data_31M # _chem_comp.id 31M _chem_comp.name ;3'-deoxy-3'-[(L-methionyl-L-phenylalanyl)amino]adenosine 5'-(dihydrogen phosphate) ; _chem_comp.type "RNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C24 H33 N8 O8 P S" _chem_comp.mon_nstd_parent_comp_id A _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2014-05-20 _chem_comp.pdbx_modified_date 2014-08-15 _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 624.606 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 31M _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag Y _chem_comp.pdbx_ideal_coordinates_details Corina _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 4QCQ _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 31M P P P 0 1 N N N 90.308 -48.533 0.216 -4.892 -4.361 1.396 P 31M 1 31M OP1 OP1 O 0 1 N N N 90.073 -47.099 -0.065 -3.891 -5.292 1.964 OP1 31M 2 31M OP2 OP2 O 0 1 N N N 91.672 -49.097 0.099 -5.740 -3.691 2.590 OP2 31M 3 31M "C1'" "C1'" C 0 1 N N R 85.475 -48.625 1.027 -3.015 0.799 -0.550 "C1'" 31M 4 31M "C2'" "C2'" C 0 1 N N R 84.638 -48.914 -0.210 -1.892 0.882 0.514 "C2'" 31M 5 31M "O2'" "O2'" O 0 1 N N N 83.856 -50.102 -0.007 -0.827 1.723 0.067 "O2'" 31M 6 31M "C3'" "C3'" C 0 1 N N S 85.656 -49.151 -1.300 -1.428 -0.591 0.612 "C3'" 31M 7 31M "N3'" "N3'" N 0 1 N N N 85.291 -50.255 -2.202 -0.233 -0.812 -0.207 "N3'" 31M 8 31M "C4'" "C4'" C 0 1 N N S 86.902 -49.624 -0.572 -2.617 -1.400 0.059 "C4'" 31M 9 31M "O4'" "O4'" O 0 1 N N N 86.733 -49.327 0.845 -3.659 -0.462 -0.267 "O4'" 31M 10 31M "C5'" "C5'" C 0 1 N N N 88.099 -48.854 -1.122 -3.115 -2.384 1.119 "C5'" 31M 11 31M "O5'" "O5'" O 0 1 N N N 89.307 -49.428 -0.657 -4.140 -3.209 0.560 "O5'" 31M 12 31M N9 N9 N 0 1 Y N N 85.754 -47.161 1.190 -3.960 1.907 -0.392 N9 31M 13 31M C8 C8 C 0 1 Y N N 86.669 -46.445 0.557 -5.108 1.890 0.342 C8 31M 14 31M N7 N7 N 0 1 Y N N 86.613 -45.195 0.992 -5.704 3.044 0.262 N7 31M 15 31M C6 C6 C 0 1 Y N N 85.232 -44.094 2.670 -5.123 5.201 -0.961 C6 31M 16 31M N6 N6 N 0 1 N N N 85.773 -42.891 2.515 -6.214 5.959 -0.572 N6 31M 17 31M C5 C5 C 0 1 Y N N 85.672 -45.104 1.930 -4.978 3.873 -0.526 C5 31M 18 31M C4 C4 C 0 1 Y N N 85.137 -46.306 2.074 -3.847 3.155 -0.950 C4 31M 19 31M N3 N3 N 0 1 Y N N 84.150 -46.524 2.957 -2.961 3.754 -1.739 N3 31M 20 31M C2 C2 C 0 1 Y N N 83.716 -45.526 3.689 -3.136 5.003 -2.118 C2 31M 21 31M N1 N1 N 0 1 Y N N 84.267 -44.271 3.543 -4.181 5.718 -1.742 N1 31M 22 31M C C C 0 1 N N N 86.007 -50.524 -3.313 0.992 -0.643 0.329 C 31M 23 31M O O O 0 1 N N N 86.916 -49.818 -3.752 1.105 -0.308 1.489 O 31M 24 31M CA CA C 0 1 N N S 85.639 -51.824 -4.016 2.220 -0.869 -0.514 CA 31M 25 31M N N N 0 1 N N N 85.505 -51.650 -5.485 3.418 -0.623 0.293 N 31M 26 31M CB CB C 0 1 N N N 86.731 -52.836 -3.664 2.234 -2.313 -1.019 CB 31M 27 31M CG CG C 0 1 Y N N 86.487 -54.052 -4.286 3.395 -2.506 -1.960 CG 31M 28 31M CD1 CD1 C 0 1 Y N N 87.293 -54.467 -5.341 3.234 -2.273 -3.313 CD1 31M 29 31M CE1 CE1 C 0 1 Y N N 87.053 -55.688 -5.960 4.300 -2.445 -4.175 CE1 31M 30 31M CZ CZ C 0 1 Y N N 86.003 -56.493 -5.527 5.528 -2.849 -3.685 CZ 31M 31 31M CE2 CE2 C 0 1 Y N N 85.198 -56.078 -4.473 5.689 -3.081 -2.332 CE2 31M 32 31M CD2 CD2 C 0 1 Y N N 85.440 -54.858 -3.851 4.623 -2.910 -1.469 CD2 31M 33 31M CTM CTM C 0 1 N N N 84.354 -51.296 -6.060 4.572 -0.266 -0.306 CTM 31M 34 31M OTM OTM O 0 1 N N N 83.367 -50.833 -5.480 4.619 -0.150 -1.512 OTM 31M 35 31M CAM CAM C 0 1 N N S 84.174 -51.411 -7.583 5.804 -0.013 0.524 CAM 31M 36 31M NM NM N 0 1 N N N 84.137 -52.818 -8.010 6.998 -0.116 -0.326 NM 31M 37 31M CBM CBM C 0 1 N N N 82.900 -50.686 -8.016 5.731 1.390 1.131 CBM 31M 38 31M CGM CGM C 0 1 N N N 83.201 -49.204 -8.240 6.918 1.601 2.072 CGM 31M 39 31M SDM SDM S 0 1 N N N 81.687 -48.231 -8.560 6.831 3.264 2.792 SDM 31M 40 31M CEM CEM C 0 1 N N N 80.894 -49.280 -9.760 8.297 3.324 3.859 CEM 31M 41 31M HOP2 HOP2 H 0 0 N N N 92.277 -48.413 -0.163 -6.416 -3.068 2.291 HOP2 31M 42 31M "H1'" "H1'" H 0 1 N N N 84.952 -49.003 1.918 -2.592 0.797 -1.555 "H1'" 31M 43 31M "H2'" "H2'" H 0 1 N N N 84.005 -48.048 -0.455 -2.286 1.231 1.469 "H2'" 31M 44 31M "HO2'" "HO2'" H 0 0 N N N 83.217 -49.948 0.679 -1.091 2.639 -0.096 "HO2'" 31M 45 31M "H3'" "H3'" H 0 1 N N N 85.857 -48.224 -1.858 -1.234 -0.860 1.651 "H3'" 31M 46 31M H3 H3 H 0 1 N N N 84.494 -50.819 -1.986 -0.324 -1.079 -1.135 H3 31M 47 31M "H4'" "H4'" H 0 1 N N N 87.045 -50.703 -0.732 -2.314 -1.940 -0.837 "H4'" 31M 48 31M H5` H5` H 0 1 N N N 88.042 -47.807 -0.788 -2.287 -3.010 1.452 H5` 31M 49 31M "H5''" "H5''" H 0 0 N N N 88.080 -48.890 -2.221 -3.516 -1.832 1.969 "H5''" 31M 50 31M H8 H8 H 0 1 N N N 87.351 -46.819 -0.193 -5.470 1.043 0.907 H8 31M 51 31M H61 H61 H 0 1 N N N 85.331 -42.244 3.136 -6.298 6.878 -0.870 H61 31M 52 31M H62 H62 H 0 1 N N N 86.750 -42.936 2.721 -6.896 5.570 -0.001 H62 31M 53 31M H2 H2 H 0 1 N N N 82.926 -45.688 4.407 -2.397 5.460 -2.759 H2 31M 54 31M HA HA H 0 1 N N N 84.683 -52.185 -3.608 2.209 -0.187 -1.364 HA 31M 55 31M H H H 0 1 N N N 86.306 -51.804 -6.064 3.381 -0.716 1.258 H 31M 56 31M HB2 HB2 H 0 1 N N N 86.749 -52.984 -2.574 2.335 -2.993 -0.172 HB2 31M 57 31M HB3 HB3 H 0 1 N N N 87.705 -52.448 -3.997 1.302 -2.523 -1.544 HB3 31M 58 31M HD1 HD1 H 0 1 N N N 88.105 -53.840 -5.679 2.275 -1.957 -3.696 HD1 31M 59 31M HE1 HE1 H 0 1 N N N 87.681 -56.012 -6.777 4.175 -2.263 -5.233 HE1 31M 60 31M HZ HZ H 0 1 N N N 85.814 -57.440 -6.010 6.361 -2.984 -4.359 HZ 31M 61 31M HE2 HE2 H 0 1 N N N 84.384 -56.703 -4.137 6.648 -3.397 -1.948 HE2 31M 62 31M HD2 HD2 H 0 1 N N N 84.815 -54.536 -3.031 4.749 -3.088 -0.411 HD2 31M 63 31M HAM HAM H 0 1 N N N 85.030 -50.916 -8.065 5.863 -0.752 1.324 HAM 31M 64 31M HNM2 HNM2 H 0 0 N N N 84.976 -53.277 -7.719 7.104 -1.053 -0.688 HNM2 31M 65 31M HNM1 HNM1 H 0 0 N N N 83.348 -53.272 -7.595 6.967 0.559 -1.075 HNM1 31M 66 31M HBM2 HBM2 H 0 0 N N N 82.136 -50.789 -7.231 5.762 2.132 0.334 HBM2 31M 67 31M HBM3 HBM3 H 0 0 N N N 82.527 -51.129 -8.951 4.801 1.495 1.690 HBM3 31M 68 31M HGM3 HGM3 H 0 0 N N N 83.874 -49.106 -9.105 6.887 0.858 2.869 HGM3 31M 69 31M HGM2 HGM2 H 0 0 N N N 83.696 -48.804 -7.343 7.848 1.495 1.514 HGM2 31M 70 31M HEM1 HEM1 H 0 0 N N N 79.940 -48.828 -10.069 8.348 4.295 4.352 HEM1 31M 71 31M HEM2 HEM2 H 0 0 N N N 81.548 -49.392 -10.638 8.231 2.538 4.612 HEM2 31M 72 31M HEM3 HEM3 H 0 0 N N N 80.705 -50.268 -9.315 9.192 3.175 3.256 HEM3 31M 73 31M OP3 OP3 O 0 1 N Y N ? ? ? -5.886 -5.169 0.421 OP3 31M 74 31M HOP3 HOP3 H 0 0 N N N ? ? ? -6.373 -5.881 0.859 HOP3 31M 75 # 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 31M CEM SDM SING N N 1 31M SDM CGM SING N N 2 31M CGM CBM SING N N 3 31M CBM CAM SING N N 4 31M NM CAM SING N N 5 31M CAM CTM SING N N 6 31M CTM N SING N N 7 31M CTM OTM DOUB N N 8 31M CE1 CZ DOUB Y N 9 31M CE1 CD1 SING Y N 10 31M CZ CE2 SING Y N 11 31M N CA SING N N 12 31M CD1 CG DOUB Y N 13 31M CE2 CD2 DOUB Y N 14 31M CG CD2 SING Y N 15 31M CG CB SING N N 16 31M CA CB SING N N 17 31M CA C SING N N 18 31M O C DOUB N N 19 31M C "N3'" SING N N 20 31M "N3'" "C3'" SING N N 21 31M "C3'" "C4'" SING N N 22 31M "C3'" "C2'" SING N N 23 31M "C5'" "O5'" SING N N 24 31M "C5'" "C4'" SING N N 25 31M "O5'" P SING N N 26 31M "C4'" "O4'" SING N N 27 31M "C2'" "O2'" SING N N 28 31M "C2'" "C1'" SING N N 29 31M OP1 P DOUB N N 30 31M OP2 P SING N N 31 31M C8 N7 DOUB Y N 32 31M C8 N9 SING Y N 33 31M "O4'" "C1'" SING N N 34 31M N7 C5 SING Y N 35 31M "C1'" N9 SING N N 36 31M N9 C4 SING Y N 37 31M C5 C4 DOUB Y N 38 31M C5 C6 SING Y N 39 31M C4 N3 SING Y N 40 31M N6 C6 SING N N 41 31M C6 N1 DOUB Y N 42 31M N3 C2 DOUB Y N 43 31M N1 C2 SING Y N 44 31M OP2 HOP2 SING N N 45 31M "C1'" "H1'" SING N N 46 31M "C2'" "H2'" SING N N 47 31M "O2'" "HO2'" SING N N 48 31M "C3'" "H3'" SING N N 49 31M "N3'" H3 SING N N 50 31M "C4'" "H4'" SING N N 51 31M "C5'" H5` SING N N 52 31M "C5'" "H5''" SING N N 53 31M C8 H8 SING N N 54 31M N6 H61 SING N N 55 31M N6 H62 SING N N 56 31M C2 H2 SING N N 57 31M CA HA SING N N 58 31M N H SING N N 59 31M CB HB2 SING N N 60 31M CB HB3 SING N N 61 31M CD1 HD1 SING N N 62 31M CE1 HE1 SING N N 63 31M CZ HZ SING N N 64 31M CE2 HE2 SING N N 65 31M CD2 HD2 SING N N 66 31M CAM HAM SING N N 67 31M NM HNM2 SING N N 68 31M NM HNM1 SING N N 69 31M CBM HBM2 SING N N 70 31M CBM HBM3 SING N N 71 31M CGM HGM3 SING N N 72 31M CGM HGM2 SING N N 73 31M CEM HEM1 SING N N 74 31M CEM HEM2 SING N N 75 31M CEM HEM3 SING N N 76 31M P OP3 SING N N 77 31M OP3 HOP3 SING N N 78 # 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 31M SMILES ACDLabs 12.01 "O=P(O)(O)OCC4OC(n2cnc1c(ncnc12)N)C(O)C4NC(=O)C(NC(=O)C(N)CCSC)Cc3ccccc3" 31M InChI InChI 1.03 ;InChI=1S/C24H33N8O8PS/c1-42-8-7-14(25)22(34)30-15(9-13-5-3-2-4-6-13)23(35)31-17-16(10-39-41(36,37)38)40-24(19(17)33)32-12-29-18-20(26)27-11-28-21(18)32/h2-6,11-12,14-17,19,24,33H,7-10,25H2,1H3,(H,30,34)(H,31,35)(H2,26,27,28)(H2,36,37,38)/t14-,15-,16+,17+,19+,24+/m0/s1 ; 31M InChIKey InChI 1.03 DNXAWIQQLHCDHP-FWHNRVPHSA-N 31M SMILES_CANONICAL CACTVS 3.385 "CSCC[C@H](N)C(=O)N[C@@H](Cc1ccccc1)C(=O)N[C@H]2[C@@H](O)[C@@H](O[C@@H]2CO[P](O)(O)=O)n3cnc4c(N)ncnc34" 31M SMILES CACTVS 3.385 "CSCC[CH](N)C(=O)N[CH](Cc1ccccc1)C(=O)N[CH]2[CH](O)[CH](O[CH]2CO[P](O)(O)=O)n3cnc4c(N)ncnc34" 31M SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "CSCC[C@@H](C(=O)N[C@@H](Cc1ccccc1)C(=O)N[C@@H]2[C@H](O[C@H]([C@@H]2O)n3cnc4c3ncnc4N)COP(=O)(O)O)N" 31M SMILES "OpenEye OEToolkits" 1.7.6 "CSCCC(C(=O)NC(Cc1ccccc1)C(=O)NC2C(OC(C2O)n3cnc4c3ncnc4N)COP(=O)(O)O)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 31M "SYSTEMATIC NAME" ACDLabs 12.01 ;3'-deoxy-3'-[(L-methionyl-L-phenylalanyl)amino]adenosine 5'-(dihydrogen phosphate) ; 31M "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "[(2S,3S,4R,5R)-5-(6-aminopurin-9-yl)-3-[[(2S)-2-[[(2S)-2-azanyl-4-methylsulfanyl-butanoyl]amino]-3-phenyl-propanoyl]amino]-4-oxidanyl-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 31M "Create component" 2014-05-20 RCSB 31M "Initial release" 2014-08-20 RCSB #