data_MDK # _chem_comp.id MDK _chem_comp.name "4-amino-1-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-3-methylpyridin-2(1H)-one" _chem_comp.type "DNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C11 H17 N2 O7 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 320.236 _chem_comp.one_letter_code ? _chem_comp.three_letter_code MDK _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 3O1R _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 MDK P P P 0 1 N N N 0.680 0.731 -1.299 4.339 1.041 0.101 P MDK 1 MDK N1 N1 N 0 1 N N N 1.144 -2.182 3.156 -2.233 -0.278 0.118 N1 MDK 2 MDK C2 C2 C 0 1 N N N 0.816 -3.135 4.100 -3.308 -0.065 0.900 C2 MDK 3 MDK O2 O2 O 0 1 N N N 1.717 -3.851 4.603 -3.346 -0.541 2.024 O2 MDK 4 MDK C3 C3 C 0 1 N N N -0.527 -3.332 4.525 -4.380 0.698 0.428 C3 MDK 5 MDK C4 C4 C 0 1 N N N -1.533 -2.516 3.953 -4.318 1.229 -0.850 C4 MDK 6 MDK N4 N4 N 0 1 N N N -2.887 -2.662 4.293 -5.361 1.989 -1.347 N4 MDK 7 MDK C5 C5 C 0 1 N N N -1.184 -1.528 3.020 -3.173 0.982 -1.637 C5 MDK 8 MDK C6 C6 C 0 1 N N N 0.159 -1.376 2.645 -2.163 0.239 -1.137 C6 MDK 9 MDK "C1'" C1* C 0 1 N N R 2.522 -2.050 2.688 -1.116 -1.075 0.631 C1* MDK 10 MDK O1P O1P O 0 1 N N N 0.079 -0.241 -2.234 4.045 1.913 -1.059 O1P MDK 11 MDK "C2'" C2* C 0 1 N N N 2.967 -3.270 1.842 -0.978 -2.372 -0.188 C2* MDK 12 MDK C21 C21 C 0 1 N N N -0.902 -4.351 5.543 -5.586 0.940 1.298 C21 MDK 13 MDK O2P O2P O 0 1 N N N 1.136 1.956 -2.059 4.763 1.949 1.361 O2P MDK 14 MDK "C3'" C3* C 0 1 N N S 3.927 -2.665 0.814 0.461 -2.312 -0.756 C3* MDK 15 MDK "O3'" O3* O 0 1 N N N 5.255 -2.592 1.337 1.088 -3.594 -0.693 O3* MDK 16 MDK "C4'" C4* C 0 1 N N R 3.349 -1.248 0.626 1.149 -1.312 0.209 C4* MDK 17 MDK "O4'" O4* O 0 1 N N N 2.814 -0.871 1.906 0.114 -0.345 0.485 O4* MDK 18 MDK "C5'" C5* C 0 1 N N N 2.254 -1.137 -0.469 2.345 -0.643 -0.471 C5* MDK 19 MDK "O5'" O5* O 0 1 N N N 1.881 0.143 -0.575 3.029 0.183 0.473 O5* MDK 20 MDK HN4 HN4 H 0 1 N N N -3.433 -1.996 3.784 -6.144 2.154 -0.799 HN4 MDK 21 MDK HN4A HN4A H 0 0 N N N -3.190 -3.587 4.063 -5.310 2.357 -2.243 HN4A MDK 22 MDK H5 H5 H 0 1 N N N -1.944 -0.889 2.594 -3.104 1.387 -2.636 H5 MDK 23 MDK H6 H6 H 0 1 N N N 0.424 -0.605 1.936 -1.289 0.053 -1.742 H6 MDK 24 MDK "H1'" H1* H 0 1 N N N 3.081 -1.974 3.632 -1.284 -1.316 1.681 H1* MDK 25 MDK "H2'" H2* H 0 1 N N N 3.467 -4.029 2.462 -1.098 -3.244 0.455 H2* MDK 26 MDK "H2'A" H2*A H 0 0 N N N 2.109 -3.756 1.354 -1.707 -2.391 -0.998 H2*A MDK 27 MDK H21 H21 H 0 1 N N N -1.989 -4.321 5.710 -5.437 1.848 1.882 H21 MDK 28 MDK H21A H21A H 0 0 N N N -0.614 -5.350 5.185 -6.470 1.053 0.670 H21A MDK 29 MDK H21B H21B H 0 0 N N N -0.380 -4.135 6.487 -5.725 0.093 1.971 H21B MDK 30 MDK "H3'" H3* H 0 1 N N N 4.001 -3.249 -0.115 0.461 -1.930 -1.777 H3* MDK 31 MDK "HO3'" HO3* H 0 0 N N N 5.833 -2.214 0.684 0.640 -4.277 -1.211 HO3* MDK 32 MDK "H4'" H4* H 0 1 N N N 4.150 -0.581 0.276 1.459 -1.815 1.125 H4* MDK 33 MDK "H5'" H5* H 0 1 N N N 2.655 -1.488 -1.432 3.025 -1.408 -0.844 H5* MDK 34 MDK "H5'A" H5*A H 0 0 N N N 1.387 -1.754 -0.191 1.994 -0.032 -1.302 H5*A MDK 35 MDK O7 O7 O 0 1 N N N -0.341 1.151 -0.267 5.546 0.042 -0.271 O7 MDK 36 MDK H16 H16 H 0 1 N N N 0.941 1.847 -2.982 5.547 2.493 1.208 H16 MDK 37 MDK H17 H17 H 0 1 N N N -1.162 0.702 -0.432 5.793 -0.560 0.444 H17 MDK 38 # 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 MDK P O1P DOUB N N 1 MDK P O2P SING N N 2 MDK P "O5'" SING N N 3 MDK N1 C2 SING N N 4 MDK N1 C6 SING N N 5 MDK N1 "C1'" SING N N 6 MDK C2 O2 DOUB N N 7 MDK C2 C3 SING N N 8 MDK C3 C4 DOUB N N 9 MDK C3 C21 SING N N 10 MDK C4 N4 SING N N 11 MDK C4 C5 SING N N 12 MDK N4 HN4 SING N N 13 MDK N4 HN4A SING N N 14 MDK C5 C6 DOUB N N 15 MDK C5 H5 SING N N 16 MDK C6 H6 SING N N 17 MDK "C1'" "C2'" SING N N 18 MDK "C1'" "O4'" SING N N 19 MDK "C1'" "H1'" SING N N 20 MDK "C2'" "C3'" SING N N 21 MDK "C2'" "H2'" SING N N 22 MDK "C2'" "H2'A" SING N N 23 MDK C21 H21 SING N N 24 MDK C21 H21A SING N N 25 MDK C21 H21B SING N N 26 MDK "C3'" "O3'" SING N N 27 MDK "C3'" "C4'" SING N N 28 MDK "C3'" "H3'" SING N N 29 MDK "O3'" "HO3'" SING N N 30 MDK "C4'" "O4'" SING N N 31 MDK "C4'" "C5'" SING N N 32 MDK "C4'" "H4'" SING N N 33 MDK "C5'" "O5'" SING N N 34 MDK "C5'" "H5'" SING N N 35 MDK "C5'" "H5'A" SING N N 36 MDK O7 P SING N N 37 MDK O2P H16 SING N N 38 MDK O7 H17 SING N N 39 # 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 MDK SMILES ACDLabs 12.01 "O=P(O)(O)OCC2OC(N1C(=O)C(=C(N)C=C1)C)CC2O" MDK SMILES_CANONICAL CACTVS 3.370 "CC1=C(N)C=CN([C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=O)O2)C1=O" MDK SMILES CACTVS 3.370 "CC1=C(N)C=CN([CH]2C[CH](O)[CH](CO[P](O)(O)=O)O2)C1=O" MDK SMILES_CANONICAL "OpenEye OEToolkits" 1.7.0 "CC1=C(C=CN(C1=O)[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)O)O)N" MDK SMILES "OpenEye OEToolkits" 1.7.0 "CC1=C(C=CN(C1=O)C2CC(C(O2)COP(=O)(O)O)O)N" MDK InChI InChI 1.03 "InChI=1S/C11H17N2O7P/c1-6-7(12)2-3-13(11(6)15)10-4-8(14)9(20-10)5-19-21(16,17)18/h2-3,8-10,14H,4-5,12H2,1H3,(H2,16,17,18)/t8-,9+,10+/m0/s1" MDK InChIKey InChI 1.03 OHKFCCHWVFFUOJ-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 MDK "SYSTEMATIC NAME" ACDLabs 12.01 "4-amino-1-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-3-methylpyridin-2(1H)-one" MDK "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.0 "[(2R,3S,5R)-5-(4-azanyl-3-methyl-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 MDK "Create component" 2010-07-23 RCSB MDK "Modify descriptor" 2011-06-04 RCSB #