data_NYM # _chem_comp.id NYM _chem_comp.name "3'-DEOXY-3'-AMINOTHYMIDINE MONOPHOSPHATE" _chem_comp.type "DNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C10 H16 N3 O7 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "PHOSPHORIC ACID MONO-[3-AMINO-5-(5-METHYL-2,4-DIOXO-3,4-DIHYDRO-2H-PYRIMIDIN-1-YL)-TETRAHYDRO-FURAN-2-YLMETHYL] ESTER" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2003-01-15 _chem_comp.pdbx_modified_date 2021-03-13 _chem_comp.pdbx_ambiguous_flag N _chem_comp.pdbx_release_status REL _chem_comp.pdbx_replaced_by ? _chem_comp.pdbx_replaces T37 _chem_comp.formula_weight 321.224 _chem_comp.one_letter_code N _chem_comp.three_letter_code NYM _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag N _chem_comp.pdbx_ideal_coordinates_details ? _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 1NMZ _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 NYM N1 N1 N 0 1 N N N 13.411 77.709 24.069 2.302 -0.342 -0.391 N1 NYM 1 NYM C6 C6 C 0 1 N N N 12.696 76.830 23.319 3.408 -0.195 -1.184 C6 NYM 2 NYM C2 C2 C 0 1 N N N 13.808 79.004 23.630 2.249 0.232 0.825 C2 NYM 3 NYM O2 O2 O 0 1 N N N 14.484 79.727 24.367 1.257 0.087 1.513 O2 NYM 4 NYM N3 N3 N 0 1 N N N 13.336 79.377 22.417 3.279 0.964 1.290 N3 NYM 5 NYM C4 C4 C 0 1 N N N 12.575 78.536 21.592 4.388 1.129 0.541 C4 NYM 6 NYM O4 O4 O 0 1 N N N 12.240 79.043 20.399 5.320 1.791 0.961 O4 NYM 7 NYM C5 C5 C 0 1 N N N 12.241 77.175 22.107 4.455 0.535 -0.742 C5 NYM 8 NYM C7 C7 C 0 1 N N N 11.395 76.340 21.134 5.681 0.708 -1.601 C7 NYM 9 NYM "O4'" O4* O 0 1 N N N 14.642 76.069 25.048 -0.042 -0.359 -0.780 "O4'" NYM 10 NYM "N3'" N3* N 0 1 N N N 14.220 76.133 28.361 -1.142 -3.544 0.572 "N3'" NYM 11 NYM "C1'" C1* C 0 1 N N R 13.969 77.201 25.374 1.166 -1.133 -0.870 "C1'" NYM 12 NYM "C2'" C2* C 0 1 N N N 12.916 76.698 26.381 0.983 -2.379 0.019 "C2'" NYM 13 NYM "C3'" C3* C 0 1 N N S 13.594 75.540 27.101 -0.459 -2.244 0.568 "C3'" NYM 14 NYM "C4'" C4* C 0 1 N N S 14.787 75.246 26.192 -1.108 -1.280 -0.457 "C4'" NYM 15 NYM "O5'" O5* O 0 1 N N N 13.498 73.264 25.851 -2.942 0.250 -0.824 "O5'" NYM 16 NYM "C5'" C5* C 0 1 N N N 14.888 73.703 25.935 -2.291 -0.542 0.172 "C5'" NYM 17 NYM P1 P1 P 0 1 N N N 13.018 71.741 26.106 -4.170 0.995 -0.096 P1 NYM 18 NYM OP2 OP2 O 0 1 N N N 13.627 71.047 27.280 -4.871 2.010 -1.131 OP2 NYM 19 NYM OP1 OP1 O 0 1 N N N 11.587 71.814 25.809 -3.666 1.752 1.072 OP1 NYM 20 NYM OP3 OP3 O 0 1 N N N 14.039 71.077 24.986 -5.245 -0.098 0.395 OP3 NYM 21 NYM HC61 1HC6 H 0 0 N N N 12.481 75.817 23.701 3.442 -0.659 -2.158 HC61 NYM 22 NYM HN31 1HN3 H 0 0 N N N 13.561 80.324 22.114 3.224 1.371 2.169 HN31 NYM 23 NYM HC71 1HC7 H 0 0 N N N 11.016 76.627 20.125 5.565 1.594 -2.225 HC71 NYM 24 NYM HC72 2HC7 H 0 0 N N N 11.960 75.390 20.983 6.557 0.825 -0.963 HC72 NYM 25 NYM HC73 3HC7 H 0 0 N N N 10.496 76.023 21.713 5.807 -0.170 -2.235 HC73 NYM 26 NYM "H3'1" 1H3* H 0 0 N N N 14.674 75.357 28.843 -0.613 -4.148 1.183 "H3'1" NYM 27 NYM "H3'2" 2H3* H 0 0 N N N 13.555 76.640 28.944 -2.038 -3.400 1.011 "H3'2" NYM 28 NYM "H1'1" 1H1* H 0 0 N N N 14.537 78.041 25.835 1.335 -1.437 -1.903 "H1'1" NYM 29 NYM "H2'1" 1H2* H 0 0 N N N 12.524 77.489 27.062 1.082 -3.288 -0.573 "H2'1" NYM 30 NYM "H2'2" 2H2* H 0 0 N N N 11.935 76.434 25.919 1.704 -2.374 0.836 "H2'2" NYM 31 NYM HC31 1HC3 H 0 0 N N N 12.921 74.677 27.319 -0.455 -1.806 1.566 HC31 NYM 32 NYM "H4'1" 1H4* H 0 0 N N N 15.773 75.500 26.645 -1.425 -1.823 -1.347 "H4'1" NYM 33 NYM "H5'1" 1H5* H 0 0 N N N 15.509 73.425 25.051 -2.997 -1.266 0.578 "H5'1" NYM 34 NYM "H5'2" 2H5* H 0 0 N N N 15.497 73.152 26.689 -1.932 0.104 0.973 "H5'2" NYM 35 NYM HP31 1HP3 H 0 0 N N N 13.345 70.152 27.429 -5.600 2.434 -0.657 HP31 NYM 36 NYM HP21 1HP2 H 0 0 N N N 13.757 70.182 25.135 -5.548 -0.567 -0.394 HP21 NYM 37 # # 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 NYM N1 C6 SING N N 1 NYM N1 C2 SING N N 2 NYM N1 "C1'" SING N N 3 NYM C6 C5 DOUB N N 4 NYM C6 HC61 SING N N 5 NYM C2 O2 DOUB N N 6 NYM C2 N3 SING N N 7 NYM N3 C4 SING N N 8 NYM N3 HN31 SING N N 9 NYM C4 O4 DOUB N N 10 NYM C4 C5 SING N N 11 NYM C5 C7 SING N N 12 NYM C7 HC71 SING N N 13 NYM C7 HC72 SING N N 14 NYM C7 HC73 SING N N 15 NYM "O4'" "C1'" SING N N 16 NYM "O4'" "C4'" SING N N 17 NYM "N3'" "C3'" SING N N 18 NYM "N3'" "H3'1" SING N N 19 NYM "N3'" "H3'2" SING N N 20 NYM "C1'" "C2'" SING N N 21 NYM "C1'" "H1'1" SING N N 22 NYM "C2'" "C3'" SING N N 23 NYM "C2'" "H2'1" SING N N 24 NYM "C2'" "H2'2" SING N N 25 NYM "C3'" "C4'" SING N N 26 NYM "C3'" HC31 SING N N 27 NYM "C4'" "C5'" SING N N 28 NYM "C4'" "H4'1" SING N N 29 NYM "O5'" "C5'" SING N N 30 NYM "O5'" P1 SING N N 31 NYM "C5'" "H5'1" SING N N 32 NYM "C5'" "H5'2" SING N N 33 NYM P1 OP2 SING N N 34 NYM P1 OP1 DOUB N N 35 NYM P1 OP3 SING N N 36 NYM OP2 HP31 SING N N 37 NYM OP3 HP21 SING N N 38 # # 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 NYM SMILES ACDLabs 10.04 "O=C1NC(=O)N(C=C1C)C2OC(C(N)C2)COP(=O)(O)O" NYM SMILES_CANONICAL CACTVS 3.341 "CC1=CN([C@H]2C[C@H](N)[C@@H](CO[P](O)(O)=O)O2)C(=O)NC1=O" NYM SMILES CACTVS 3.341 "CC1=CN([CH]2C[CH](N)[CH](CO[P](O)(O)=O)O2)C(=O)NC1=O" NYM SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)O)N" NYM SMILES "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(O)O)N" NYM InChI InChI 1.03 "InChI=1S/C10H16N3O7P/c1-5-3-13(10(15)12-9(5)14)8-2-6(11)7(20-8)4-19-21(16,17)18/h3,6-8H,2,4,11H2,1H3,(H,12,14,15)(H2,16,17,18)/t6-,7+,8+/m0/s1" NYM InChIKey InChI 1.03 BQZMHQZNZNBJNF-XLPZGREQSA-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 NYM "SYSTEMATIC NAME" ACDLabs 10.04 "3'-amino-3'-deoxythymidine 5'-(dihydrogen phosphate)" NYM "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2S,3S,5R)-3-amino-5-(5-methyl-2,4-dioxo-pyrimidin-1-yl)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 NYM "Create component" 2003-01-15 RCSB NYM "Modify descriptor" 2011-06-04 RCSB NYM "Modify synonyms" 2021-03-13 RCSB # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id NYM _pdbx_chem_comp_synonyms.name "PHOSPHORIC ACID MONO-[3-AMINO-5-(5-METHYL-2,4-DIOXO-3,4-DIHYDRO-2H-PYRIMIDIN-1-YL)-TETRAHYDRO-FURAN-2-YLMETHYL] ESTER" _pdbx_chem_comp_synonyms.provenance PDB _pdbx_chem_comp_synonyms.type ? ##