data_YMP # _chem_comp.id YMP _chem_comp.name "O-(ADENOSINE-5'-O-YL)-N-(L-TYROSYL)PHOSPHORAMIDATE" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C19 H24 N7 O8 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "TYROSYL-ADENYLATE ANALOGUE; TYR-AMP ANALOGUE" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2006-05-02 _chem_comp.pdbx_modified_date 2020-05-26 _chem_comp.pdbx_ambiguous_flag ? _chem_comp.pdbx_release_status REL _chem_comp.pdbx_replaced_by ? _chem_comp.pdbx_replaces ? _chem_comp.formula_weight 509.410 _chem_comp.one_letter_code ? _chem_comp.three_letter_code YMP _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 ? _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 YMP N N N 0 1 N N N 8.261 30.255 160.434 5.465 1.361 1.720 N YMP 1 YMP CA CA C 0 1 N N S 8.118 31.568 159.734 4.723 1.142 0.471 CA YMP 2 YMP CB CB C 0 1 N N N 9.501 32.146 159.423 4.558 -0.360 0.232 CB YMP 3 YMP CG CG C 0 1 Y N N 10.268 32.506 160.675 5.911 -0.984 0.007 CG YMP 4 YMP CD1 CD1 C 0 1 Y N N 9.699 33.340 161.639 6.635 -1.469 1.080 CD1 YMP 5 YMP CE1 CE1 C 0 1 Y N N 10.416 33.674 162.784 7.876 -2.041 0.876 CE1 YMP 6 YMP CZ CZ C 0 1 Y N N 11.704 33.173 162.975 8.395 -2.130 -0.407 CZ YMP 7 YMP OH OH O 0 1 N N N 12.372 33.494 164.078 9.615 -2.693 -0.610 OH YMP 8 YMP CE2 CE2 C 0 1 Y N N 12.280 32.337 162.015 7.666 -1.643 -1.483 CE2 YMP 9 YMP CD2 CD2 C 0 1 Y N N 11.558 32.003 160.869 6.424 -1.077 -1.274 CD2 YMP 10 YMP C C C 0 1 N N N 7.308 31.413 158.469 3.365 1.787 0.574 C YMP 11 YMP O O O 0 1 N N N 6.785 30.344 158.202 2.898 2.046 1.663 O YMP 12 YMP N3P N3P N 0 1 N N N 7.213 32.502 157.702 2.669 2.075 -0.544 N3P YMP 13 YMP P P P 0 1 N N S 6.429 32.648 156.226 1.191 2.777 -0.431 P YMP 14 YMP O1P O1P O 0 1 N N N 5.777 31.383 155.759 0.641 2.988 -1.789 O1P YMP 15 YMP O2P O2P O 0 1 N N N 7.390 33.312 155.279 1.325 4.194 0.320 O2P YMP 16 YMP "O5'" O5* O 0 1 N N N 5.212 33.669 156.482 0.204 1.818 0.405 "O5'" YMP 17 YMP "C5'" C5* C 0 1 N N N 5.441 34.972 157.013 -0.061 0.680 -0.419 "C5'" YMP 18 YMP "C4'" C4* C 0 1 N N R 4.272 35.381 157.902 -0.999 -0.277 0.321 "C4'" YMP 19 YMP "O4'" O4* O 0 1 N N N 3.176 35.859 157.108 -2.290 0.334 0.485 "O4'" YMP 20 YMP "C1'" C1* C 0 1 N N R 1.997 35.110 157.408 -3.270 -0.723 0.398 "C1'" YMP 21 YMP "C2'" C2* C 0 1 N N R 2.359 33.977 158.365 -2.730 -1.623 -0.742 "C2'" YMP 22 YMP "C3'" C3* C 0 1 N N S 3.796 34.222 158.762 -1.198 -1.560 -0.509 "C3'" YMP 23 YMP "O3'" O3* O 0 1 N N N 3.815 34.722 160.090 -0.755 -2.708 0.219 "O3'" YMP 24 YMP "O2'" O2* O 0 1 N N N 1.441 33.780 159.426 -3.211 -2.962 -0.606 "O2'" YMP 25 YMP N9 N9 N 0 1 Y N N 1.201 34.584 156.285 -4.585 -0.179 0.052 N9 YMP 26 YMP C4 C4 C 0 1 Y N N -0.089 34.816 156.131 -5.799 -0.764 0.309 C4 YMP 27 YMP N3 N3 N 0 1 Y N N -0.846 35.595 156.952 -6.193 -1.887 0.901 N3 YMP 28 YMP C5 C5 C 0 1 Y N N -0.577 34.175 155.035 -6.769 0.117 -0.198 C5 YMP 29 YMP N7 N7 N 0 1 Y N N 0.468 33.518 154.494 -6.109 1.171 -0.736 N7 YMP 30 YMP C8 C8 C 0 1 Y N N 1.556 33.767 155.274 -4.827 0.999 -0.590 C8 YMP 31 YMP C6 C6 C 0 1 Y N N -2.006 34.332 154.710 -8.122 -0.238 -0.064 C6 YMP 32 YMP N6 N6 N 0 1 N N N -2.543 33.743 153.651 -9.122 0.588 -0.550 N6 YMP 33 YMP N1 N1 N 0 1 Y N N -2.724 35.096 155.529 -8.420 -1.384 0.538 N1 YMP 34 YMP C2 C2 C 0 1 Y N N -2.263 35.809 156.718 -7.473 -2.178 1.004 C2 YMP 35 YMP HN1 1HN H 0 1 N N N 9.106 30.253 160.969 5.460 2.355 1.890 HN1 YMP 36 YMP HN2 2HN H 0 1 N N N 8.293 29.518 159.759 4.922 0.937 2.458 HN2 YMP 37 YMP HA HA H 0 1 N N N 7.583 32.265 160.396 5.273 1.584 -0.360 HA YMP 38 YMP HB1 1HB H 0 1 N N N 9.359 33.066 158.838 4.088 -0.817 1.103 HB1 YMP 39 YMP HB2 2HB H 0 1 N N N 10.077 31.393 158.865 3.933 -0.522 -0.646 HB2 YMP 40 YMP HD1 HD1 H 0 1 N N N 8.701 33.727 161.496 6.231 -1.400 2.079 HD1 YMP 41 YMP HE1 HE1 H 0 1 N N N 9.974 34.322 163.526 8.441 -2.419 1.715 HE1 YMP 42 YMP HOH HOH H 0 1 N N N 13.297 33.571 163.877 9.466 -3.637 -0.757 HOH YMP 43 YMP HE2 HE2 H 0 1 N N N 13.279 31.952 162.159 8.069 -1.711 -2.483 HE2 YMP 44 YMP HD2 HD2 H 0 1 N N N 11.998 31.352 160.128 5.856 -0.698 -2.111 HD2 YMP 45 YMP H3P H3P H 0 1 N N N 7.661 33.326 158.048 3.043 1.868 -1.414 H3P YMP 46 YMP H2P H2P H 0 1 N N N 6.964 33.452 154.441 1.686 4.012 1.198 H2P YMP 47 YMP "H5'1" 1H5* H 0 0 N N N 5.536 35.690 156.185 -0.532 1.005 -1.347 "H5'1" YMP 48 YMP "H5'2" 2H5* H 0 0 N N N 6.366 34.966 157.608 0.874 0.169 -0.645 "H5'2" YMP 49 YMP "H4'" H4* H 0 1 N N N 4.630 36.186 158.560 -0.580 -0.527 1.295 "H4'" YMP 50 YMP "H1'" H1* H 0 1 N N N 1.321 35.854 157.855 -3.320 -1.278 1.335 "H1'" YMP 51 YMP "H2'" H2* H 0 1 N N N 2.274 32.997 157.872 -2.994 -1.215 -1.718 "H2'" YMP 52 YMP "H3'" H3* H 0 1 N N N 4.396 33.306 158.659 -0.670 -1.486 -1.459 "H3'" YMP 53 YMP H2 H2 H 0 1 N N N 3.819 33.996 160.702 -0.961 -3.480 -0.325 H2 YMP 54 YMP H1 H1 H 0 1 N N N 1.913 33.736 160.249 -2.841 -3.468 -1.342 H1 YMP 55 YMP H8 H8 H 0 1 N N N 2.547 33.372 155.108 -4.068 1.688 -0.928 H8 YMP 56 YMP HN61 1HN6 H 0 0 N N N -2.054 33.162 153.000 -8.892 1.422 -0.988 HN61 YMP 57 YMP HN62 2HN6 H 0 0 N N N -3.515 33.972 153.607 -10.052 0.332 -0.451 HN62 YMP 58 YMP H3 H3 H 0 1 N N N -2.897 36.419 157.345 -7.759 -3.100 1.487 H3 YMP 59 # 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 YMP N CA SING N N 1 YMP N HN1 SING N N 2 YMP N HN2 SING N N 3 YMP CA CB SING N N 4 YMP CA C SING N N 5 YMP CA HA SING N N 6 YMP CB CG SING N N 7 YMP CB HB1 SING N N 8 YMP CB HB2 SING N N 9 YMP CG CD1 DOUB Y N 10 YMP CG CD2 SING Y N 11 YMP CD1 CE1 SING Y N 12 YMP CD1 HD1 SING N N 13 YMP CE1 CZ DOUB Y N 14 YMP CE1 HE1 SING N N 15 YMP CZ OH SING N N 16 YMP CZ CE2 SING Y N 17 YMP OH HOH SING N N 18 YMP CE2 CD2 DOUB Y N 19 YMP CE2 HE2 SING N N 20 YMP CD2 HD2 SING N N 21 YMP C O DOUB N N 22 YMP C N3P SING N N 23 YMP N3P P SING N N 24 YMP N3P H3P SING N N 25 YMP P O1P DOUB N N 26 YMP P O2P SING N N 27 YMP P "O5'" SING N N 28 YMP O2P H2P SING N N 29 YMP "O5'" "C5'" SING N N 30 YMP "C5'" "C4'" SING N N 31 YMP "C5'" "H5'1" SING N N 32 YMP "C5'" "H5'2" SING N N 33 YMP "C4'" "O4'" SING N N 34 YMP "C4'" "C3'" SING N N 35 YMP "C4'" "H4'" SING N N 36 YMP "O4'" "C1'" SING N N 37 YMP "C1'" "C2'" SING N N 38 YMP "C1'" N9 SING N N 39 YMP "C1'" "H1'" SING N N 40 YMP "C2'" "C3'" SING N N 41 YMP "C2'" "O2'" SING N N 42 YMP "C2'" "H2'" SING N N 43 YMP "C3'" "O3'" SING N N 44 YMP "C3'" "H3'" SING N N 45 YMP "O3'" H2 SING N N 46 YMP "O2'" H1 SING N N 47 YMP N9 C4 SING Y N 48 YMP N9 C8 SING Y N 49 YMP C4 N3 SING Y N 50 YMP C4 C5 DOUB Y N 51 YMP N3 C2 DOUB Y N 52 YMP C5 N7 SING Y N 53 YMP C5 C6 SING Y N 54 YMP N7 C8 DOUB Y N 55 YMP C8 H8 SING N N 56 YMP C6 N6 SING N N 57 YMP C6 N1 DOUB Y N 58 YMP N6 HN61 SING N N 59 YMP N6 HN62 SING N N 60 YMP N1 C2 SING Y N 61 YMP C2 H3 SING N N 62 # 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 YMP SMILES ACDLabs 10.04 "O=C(NP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O)C(N)Cc4ccc(O)cc4" YMP SMILES_CANONICAL CACTVS 3.341 "N[C@@H](Cc1ccc(O)cc1)C(=O)N[P@@](O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)n3cnc4c(N)ncnc34" YMP SMILES CACTVS 3.341 "N[CH](Cc1ccc(O)cc1)C(=O)N[P](O)(=O)OC[CH]2O[CH]([CH](O)[CH]2O)n3cnc4c(N)ncnc34" YMP SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "c1cc(ccc1C[C@@H](C(=O)N[P@](=O)(O)OC[C@@H]2[C@H]([C@H]([C@@H](O2)n3cnc4c3ncnc4N)O)O)N)O" YMP SMILES "OpenEye OEToolkits" 1.5.0 "c1cc(ccc1CC(C(=O)NP(=O)(O)OCC2C(C(C(O2)n3cnc4c3ncnc4N)O)O)N)O" YMP InChI InChI 1.03 "InChI=1S/C19H24N7O8P/c20-11(5-9-1-3-10(27)4-2-9)18(30)25-35(31,32)33-6-12-14(28)15(29)19(34-12)26-8-24-13-16(21)22-7-23-17(13)26/h1-4,7-8,11-12,14-15,19,27-29H,5-6,20H2,(H2,21,22,23)(H2,25,30,31,32)/t11-,12+,14+,15+,19+/m0/s1" YMP InChIKey InChI 1.03 WJKRKCCMHCWYJU-QTOWJTHWSA-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 YMP "SYSTEMATIC NAME" ACDLabs 10.04 "5'-O-[(S)-hydroxy(L-tyrosylamino)phosphoryl]adenosine" YMP "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "N-[(2S)-2-amino-3-(4-hydroxyphenyl)propanoyl]-[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy]phosphonamidic acid" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site YMP "Create component" 2006-05-02 RCSB YMP "Modify descriptor" 2011-06-04 RCSB YMP "Modify synonyms" 2020-05-26 PDBE # loop_ _pdbx_chem_comp_synonyms.ordinal _pdbx_chem_comp_synonyms.comp_id _pdbx_chem_comp_synonyms.name _pdbx_chem_comp_synonyms.provenance _pdbx_chem_comp_synonyms.type 1 YMP "TYROSYL-ADENYLATE ANALOGUE" ? ? 2 YMP "TYR-AMP ANALOGUE" ? ? #