data_N5P # _chem_comp.id N5P _chem_comp.name ;1-{2-DEOXY-5-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}PHOSPHORYL]-BETA-D-ERYTHRO-PENTOFURANOSYL}-5-NITRO -1H-INDOLE ; _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C13 H17 N2 O14 P3" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "5-NITRO-1-INDOLYL-2'-DEOXYRIBOSIDE-5'-TRIPHOSPHATE" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2007-03-21 _chem_comp.pdbx_modified_date 2020-06-17 _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 518.200 _chem_comp.one_letter_code ? _chem_comp.three_letter_code N5P _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 ? _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 N5P OR2 OR2 O 0 1 N N N -11.998 65.837 38.494 -9.522 2.250 1.175 OR2 N5P 1 N5P NRO NRO N 1 1 N N N -12.083 64.841 39.197 -8.869 2.213 0.148 NRO N5P 2 N5P OR1 OR1 O -1 1 N N N -11.065 64.372 39.684 -9.295 2.739 -0.865 OR1 N5P 3 N5P CZ3 CZ3 C 0 1 Y N N -13.379 64.215 39.448 -7.553 1.535 0.131 CZ3 N5P 4 N5P CE3 CE3 C 0 1 Y N N -13.435 63.087 40.255 -6.822 1.502 -1.023 CE3 N5P 5 N5P CD2 CD2 C 0 1 Y N N -14.689 62.505 40.486 -5.581 0.862 -1.039 CD2 N5P 6 N5P CH2 CH2 C 0 1 Y N N -14.522 64.788 38.877 -7.070 0.942 1.289 CH2 N5P 7 N5P CZ2 CZ2 C 0 1 Y N N -15.762 64.242 39.088 -5.848 0.306 1.296 CZ2 N5P 8 N5P CE2 CE2 C 0 1 Y N N -15.834 63.091 39.891 -5.089 0.255 0.130 CE2 N5P 9 N5P NE1 NE1 N 0 1 Y N N -16.913 62.339 40.275 -3.863 -0.289 -0.179 NE1 N5P 10 N5P CD1 CD1 C 0 1 Y N N -16.491 61.309 41.080 -3.566 -0.049 -1.493 CD1 N5P 11 N5P CG CG C 0 1 Y N N -15.136 61.368 41.238 -4.563 0.642 -2.069 CG N5P 12 N5P "C1'" "C1'" C 0 1 N N R -18.346 62.553 39.911 -3.004 -1.017 0.758 "C1'" N5P 13 N5P "O4'" "O4'" O 0 1 N N N -19.140 61.497 40.459 -1.641 -0.977 0.304 "O4'" N5P 14 N5P "C4'" "C4'" C 0 1 N N R -19.839 60.808 39.424 -1.035 -2.233 0.679 "C4'" N5P 15 N5P "C3'" "C3'" C 0 1 N N S -19.933 61.809 38.279 -2.150 -3.271 0.398 "C3'" N5P 16 N5P "O3'" "O3'" O 0 1 N N N -21.050 62.687 38.470 -1.975 -4.438 1.204 "O3'" N5P 17 N5P "C2'" "C2'" C 0 1 N N N -18.617 62.561 38.407 -3.425 -2.498 0.813 "C2'" N5P 18 N5P "C5'" "C5'" C 0 1 N N N -19.116 59.497 39.113 0.196 -2.516 -0.185 "C5'" N5P 19 N5P "O5'" "O5'" O 0 1 N N N -19.882 58.704 38.212 1.212 -1.553 0.103 "O5'" N5P 20 N5P PA PA P 0 1 N N N -19.480 57.178 37.897 2.648 -1.549 -0.626 PA N5P 21 N5P O1A O1A O 0 1 N N N -18.003 57.138 37.578 3.289 -2.873 -0.459 O1A N5P 22 N5P O2A O2A O 0 1 N N N -20.008 56.330 39.030 2.453 -1.241 -2.194 O2A N5P 23 N5P O3A O3A O 0 1 N N N -20.269 56.735 36.564 3.581 -0.414 0.033 O3A N5P 24 N5P PB PB P 0 1 N N N -21.441 57.639 35.922 5.159 -0.101 -0.008 PB N5P 25 N5P O1B O1B O 0 1 N N N -20.892 58.294 34.677 5.649 -0.216 -1.400 O1B N5P 26 N5P O2B O2B O 0 1 N N N -22.078 58.503 36.990 5.940 -1.156 0.924 O2B N5P 27 N5P O3B O3B O 0 1 N N N -22.512 56.523 35.471 5.425 1.392 0.532 O3B N5P 28 N5P PG PG P 0 1 N N N -23.685 56.000 36.449 6.640 2.437 0.380 PG N5P 29 N5P O3G O3G O 0 1 N N N -23.759 54.517 36.153 6.146 3.903 0.824 O3G N5P 30 N5P O2G O2G O 0 1 N N N -23.229 56.314 37.860 7.864 1.977 1.319 O2G N5P 31 N5P O1G O1G O 0 1 N N N -24.900 56.779 35.998 7.087 2.472 -1.030 O1G N5P 32 N5P HE3 HE3 H 0 1 N N N -12.539 62.670 40.692 -7.203 1.969 -1.919 HE3 N5P 33 N5P HH2 HH2 H 0 1 N N N -14.426 65.671 38.263 -7.657 0.980 2.195 HH2 N5P 34 N5P HZ2 HZ2 H 0 1 N N N -16.649 64.680 38.654 -5.480 -0.152 2.202 HZ2 N5P 35 N5P HD1 HD1 H 0 1 N N N -17.135 60.563 41.522 -2.663 -0.368 -1.993 HD1 N5P 36 N5P HG HG H 0 1 N N N -14.522 60.692 41.815 -4.606 0.973 -3.096 HG N5P 37 N5P "H1'" "H1'" H 0 1 N N N -18.602 63.544 40.315 -3.079 -0.573 1.751 "H1'" N5P 38 N5P "H4'" "H4'" H 0 1 N N N -20.859 60.488 39.683 -0.770 -2.230 1.737 "H4'" N5P 39 N5P "H3'" "H3'" H 0 1 N N N -20.084 61.350 37.291 -2.181 -3.532 -0.660 "H3'" N5P 40 N5P "HO3'" "HO3'" H 0 0 N N N -21.095 63.304 37.749 -2.649 -5.117 1.064 "HO3'" N5P 41 N5P "H2'1" "H2'1" H 0 0 N N N -18.699 63.586 38.017 -3.725 -2.772 1.825 "H2'1" N5P 42 N5P "H2'2" "H2'2" H 0 0 N N N -17.811 62.061 37.849 -4.235 -2.691 0.109 "H2'2" N5P 43 N5P "H5'1" "H5'1" H 0 0 N N N -18.142 59.723 38.655 0.571 -3.516 0.034 "H5'1" N5P 44 N5P "H5'2" "H5'2" H 0 0 N N N -18.968 58.937 40.048 -0.077 -2.453 -1.238 "H5'2" N5P 45 N5P HO2A HO2A H 0 0 N N N -19.292 55.846 39.424 2.038 -0.387 -2.378 HO2A N5P 46 N5P HO2B HO2B H 0 0 N N N -22.049 59.414 36.721 5.670 -1.137 1.852 HO2B N5P 47 N5P HOG3 HOG3 H 0 0 N N N -24.582 54.321 35.721 6.828 4.585 0.758 HOG3 N5P 48 N5P HOG2 HOG2 H 0 0 N N N -23.801 56.970 38.240 7.643 1.931 2.260 HOG2 N5P 49 # # 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 N5P OR2 NRO DOUB N N 1 N5P NRO CZ3 SING N N 2 N5P NRO OR1 SING N N 3 N5P CZ3 CH2 SING Y N 4 N5P CZ3 CE3 DOUB Y N 5 N5P CE3 CD2 SING Y N 6 N5P CE3 HE3 SING N N 7 N5P CD2 CE2 DOUB Y N 8 N5P CD2 CG SING Y N 9 N5P CH2 CZ2 DOUB Y N 10 N5P CH2 HH2 SING N N 11 N5P CZ2 CE2 SING Y N 12 N5P CZ2 HZ2 SING N N 13 N5P CE2 NE1 SING Y N 14 N5P NE1 "C1'" SING N N 15 N5P NE1 CD1 SING Y N 16 N5P CD1 CG DOUB Y N 17 N5P CD1 HD1 SING N N 18 N5P CG HG SING N N 19 N5P "C1'" "C2'" SING N N 20 N5P "C1'" "O4'" SING N N 21 N5P "C1'" "H1'" SING N N 22 N5P "O4'" "C4'" SING N N 23 N5P "C4'" "C3'" SING N N 24 N5P "C4'" "C5'" SING N N 25 N5P "C4'" "H4'" SING N N 26 N5P "C3'" "C2'" SING N N 27 N5P "C3'" "O3'" SING N N 28 N5P "C3'" "H3'" SING N N 29 N5P "O3'" "HO3'" SING N N 30 N5P "C2'" "H2'1" SING N N 31 N5P "C2'" "H2'2" SING N N 32 N5P "C5'" "O5'" SING N N 33 N5P "C5'" "H5'1" SING N N 34 N5P "C5'" "H5'2" SING N N 35 N5P "O5'" PA SING N N 36 N5P PA O3A SING N N 37 N5P PA O1A DOUB N N 38 N5P PA O2A SING N N 39 N5P O2A HO2A SING N N 40 N5P O3A PB SING N N 41 N5P PB O1B DOUB N N 42 N5P PB O3B SING N N 43 N5P PB O2B SING N N 44 N5P O2B HO2B SING N N 45 N5P O3B PG SING N N 46 N5P PG O1G DOUB N N 47 N5P PG O3G SING N N 48 N5P PG O2G SING N N 49 N5P O3G HOG3 SING N N 50 N5P O2G HOG2 SING N N 51 # # 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 N5P SMILES ACDLabs 12.01 "[O-][N+](=O)c2cc1ccn(c1cc2)C3OC(C(O)C3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O" N5P InChI InChI 1.03 "InChI=1S/C13H17N2O14P3/c16-11-6-13(14-4-3-8-5-9(15(17)18)1-2-10(8)14)27-12(11)7-26-31(22,23)29-32(24,25)28-30(19,20)21/h1-5,11-13,16H,6-7H2,(H,22,23)(H,24,25)(H2,19,20,21)/t11-,12+,13+/m0/s1" N5P InChIKey InChI 1.03 JJJBDAFRCKSXDR-YNEHKIRRSA-N N5P SMILES_CANONICAL CACTVS 3.370 "O[C@H]1C[C@@H](O[C@@H]1CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)n2ccc3cc(ccc23)[N+]([O-])=O" N5P SMILES CACTVS 3.370 "O[CH]1C[CH](O[CH]1CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)n2ccc3cc(ccc23)[N+]([O-])=O" N5P SMILES_CANONICAL "OpenEye OEToolkits" 1.7.2 "c1cc2c(ccn2C3CC(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)cc1[N+](=O)[O-]" N5P SMILES "OpenEye OEToolkits" 1.7.2 "c1cc2c(ccn2C3CC(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)cc1[N+](=O)[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 N5P "SYSTEMATIC NAME" ACDLabs 12.01 "1-{2-deoxy-5-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-erythro-pentofuranosyl}-5-nitro-1H-indole" N5P "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.2 "[[5-(5-nitroindol-1-yl)-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen 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 N5P "Create component" 2007-03-21 RCSB N5P "Modify descriptor" 2011-06-04 RCSB N5P "Modify synonyms" 2020-06-05 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id N5P _pdbx_chem_comp_synonyms.name "5-NITRO-1-INDOLYL-2'-DEOXYRIBOSIDE-5'-TRIPHOSPHATE" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##