SMILES_CANONICAL "OpenEye OEToolkits" 1.7.0 "C1[C@@H]([C@H](O[C@H]1N2C=CC(=C(C2=O)CO)N)COP(=O)(O)O)O" MDJ SMILES "OpenEye OEToolkits" 1.7.0 "C1C(C(OC1N2C=CC(=C(C2=O)CO)N)COP(=O)(O)O)O" MDJ InChI InChI 1.03 "InChI=1S/C11H17N2O8P/c12-7-1-2-13(11(16)6(7)4-14)10-3-8(15)9(21-10)5-20-22(17,18)19/h1-2,8-10,14-15H,3-5,12H2,(H2,17,18,19)/t8-,9+,10+/m0/s1" MDJ InChIKey InChI 1.03 FIHVBWHWCWOFPJ-IVZWLZJFSA-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 MDJ "SYSTEMATIC NAME" ACDLabs 12.01 "4-amino-1-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-3-(hydroxymethyl)pyridin-2(1H)-one" MDJ "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.0 "[(2R,3S,5R)-5-[4-azanyl-3-(hydroxymethyl)-2-oxo-pyridin-1-yl]-3-hydroxy-oxolan-2-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 MDJ "Create component" 2010-07-23 RCSB MDJ "Modify descriptor" 2011-06-04 RCSB #