data_RA4 # _chem_comp.id RA4 _chem_comp.name "N-(4-NITROBENZOYL)-L-LEUCYL-N-(4-{[AMINO(IMINO)METHYL]AMINO}BUTYL)-L-PROLINAMIDE" _chem_comp.type peptide-like _chem_comp.pdbx_type HETAIN _chem_comp.formula "C23 H35 N7 O5" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "1-GUANIDINO-4-(N-NITRO-BENZOYLAMINO-L-LEUCYL-L-PROLYLAMINO)BUTANE" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2005-02-03 _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 489.568 _chem_comp.one_letter_code ? _chem_comp.three_letter_code RA4 _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 1YPM _chem_comp.pdbx_subcomponent_list "4NB LEU PRO AG2" _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 RA4 C26 C26 C 0 1 N N N 18.868 -16.772 24.152 4.233 0.957 0.073 C 4NB 1 RA4 O25 O25 O 0 1 N N N 19.550 -17.157 25.096 4.697 2.079 0.123 O2 4NB 2 RA4 C27 C27 C 0 1 Y N N 17.464 -17.318 24.074 5.125 -0.217 0.178 C1 4NB 3 RA4 C28 C28 C 0 1 Y N N 17.002 -18.044 25.179 6.501 -0.041 0.333 C2 4NB 4 RA4 C29 C29 C 0 1 Y N N 15.851 -18.825 25.081 7.327 -1.141 0.430 C3 4NB 5 RA4 C30 C30 C 0 1 Y N N 15.137 -18.896 23.881 6.796 -2.417 0.373 C4 4NB 6 RA4 C34 C34 C 0 1 Y N N 15.602 -18.169 22.783 5.433 -2.599 0.219 C5 4NB 7 RA4 C35 C35 C 0 1 Y N N 16.761 -17.389 22.873 4.594 -1.507 0.126 C6 4NB 8 RA4 N31 N31 N 1 1 N N N 14.024 -19.664 23.814 7.689 -3.593 0.477 N 4NB 9 RA4 O32 O32 O -1 1 N N N 13.592 -20.376 24.946 8.889 -3.436 0.612 "O1'" 4NB 10 RA4 O33 O33 O 0 1 N N N 13.379 -19.757 22.795 7.223 -4.717 0.426 "O2'" 4NB 11 RA4 N24 N24 N 0 1 N N N 19.295 -15.861 23.269 2.905 0.784 -0.077 N LEU 12 RA4 C23 C23 C 0 1 N N S 19.263 -14.448 23.538 2.010 1.943 -0.078 CA LEU 13 RA4 C18 C18 C 0 1 N N N 18.645 -13.608 22.443 0.644 1.524 0.402 C LEU 14 RA4 O17 O17 O 0 1 N N N 17.598 -13.077 22.829 0.351 0.348 0.444 O LEU 15 RA4 C22 C22 C 0 1 N N N 20.596 -13.886 24.018 1.902 2.504 -1.497 CB LEU 16 RA4 C21 C21 C 0 1 N N N 20.781 -13.907 25.532 1.697 1.354 -2.486 CG LEU 17 RA4 C19 C19 C 0 1 N N N 21.335 -12.570 26.056 2.096 1.811 -3.890 CD1 LEU 18 RA4 C20 C20 C 0 1 N N N 19.491 -14.310 26.258 0.225 0.936 -2.484 CD2 LEU 19 RA4 N16 N16 N 0 1 N N N 19.303 -13.046 21.395 -0.252 2.456 0.783 N PRO 20 RA4 C12 C12 C 0 1 N N S 18.872 -11.802 20.775 -1.560 2.186 1.396 CA PRO 21 RA4 C11 C11 C 0 1 N N N 17.436 -11.857 20.319 -2.418 1.392 0.445 C PRO 22 RA4 O10 O10 O 0 1 N N N 17.064 -12.804 19.632 -2.034 1.183 -0.686 O PRO 23 RA4 C13 C13 C 0 1 N N N 19.759 -11.719 19.511 -2.220 3.551 1.687 CB PRO 24 RA4 C14 C14 C 0 1 N N N 20.940 -12.685 19.768 -1.010 4.521 1.733 CG PRO 25 RA4 C15 C15 C 0 1 N N N 20.379 -13.761 20.735 -0.084 3.915 0.650 CD PRO 26 RA4 N9 N9 N 0 1 N N N 16.793 -10.758 20.415 -3.611 0.914 0.852 N AG2 27 RA4 C8 C8 C 0 1 N N N 15.432 -10.908 19.933 -4.444 0.142 -0.073 CA AG2 28 RA4 C7 C7 C 0 1 N N N 14.556 -9.949 20.768 -5.735 -0.278 0.633 CB AG2 29 RA4 C6 C6 C 0 1 N N N 13.293 -10.693 21.213 -6.606 -1.084 -0.333 CG AG2 30 RA4 C5 C5 C 0 1 N N N 12.584 -9.902 22.342 -7.896 -1.504 0.374 CD AG2 31 RA4 N4 N4 N 0 1 N N N 11.998 -10.916 23.174 -8.730 -2.276 -0.551 NE AG2 32 RA4 C2 C2 C 0 1 N N N 11.172 -10.577 24.064 -9.947 -2.763 -0.136 CZ AG2 33 RA4 N1 N1 N 0 1 N N N 10.885 -9.391 24.419 -10.359 -2.538 1.079 NH1 AG2 34 RA4 N3 N3 N 0 1 N N N 10.586 -11.562 24.648 -10.729 -3.488 -1.004 NH2 AG2 35 RA4 H28 H28 H 0 1 N N N 17.541 -17.999 26.114 6.917 0.955 0.378 H2 4NB 36 RA4 H29 H29 H 0 1 N N N 15.507 -19.381 25.941 8.392 -1.006 0.551 H3 4NB 37 RA4 H34 H34 H 0 1 N N N 15.059 -18.209 21.850 5.024 -3.598 0.175 H5 4NB 38 RA4 H35 H35 H 0 1 N N N 17.111 -16.841 22.010 3.530 -1.650 0.011 H6 4NB 39 RA4 H24 H24 H 0 1 N N N 19.650 -16.175 22.388 2.542 -0.109 -0.185 H LEU 40 RA4 H23 H23 H 0 1 N N N 18.568 -14.366 24.387 2.408 2.710 0.586 HA LEU 41 RA4 H221 H221 H 0 0 N N N 21.398 -14.493 23.572 1.055 3.188 -1.555 HB2 LEU 42 RA4 H222 H222 H 0 0 N N N 20.660 -12.840 23.685 2.819 3.038 -1.747 HB3 LEU 43 RA4 H21 H21 H 0 1 N N N 21.532 -14.680 25.755 2.315 0.506 -2.190 HG LEU 44 RA4 H191 H191 H 0 0 N N N 21.454 -12.625 27.148 3.144 2.108 -3.891 HD11 LEU 45 RA4 H192 H192 H 0 0 N N N 22.311 -12.370 25.590 1.949 0.992 -4.594 HD12 LEU 46 RA4 H193 H193 H 0 0 N N N 20.636 -11.759 25.804 1.477 2.659 -4.186 HD13 LEU 47 RA4 H201 H201 H 0 0 N N N 19.666 -14.313 27.344 0.056 0.197 -3.266 HD21 LEU 48 RA4 H202 H202 H 0 0 N N N 18.695 -13.590 26.017 -0.029 0.505 -1.515 HD22 LEU 49 RA4 H203 H203 H 0 0 N N N 19.187 -15.316 25.933 -0.400 1.810 -2.668 HD23 LEU 50 RA4 H12 H12 H 0 1 N N N 18.955 -10.957 21.475 -1.427 1.635 2.327 HA PRO 51 RA4 H131 H131 H 0 0 N N N 20.121 -10.692 19.355 -2.738 3.535 2.646 HB2 PRO 52 RA4 H132 H132 H 0 0 N N N 19.194 -12.022 18.617 -2.903 3.824 0.883 HB3 PRO 53 RA4 H141 H141 H 0 0 N N N 21.791 -12.155 20.221 -0.531 4.503 2.712 HG2 PRO 54 RA4 H142 H142 H 0 0 N N N 21.286 -13.142 18.829 -1.311 5.534 1.467 HG3 PRO 55 RA4 H151 H151 H 0 0 N N N 21.140 -14.111 21.448 0.953 4.196 0.836 HD2 PRO 56 RA4 H152 H152 H 0 0 N N N 20.015 -14.649 20.197 -0.394 4.243 -0.342 HD3 PRO 57 RA4 HN9 HN9 H 0 1 N N N 17.176 -9.907 20.774 -3.918 1.082 1.757 HN1 AG2 58 RA4 H81 H81 H 0 1 N N N 15.373 -10.650 18.865 -4.688 0.755 -0.941 HA1 AG2 59 RA4 H82 H82 H 0 1 N N N 15.092 -11.946 20.061 -3.902 -0.746 -0.396 HA2 AG2 60 RA4 H71 H71 H 0 1 N N N 15.117 -9.610 21.651 -5.491 -0.891 1.501 HB1 AG2 61 RA4 H72 H72 H 0 1 N N N 14.277 -9.077 20.158 -6.278 0.610 0.956 HB2 AG2 62 RA4 H61 H61 H 0 1 N N N 12.610 -10.796 20.357 -6.849 -0.471 -1.200 HG1 AG2 63 RA4 H62 H62 H 0 1 N N N 13.570 -11.690 21.586 -6.063 -1.972 -0.656 HG2 AG2 64 RA4 H51 H51 H 0 1 N N N 13.300 -9.288 22.908 -7.653 -2.117 1.241 HD1 AG2 65 RA4 H52 H52 H 0 1 N N N 11.816 -9.229 21.934 -8.439 -0.616 0.697 HD2 AG2 66 RA4 HN4 HN4 H 0 1 N N N 12.242 -11.878 23.049 -8.423 -2.444 -1.456 HE1 AG2 67 RA4 HN1 HN1 H 0 1 N N N 10.201 -9.373 25.149 -11.217 -2.882 1.372 HH11 AG2 68 RA4 HN31 HN31 H 0 0 N N N 9.916 -11.388 25.370 -10.422 -3.656 -1.909 HH21 AG2 69 RA4 HN32 HN32 H 0 0 N N N 10.801 -12.501 24.380 -11.588 -3.832 -0.712 HH22 AG2 70 # # 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 RA4 C27 C26 SING N N 1 RA4 C27 C28 DOUB Y N 2 RA4 C27 C35 SING Y N 3 RA4 C26 O25 DOUB N N 4 RA4 C26 N24 SING N N 5 RA4 N24 C23 SING N N 6 RA4 N24 H24 SING N N 7 RA4 C23 C22 SING N N 8 RA4 C23 C18 SING N N 9 RA4 C23 H23 SING N N 10 RA4 C22 C21 SING N N 11 RA4 C22 H221 SING N N 12 RA4 C22 H222 SING N N 13 RA4 C21 C20 SING N N 14 RA4 C21 C19 SING N N 15 RA4 C21 H21 SING N N 16 RA4 C20 H201 SING N N 17 RA4 C20 H202 SING N N 18 RA4 C20 H203 SING N N 19 RA4 C19 H191 SING N N 20 RA4 C19 H192 SING N N 21 RA4 C19 H193 SING N N 22 RA4 C18 O17 DOUB N N 23 RA4 C18 N16 SING N N 24 RA4 N16 C15 SING N N 25 RA4 N16 C12 SING N N 26 RA4 C15 C14 SING N N 27 RA4 C15 H151 SING N N 28 RA4 C15 H152 SING N N 29 RA4 C14 C13 SING N N 30 RA4 C14 H141 SING N N 31 RA4 C14 H142 SING N N 32 RA4 C13 C12 SING N N 33 RA4 C13 H131 SING N N 34 RA4 C13 H132 SING N N 35 RA4 C12 C11 SING N N 36 RA4 C12 H12 SING N N 37 RA4 C11 O10 DOUB N N 38 RA4 C11 N9 SING N N 39 RA4 N9 C8 SING N N 40 RA4 N9 HN9 SING N N 41 RA4 C8 C7 SING N N 42 RA4 C8 H81 SING N N 43 RA4 C8 H82 SING N N 44 RA4 C7 C6 SING N N 45 RA4 C7 H71 SING N N 46 RA4 C7 H72 SING N N 47 RA4 C6 C5 SING N N 48 RA4 C6 H61 SING N N 49 RA4 C6 H62 SING N N 50 RA4 C5 N4 SING N N 51 RA4 C5 H51 SING N N 52 RA4 C5 H52 SING N N 53 RA4 N4 C2 SING N N 54 RA4 N4 HN4 SING N N 55 RA4 C2 N1 DOUB N N 56 RA4 C2 N3 SING N N 57 RA4 N1 HN1 SING N N 58 RA4 N3 HN31 SING N N 59 RA4 N3 HN32 SING N N 60 RA4 C28 C29 SING Y N 61 RA4 C28 H28 SING N N 62 RA4 C29 C30 DOUB Y N 63 RA4 C29 H29 SING N N 64 RA4 C30 N31 SING N N 65 RA4 C30 C34 SING Y N 66 RA4 N31 O32 SING N N 67 RA4 N31 O33 DOUB N N 68 RA4 C34 C35 DOUB Y N 69 RA4 C34 H34 SING N N 70 RA4 C35 H35 SING N N 71 # # 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 RA4 SMILES ACDLabs 12.01 "O=C(NCCCCNC(=[N@H])N)C2N(C(=O)C(NC(=O)c1ccc([N+]([O-])=O)cc1)CC(C)C)CCC2" RA4 InChI InChI 1.03 "InChI=1S/C23H35N7O5/c1-15(2)14-18(28-20(31)16-7-9-17(10-8-16)30(34)35)22(33)29-13-5-6-19(29)21(32)26-11-3-4-12-27-23(24)25/h7-10,15,18-19H,3-6,11-14H2,1-2H3,(H,26,32)(H,28,31)(H4,24,25,27)/t18-,19-/m0/s1" RA4 InChIKey InChI 1.03 FIZYZWLGMGGGBJ-OALUTQOASA-N RA4 SMILES_CANONICAL CACTVS 3.385 "CC(C)C[C@H](NC(=O)c1ccc(cc1)[N+]([O-])=O)C(=O)N2CCC[C@H]2C(=O)NCCCCNC(N)=N" RA4 SMILES CACTVS 3.385 "CC(C)C[CH](NC(=O)c1ccc(cc1)[N+]([O-])=O)C(=O)N2CCC[CH]2C(=O)NCCCCNC(N)=N" RA4 SMILES_CANONICAL "OpenEye OEToolkits" 1.7.5 "[H]/N=C(\N)/NCCCCNC(=O)[C@@H]1CCCN1C(=O)[C@H](CC(C)C)NC(=O)c2ccc(cc2)[N+](=O)[O-]" RA4 SMILES "OpenEye OEToolkits" 1.7.5 "CC(C)CC(C(=O)N1CCCC1C(=O)NCCCCNC(=N)N)NC(=O)c2ccc(cc2)[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 RA4 "SYSTEMATIC NAME" ACDLabs 12.01 "N-(4-nitrobenzoyl)-L-leucyl-N-(4-carbamimidamidobutyl)-L-prolinamide" RA4 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.0 "(2S)-N-(4-carbamimidamidobutyl)-1-[(2S)-4-methyl-2-[(4-nitrophenyl)carbonylamino]pentanoyl]pyrrolidine-2-carboxamide" # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site RA4 "Create component" 2005-02-03 RCSB RA4 "Modify subcomponent list" 2011-02-24 RCSB RA4 "Modify descriptor" 2011-06-04 RCSB RA4 "Modify descriptor" 2012-01-05 RCSB RA4 "Modify synonyms" 2020-06-05 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id RA4 _pdbx_chem_comp_synonyms.name "1-GUANIDINO-4-(N-NITRO-BENZOYLAMINO-L-LEUCYL-L-PROLYLAMINO)BUTANE" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##