data_PRDCC_000940 # _chem_comp.id PRD_000940 _chem_comp.name "D-PHE-PRO-D-ARG-D-THR DERIVED DIRECT THROMBIN INHIBITOR" _chem_comp.formula "C24 H39 N8 O5" _chem_comp.formula_weight 519.617 _chem_comp.pdbx_release_status REF_ONLY _chem_comp.type peptide-like _chem_comp.pdbx_type ? _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge ? _chem_comp.pdbx_initial_date ? _chem_comp.pdbx_modified_date ? _chem_comp.pdbx_ambiguous_flag ? _chem_comp.pdbx_replaced_by ? _chem_comp.pdbx_replaces ? _chem_comp.one_letter_code ? _chem_comp.three_letter_code ? _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag ? _chem_comp.pdbx_ideal_coordinates_details ? _chem_comp.pdbx_ideal_coordinates_missing_flag ? _chem_comp.pdbx_model_coordinates_db_code ? _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site ? # 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_comp_id _chem_comp_atom.pdbx_residue_numbering _chem_comp_atom.pdbx_component_atom_id _chem_comp_atom.pdbx_polymer_type _chem_comp_atom.pdbx_ref_id _chem_comp_atom.pdbx_component_id _chem_comp_atom.pdbx_ordinal _chem_comp_atom.pdbx_backbone_atom_flag _chem_comp_atom.pdbx_n_terminal_atom_flag _chem_comp_atom.pdbx_c_terminal_atom_flag PRD_000940 N1 N1 N 0 1 N N N -15.596 -25.592 18.529 4.599 1.451 0.745 DPN 1 N polymer 1 1 1 ? ? ? PRD_000940 C1 C1 C 0 1 N N R -17.034 -25.172 18.574 4.364 0.104 0.206 DPN 1 CA polymer 1 1 2 ? ? ? PRD_000940 C2 C2 C 0 1 N N N -16.997 -23.667 18.529 3.003 0.051 -0.437 DPN 1 C polymer 1 1 3 ? ? ? PRD_000940 O1 O1 O 0 1 N N N -16.354 -23.080 17.659 2.451 1.077 -0.775 DPN 1 O polymer 1 1 4 ? ? ? PRD_000940 C3 C3 C 0 1 N N N -17.800 -25.775 17.403 5.435 -0.221 -0.838 DPN 1 CB polymer 1 1 5 ? ? ? PRD_000940 C4 C4 C 0 1 Y N N -19.250 -25.403 17.432 6.784 -0.288 -0.170 DPN 1 CG polymer 1 1 6 ? ? ? PRD_000940 C5 C5 C 0 1 Y N N -19.793 -24.589 16.486 7.244 -1.488 0.338 DPN 1 CD1 polymer 1 1 7 ? ? ? PRD_000940 C6 C6 C 0 1 Y N N -20.067 -25.914 18.449 7.563 0.849 -0.071 DPN 1 CD2 polymer 1 1 8 ? ? ? PRD_000940 C7 C7 C 0 1 Y N N -21.129 -24.249 16.500 8.482 -1.550 0.951 DPN 1 CE1 polymer 1 1 9 ? ? ? PRD_000940 C8 C8 C 0 1 Y N N -21.399 -25.553 18.464 8.801 0.787 0.542 DPN 1 CE2 polymer 1 1 10 ? ? ? PRD_000940 C9 C9 C 0 1 Y N N -21.944 -24.727 17.492 9.259 -0.412 1.055 DPN 1 CZ polymer 1 1 11 ? ? ? PRD_000940 N2 N2 N 0 1 N N N -17.684 -22.972 19.464 2.398 -1.137 -0.638 PRO 2 N polymer 1 1 12 ? ? ? PRD_000940 C10 C10 C 0 1 N N S -17.642 -21.518 19.425 1.077 -1.333 -1.252 PRO 2 CA polymer 1 1 13 ? ? ? PRD_000940 C11 C11 C 0 1 N N N -16.229 -20.994 19.510 0.026 -0.611 -0.448 PRO 2 C polymer 1 1 14 ? ? ? PRD_000940 O2 O2 O 0 1 N N N -15.374 -21.574 20.178 0.343 0.011 0.544 PRO 2 O polymer 1 1 15 ? ? ? PRD_000940 C12 C12 C 0 1 N N N -18.423 -21.111 20.657 0.790 -2.849 -1.248 PRO 2 CB polymer 1 1 16 ? ? ? PRD_000940 C13 C13 C 0 1 N N N -19.389 -22.258 20.919 1.717 -3.375 -0.120 PRO 2 CG polymer 1 1 17 ? ? ? PRD_000940 C14 C14 C 0 1 N N N -18.502 -23.492 20.581 2.955 -2.455 -0.284 PRO 2 CD polymer 1 1 18 ? ? ? PRD_000940 N3 N3 N 0 1 N N N -16.010 -19.853 18.860 -1.265 -0.656 -0.832 DAR 3 N polymer 1 1 19 ? ? ? PRD_000940 C15 C15 C 0 1 N N R -14.729 -19.175 18.871 -2.286 0.046 -0.050 DAR 3 CA polymer 1 1 20 ? ? ? PRD_000940 C16 C16 C 0 1 N N N -13.772 -19.755 17.862 -3.645 -0.621 -0.271 DAR 3 CB polymer 1 1 21 ? ? ? PRD_000940 C17 C17 C 0 1 N N N -12.640 -18.851 17.417 -3.613 -2.044 0.291 DAR 3 CG polymer 1 1 22 ? ? ? PRD_000940 C18 C18 C 0 1 N N N -12.393 -18.907 15.893 -4.972 -2.711 0.070 DAR 3 CD polymer 1 1 23 ? ? ? PRD_000940 N4 N4 N 0 1 N N N -11.811 -20.204 15.540 -4.940 -4.073 0.608 DAR 3 NE polymer 1 1 24 ? ? ? PRD_000940 C19 C19 C 0 1 N N N -11.189 -20.459 14.366 -6.051 -4.867 0.524 DAR 3 CZ polymer 1 1 25 ? ? ? PRD_000940 N5 N5 N 0 1 N N N -11.272 -19.586 13.366 -7.161 -4.402 -0.047 DAR 3 NH1 polymer 1 1 26 ? ? ? PRD_000940 N6 N6 N 1 1 N N N -10.547 -21.559 14.209 -6.022 -6.106 1.013 DAR 3 NH2 polymer 1 1 27 ? ? ? PRD_000940 C20 C20 C 0 1 N N N -14.157 -19.132 20.296 -2.355 1.485 -0.492 DAR 3 C polymer 1 1 28 ? ? ? PRD_000940 O3 O3 O 0 1 N N N -13.023 -19.602 20.540 -1.624 1.885 -1.372 DAR 3 O polymer 1 1 29 ? ? ? PRD_000940 N7 N7 N 0 1 N N N -14.926 -18.542 21.215 -3.231 2.328 0.092 DTH 4 N polymer 1 1 30 ? ? ? PRD_000940 C21 C21 C 0 1 N N R -14.497 -18.434 22.612 -3.298 3.727 -0.337 DTH 4 CA polymer 1 1 31 ? ? ? PRD_000940 C22 C22 C 0 1 N N S -15.632 -17.723 23.414 -2.240 4.541 0.411 DTH 4 CB polymer 1 1 32 ? ? ? PRD_000940 C23 C23 C 0 1 N N N -15.803 -16.264 23.068 -0.850 3.984 0.095 DTH 4 CG2 polymer 1 1 33 ? ? ? PRD_000940 O4 O4 O 0 1 N N N -15.283 -17.787 24.786 -2.479 4.456 1.817 DTH 4 OG1 polymer 1 1 34 ? ? ? PRD_000940 C24 C24 C 0 1 N N N -13.253 -17.643 22.714 -4.666 4.281 -0.032 DTH 4 C polymer 1 1 35 ? ? ? PRD_000940 O5 O5 O 0 1 N N N -12.870 -16.765 21.921 -5.369 3.739 0.794 DTH 4 O polymer 1 1 36 ? ? ? PRD_000940 N8 N8 N 0 1 N N N -12.465 -17.941 23.776 -5.108 5.378 -0.678 NH2 5 N polymer 1 1 37 ? ? ? PRD_000940 H1 H1 H 0 1 N N N -15.539 -26.590 18.556 5.478 1.495 1.238 DPN 1 H polymer 1 1 38 ? ? ? PRD_000940 H2 H2 H 0 1 N Y N -15.177 -25.257 17.685 4.559 2.145 0.014 DPN 1 H2 polymer 1 1 39 ? ? ? PRD_000940 H3 H3 H 0 1 N N N -17.489 -25.503 19.519 4.413 -0.624 1.015 DPN 1 HA polymer 1 1 40 ? ? ? PRD_000940 H4 H4 H 0 1 N N N -17.358 -25.410 16.464 5.210 -1.181 -1.301 DPN 1 HB2 polymer 1 1 41 ? ? ? PRD_000940 H5 H5 H 0 1 N N N -17.713 -26.871 17.448 5.446 0.557 -1.602 DPN 1 HB3 polymer 1 1 42 ? ? ? PRD_000940 H6 H6 H 0 1 N N N -19.160 -24.199 15.703 6.637 -2.378 0.257 DPN 1 HD1 polymer 1 1 43 ? ? ? PRD_000940 H7 H7 H 0 1 N N N -19.664 -26.574 19.203 7.206 1.786 -0.472 DPN 1 HD2 polymer 1 1 44 ? ? ? PRD_000940 H8 H8 H 0 1 N N N -21.532 -23.607 15.731 8.841 -2.488 1.349 DPN 1 HE1 polymer 1 1 45 ? ? ? PRD_000940 H9 H9 H 0 1 N N N -22.035 -25.924 19.254 9.410 1.676 0.619 DPN 1 HE2 polymer 1 1 46 ? ? ? PRD_000940 H10 H10 H 0 1 N N N -22.992 -24.466 17.517 10.226 -0.460 1.534 DPN 1 HZ polymer 1 1 47 ? ? ? PRD_000940 H11 H11 H 0 1 N N N -18.136 -21.134 18.520 1.084 -0.957 -2.275 PRO 2 HA polymer 1 1 48 ? ? ? PRD_000940 H12 H12 H 0 1 N N N -17.747 -20.974 21.514 -0.255 -3.044 -1.009 PRO 2 HB2 polymer 1 1 49 ? ? ? PRD_000940 H13 H13 H 0 1 N N N -18.975 -20.177 20.472 1.058 -3.295 -2.206 PRO 2 HB3 polymer 1 1 50 ? ? ? PRD_000940 H14 H14 H 0 1 N N N -19.718 -22.275 21.968 1.255 -3.244 0.858 PRO 2 HG2 polymer 1 1 51 ? ? ? PRD_000940 H15 H15 H 0 1 N N N -20.268 -22.202 20.260 1.984 -4.419 -0.289 PRO 2 HG3 polymer 1 1 52 ? ? ? PRD_000940 H16 H16 H 0 1 N N N -19.112 -24.351 20.266 3.600 -2.821 -1.083 PRO 2 HD2 polymer 1 1 53 ? ? ? PRD_000940 H17 H17 H 0 1 N N N -17.875 -23.782 21.437 3.509 -2.394 0.653 PRO 2 HD3 polymer 1 1 54 ? ? ? PRD_000940 H18 H18 H 0 1 N N N -16.762 -19.446 18.342 -1.518 -1.153 -1.625 DAR 3 H polymer 1 1 55 ? ? ? PRD_000940 H19 H19 H 0 1 N N N -14.906 -18.130 18.576 -2.028 0.002 1.008 DAR 3 HA polymer 1 1 56 ? ? ? PRD_000940 H20 H20 H 0 1 N N N -13.326 -20.659 18.303 -4.419 -0.047 0.238 DAR 3 HB2 polymer 1 1 57 ? ? ? PRD_000940 H21 H21 H 0 1 N N N -14.352 -20.031 16.969 -3.863 -0.657 -1.339 DAR 3 HB3 polymer 1 1 58 ? ? ? PRD_000940 H22 H22 H 0 1 N N N -12.887 -17.816 17.695 -2.839 -2.618 -0.219 DAR 3 HG2 polymer 1 1 59 ? ? ? PRD_000940 H23 H23 H 0 1 N N N -11.719 -19.160 17.934 -3.395 -2.008 1.358 DAR 3 HG3 polymer 1 1 60 ? ? ? PRD_000940 H24 H24 H 0 1 N N N -13.347 -18.777 15.362 -5.746 -2.137 0.579 DAR 3 HD2 polymer 1 1 61 ? ? ? PRD_000940 H25 H25 H 0 1 N N N -11.700 -18.103 15.604 -5.190 -2.747 -0.998 DAR 3 HD3 polymer 1 1 62 ? ? ? PRD_000940 H26 H26 H 0 1 N N N -11.877 -20.946 16.207 -4.132 -4.412 1.024 DAR 3 HE polymer 1 1 63 ? ? ? PRD_000940 H27 H27 H 0 0 N N N -10.834 -19.786 12.490 -7.181 -3.500 -0.404 DAR 3 HH11 polymer 1 1 64 ? ? ? PRD_000940 H28 H28 H 0 0 N N N -11.773 -18.729 13.490 -7.948 -4.965 -0.107 DAR 3 HH12 polymer 1 1 65 ? ? ? PRD_000940 H29 H29 H 0 0 N N N -10.108 -21.761 13.334 -6.810 -6.669 0.953 DAR 3 HH21 polymer 1 1 66 ? ? ? PRD_000940 H30 H30 H 0 0 N N N -10.486 -22.214 14.962 -5.214 -6.445 1.429 DAR 3 HH22 polymer 1 1 67 ? ? ? PRD_000940 H31 H31 H 0 1 N N N -15.812 -18.166 20.944 -3.816 2.008 0.796 DTH 4 H polymer 1 1 68 ? ? ? PRD_000940 H32 H32 H 0 1 N N N -14.338 -19.436 23.036 -3.112 3.788 -1.409 DTH 4 HA polymer 1 1 69 ? ? ? PRD_000940 H33 H33 H 0 1 N N N -16.578 -18.254 23.230 -2.294 5.583 0.096 DTH 4 HB polymer 1 1 70 ? ? ? PRD_000940 H34 H34 H 0 0 N N N -16.617 -15.836 23.672 -0.709 3.950 -0.985 DTH 4 HG21 polymer 1 1 71 ? ? ? PRD_000940 H35 H35 H 0 0 N N N -14.868 -15.725 23.280 -0.091 4.627 0.541 DTH 4 HG22 polymer 1 1 72 ? ? ? PRD_000940 H36 H36 H 0 0 N N N -16.049 -16.167 22.000 -0.761 2.978 0.505 DTH 4 HG23 polymer 1 1 73 ? ? ? PRD_000940 H37 H37 H 0 1 N N N -15.956 -17.361 25.305 -3.344 4.792 2.090 DTH 4 HG1 polymer 1 1 74 ? ? ? PRD_000940 H38 H38 H 0 1 N N N -11.599 -17.459 23.907 -4.520 5.853 -1.286 NH2 5 HN1 polymer 1 1 75 ? ? ? PRD_000940 H39 H39 H 0 1 N N N -12.750 -18.643 24.429 -6.015 5.692 -0.536 NH2 5 HN2 polymer 1 1 76 ? ? ? # 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 PRD_000940 N1 C1 SING N N 1 PRD_000940 N1 H1 SING N N 2 PRD_000940 N1 H2 SING N N 3 PRD_000940 C1 C2 SING N N 4 PRD_000940 C1 C3 SING N N 5 PRD_000940 C1 H3 SING N N 6 PRD_000940 C2 O1 DOUB N N 7 PRD_000940 C3 C4 SING N N 8 PRD_000940 C3 H4 SING N N 9 PRD_000940 C3 H5 SING N N 10 PRD_000940 C4 C5 DOUB Y N 11 PRD_000940 C4 C6 SING Y N 12 PRD_000940 C5 C7 SING Y N 13 PRD_000940 C5 H6 SING N N 14 PRD_000940 C6 C8 DOUB Y N 15 PRD_000940 C6 H7 SING N N 16 PRD_000940 C7 C9 DOUB Y N 17 PRD_000940 C7 H8 SING N N 18 PRD_000940 C8 C9 SING Y N 19 PRD_000940 C8 H9 SING N N 20 PRD_000940 C9 H10 SING N N 21 PRD_000940 N2 C10 SING N N 22 PRD_000940 N2 C14 SING N N 23 PRD_000940 C10 C11 SING N N 24 PRD_000940 C10 C12 SING N N 25 PRD_000940 C10 H11 SING N N 26 PRD_000940 C11 O2 DOUB N N 27 PRD_000940 C12 C13 SING N N 28 PRD_000940 C12 H12 SING N N 29 PRD_000940 C12 H13 SING N N 30 PRD_000940 C13 C14 SING N N 31 PRD_000940 C13 H14 SING N N 32 PRD_000940 C13 H15 SING N N 33 PRD_000940 C14 H16 SING N N 34 PRD_000940 C14 H17 SING N N 35 PRD_000940 N3 C15 SING N N 36 PRD_000940 N3 H18 SING N N 37 PRD_000940 C15 C16 SING N N 38 PRD_000940 C15 C20 SING N N 39 PRD_000940 C15 H19 SING N N 40 PRD_000940 C16 C17 SING N N 41 PRD_000940 C16 H20 SING N N 42 PRD_000940 C16 H21 SING N N 43 PRD_000940 C17 C18 SING N N 44 PRD_000940 C17 H22 SING N N 45 PRD_000940 C17 H23 SING N N 46 PRD_000940 C18 N4 SING N N 47 PRD_000940 C18 H24 SING N N 48 PRD_000940 C18 H25 SING N N 49 PRD_000940 N4 C19 SING N N 50 PRD_000940 N4 H26 SING N N 51 PRD_000940 C19 N5 SING N N 52 PRD_000940 C19 N6 DOUB N N 53 PRD_000940 N5 H27 SING N N 54 PRD_000940 N5 H28 SING N N 55 PRD_000940 N6 H29 SING N N 56 PRD_000940 N6 H30 SING N N 57 PRD_000940 C20 O3 DOUB N N 58 PRD_000940 N7 C21 SING N N 59 PRD_000940 N7 H31 SING N N 60 PRD_000940 C21 C22 SING N N 61 PRD_000940 C21 C24 SING N N 62 PRD_000940 C21 H32 SING N N 63 PRD_000940 C22 C23 SING N N 64 PRD_000940 C22 O4 SING N N 65 PRD_000940 C22 H33 SING N N 66 PRD_000940 C23 H34 SING N N 67 PRD_000940 C23 H35 SING N N 68 PRD_000940 C23 H36 SING N N 69 PRD_000940 O4 H37 SING N N 70 PRD_000940 C24 O5 DOUB N N 71 PRD_000940 N8 H38 SING N N 72 PRD_000940 N8 H39 SING N N 73 PRD_000940 C2 N2 SING N N 74 PRD_000940 C11 N3 SING N N 75 PRD_000940 C20 N7 SING N N 76 PRD_000940 C24 N8 SING N N 77 # 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 PRD_000940 SMILES ACDLabs 12.01 "O=C(NC(C(=O)NC(C(=O)N)C(O)C)CCCNC(=[NH2+])\N)C2N(C(=O)C(N)Cc1ccccc1)CCC2" PRD_000940 InChI InChI 1.03 "InChI=1S/C24H38N8O5/c1-14(33)19(20(26)34)31-21(35)17(9-5-11-29-24(27)28)30-22(36)18-10-6-12-32(18)23(37)16(25)13-15-7-3-2-4-8-15/h2-4,7-8,14,16-19,33H,5-6,9-13,25H2,1H3,(H2,26,34)(H,30,36)(H,31,35)(H4,27,28,29)/p+1/t14-,16-,17-,18+,19-/m1/s1" PRD_000940 InChIKey InChI 1.03 DQDTXGOXVWFJHV-RXABAKJHSA-O PRD_000940 SMILES_CANONICAL CACTVS 3.370 "C[C@@H](O)[C@@H](NC(=O)[C@@H](CCCNC(N)=[NH2+])NC(=O)[C@@H]1CCCN1C(=O)[C@H](N)Cc2ccccc2)C(N)=O" PRD_000940 SMILES CACTVS 3.370 "C[CH](O)[CH](NC(=O)[CH](CCCNC(N)=[NH2+])NC(=O)[CH]1CCCN1C(=O)[CH](N)Cc2ccccc2)C(N)=O" PRD_000940 SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "C[C@@H]([C@H](C(=O)N)NC(=O)[C@@H](CCCNC(=[NH2+])N)NC(=O)[C@@H]1CCCN1C(=O)[C@@H](Cc2ccccc2)N)O" PRD_000940 SMILES "OpenEye OEToolkits" 1.7.6 "CC(C(C(=O)N)NC(=O)C(CCCNC(=[NH2+])N)NC(=O)C1CCCN1C(=O)C(Cc2ccccc2)N)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 PRD_000940 "SYSTEMATIC NAME" ACDLabs 12.01 "D-phenylalanyl-L-prolyl-N~5~-[amino(iminio)methyl]-D-ornithyl-D-threoninamide" PRD_000940 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "[azanyl-[[(4R)-5-[[(2R,3S)-1-azanyl-3-oxidanyl-1-oxidanylidene-butan-2-yl]amino]-4-[[(2S)-1-[(2R)-2-azanyl-3-phenyl-propanoyl]pyrrolidin-2-yl]carbonylamino]-5-oxidanylidene-pentyl]amino]methylidene]azanium" #