data_ME6 # _chem_comp.id ME6 _chem_comp.name "[(2R,3S,5R)-5-(4-azanyl-3-methyl-2-oxo-pyrimidin-3-ium-1-yl)-3-hydroxy-oxolan-2-yl]methyl dihydrogen phosphate" _chem_comp.type "DNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C10 H17 N3 O7 P" _chem_comp.mon_nstd_parent_comp_id DC _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 1 _chem_comp.pdbx_initial_date 2009-05-21 _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 322.232 _chem_comp.one_letter_code ? _chem_comp.three_letter_code ME6 _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 3H8X _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 ME6 O2 O2 O 0 1 N N N -8.930 9.508 -2.417 -3.272 -0.754 1.844 O2 ME6 1 ME6 C2 C2 C 0 1 N N N -8.302 8.516 -1.984 -3.260 -0.138 0.792 C2 ME6 2 ME6 N3 N3 N 1 1 N N N -9.020 7.416 -1.742 -4.297 0.636 0.474 N3 ME6 3 ME6 C20 C20 C 0 1 N N N -10.467 7.450 -2.007 -5.434 0.737 1.391 C20 ME6 4 ME6 C4 C4 C 0 1 N N N -8.433 6.295 -1.283 -4.310 1.317 -0.665 C4 ME6 5 ME6 N4 N4 N 0 1 N N N -9.167 5.174 -1.051 -5.385 2.113 -0.983 N4 ME6 6 ME6 C5 C5 C 0 1 N N N -7.061 6.271 -1.040 -3.214 1.219 -1.548 C5 ME6 7 ME6 C6 C6 C 0 1 N N N -6.305 7.411 -1.275 -2.168 0.429 -1.210 C6 ME6 8 ME6 N1 N1 N 0 1 N N N -6.888 8.525 -1.766 -2.198 -0.247 -0.027 N1 ME6 9 ME6 "C1'" "C1'" C 0 1 N N R -5.993 9.700 -1.945 -1.070 -1.101 0.353 C1* ME6 10 ME6 "O4'" "O4'" O 0 1 N N N -6.319 10.788 -2.828 0.170 -0.365 0.265 O4* ME6 11 ME6 "C2'" "C2'" C 0 1 N N N -4.531 9.358 -2.213 -0.913 -2.264 -0.652 C2* ME6 12 ME6 "C3'" "C3'" C 0 1 N N S -4.029 10.778 -2.275 0.615 -2.446 -0.780 C3* ME6 13 ME6 "O3'" "O3'" O 0 1 N N N -4.180 11.325 -0.978 1.002 -3.753 -0.351 O3* ME6 14 ME6 "C4'" "C4'" C 0 1 N N R -5.066 11.392 -3.175 1.202 -1.370 0.164 C4* ME6 15 ME6 "C5'" "C5'" C 0 1 N N N -4.767 10.784 -4.517 2.474 -0.768 -0.436 C5* ME6 16 ME6 "O5'" "O5'" O 0 1 N N N -6.032 10.289 -4.852 3.022 0.191 0.471 O5* ME6 17 ME6 P P P 0 1 N N N -6.143 8.904 -5.616 4.366 1.022 0.163 P ME6 18 ME6 O3P O3P O 0 1 N Y N -5.452 7.861 -4.762 4.120 1.991 -1.099 O1P ME6 19 ME6 O2P O2P O 0 1 N N N -5.681 9.101 -7.047 4.757 1.906 1.450 O2P ME6 20 ME6 H20 H20 H 0 1 N N N -11.015 7.458 -1.053 -5.266 1.557 2.089 H20 ME6 21 ME6 H20A H20A H 0 0 N N N -10.714 8.356 -2.579 -6.345 0.924 0.822 H20A ME6 22 ME6 H20B H20B H 0 0 N N N -10.754 6.560 -2.587 -5.538 -0.196 1.946 H20B ME6 23 ME6 HN4 HN4 H 0 1 N N N -8.577 4.440 -0.715 -6.137 2.178 -0.373 HN4 ME6 24 ME6 H5 H5 H 0 1 N N N -6.589 5.372 -0.672 -3.210 1.767 -2.478 H5 ME6 25 ME6 H6 H6 H 0 1 N N N -5.246 7.407 -1.064 -1.318 0.337 -1.870 H6 ME6 26 ME6 "H1'" "H1'" H 0 1 N N N -6.190 10.089 -0.935 -1.211 -1.488 1.362 H1* ME6 27 ME6 "H2'" "H2'" H 0 1 N N N -4.062 8.751 -1.425 -1.375 -3.171 -0.261 H2* ME6 28 ME6 "H2'A" "H2'A" H 0 0 N N N -4.326 8.725 -3.089 -1.351 -1.999 -1.614 H2*A ME6 29 ME6 "H3'" "H3'" H 0 1 N N N -2.989 10.914 -2.606 0.936 -2.272 -1.808 H3* ME6 30 ME6 "HO3'" "HO3'" H 0 0 N Y N -4.214 10.622 -0.339 0.613 -4.469 -0.872 HO3* ME6 31 ME6 "H4'" "H4'" H 0 1 N N N -5.079 12.491 -3.128 1.411 -1.800 1.144 H4* ME6 32 ME6 "H5'" "H5'" H 0 1 N N N -4.394 11.521 -5.243 3.203 -1.559 -0.612 H5* ME6 33 ME6 "H5'A" "H5'A" H 0 0 N N N -3.967 10.029 -4.510 2.234 -0.279 -1.380 H5*A ME6 34 ME6 HO3P HO3P H 0 0 N Y N -5.307 7.075 -5.276 3.410 2.634 -0.969 HO1P ME6 35 ME6 HO2P HO2P H 0 0 N N N -6.437 9.142 -7.621 5.559 2.435 1.335 HO2P ME6 36 ME6 O1P O1P O 0 1 N N N -6.695 7.229 -6.104 5.468 0.083 -0.144 O7 ME6 37 ME6 H17 H17 H 0 1 N N N -10.153 5.095 -1.195 -5.392 2.610 -1.816 H17 ME6 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 ME6 O2 C2 DOUB N N 1 ME6 C2 N1 SING N N 2 ME6 C2 N3 SING N N 3 ME6 N3 C4 DOUB N N 4 ME6 C20 N3 SING N N 5 ME6 C20 H20 SING N N 6 ME6 C20 H20A SING N N 7 ME6 C20 H20B SING N N 8 ME6 C4 N4 SING N N 9 ME6 C4 C5 SING N N 10 ME6 N4 HN4 SING N N 11 ME6 C5 H5 SING N N 12 ME6 C6 C5 DOUB N N 13 ME6 C6 H6 SING N N 14 ME6 N1 C6 SING N N 15 ME6 "C1'" N1 SING N N 16 ME6 "C1'" "H1'" SING N N 17 ME6 "O4'" "C1'" SING N N 18 ME6 "C2'" "C1'" SING N N 19 ME6 "C2'" "H2'" SING N N 20 ME6 "C2'" "H2'A" SING N N 21 ME6 "C3'" "C2'" SING N N 22 ME6 "C3'" "O3'" SING N N 23 ME6 "C3'" "H3'" SING N N 24 ME6 "O3'" "HO3'" SING N N 25 ME6 "C4'" "O4'" SING N N 26 ME6 "C4'" "C3'" SING N N 27 ME6 "C4'" "H4'" SING N N 28 ME6 "C5'" "C4'" SING N N 29 ME6 "C5'" "H5'" SING N N 30 ME6 "C5'" "H5'A" SING N N 31 ME6 "O5'" "C5'" SING N N 32 ME6 P "O5'" SING N N 33 ME6 P O3P SING N N 34 ME6 P O1P DOUB N N 35 ME6 O3P HO3P SING N N 36 ME6 O2P P SING N N 37 ME6 O2P HO2P SING N N 38 ME6 N4 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 ME6 SMILES_CANONICAL CACTVS 3.352 "C[N+]1=C(N)C=CN([C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=O)O2)C1=O" ME6 SMILES CACTVS 3.352 "C[N+]1=C(N)C=CN([CH]2C[CH](O)[CH](CO[P](O)(O)=O)O2)C1=O" ME6 SMILES_CANONICAL "OpenEye OEToolkits" 1.6.1 "C[N+]1=C(C=CN(C1=O)[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)O)O)N" ME6 SMILES "OpenEye OEToolkits" 1.6.1 "C[N+]1=C(C=CN(C1=O)C2CC(C(O2)COP(=O)(O)O)O)N" ME6 InChI InChI 1.03 "InChI=1S/C10H16N3O7P/c1-12-8(11)2-3-13(10(12)15)9-4-6(14)7(20-9)5-19-21(16,17)18/h2-3,6-7,9,11,14H,4-5H2,1H3,(H2,16,17,18)/p+1/t6-,7+,9+/m0/s1" ME6 InChIKey InChI 1.03 SXDBYGVVLMSJDZ-LKEWCRSYSA-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 ME6 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.6.1 "[(2R,3S,5R)-5-(4-azanyl-3-methyl-2-oxo-pyrimidin-3-ium-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 ME6 "Create component" 2009-05-21 RCSB ME6 "Modify descriptor" 2011-06-04 RCSB #