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" 
# 
