data_DP2
# 
_chem_comp.id                                    DP2 
_chem_comp.name                                  "D-lysyl-N~5~-(N-nitrocarbamimidoyl)-D-ornithinamide" 
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C12 H26 N8 O4" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         "D-LYSINE-D-NITROARGININE AMIDE" 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2003-12-18 
_chem_comp.pdbx_modified_date                    2026-04-05 
_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                        346.386 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     DP2 
_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        1RS6 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  RCSB 
_chem_comp.pdbx_pcm                              ? 
# 
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.pdbx_n_terminal_atom_flag 
_chem_comp_atom.pdbx_backbone_atom_flag 
_chem_comp_atom.pdbx_c_terminal_atom_flag 
_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 
DP2 N1     N1     N 1  1 N N N N N N 14.709 1.535  21.207 6.998  -1.766 -0.079 N1     DP2 1  
DP2 O2     O2     O 0  1 N N N N N N 14.393 2.115  20.121 7.122  -1.961 1.117  O2     DP2 2  
DP2 O3     O3     O -1 1 N N N N N N 15.791 0.830  21.281 7.932  -1.980 -0.831 O3     DP2 3  
DP2 N      N      N 0  1 N N N N N N 7.017  2.606  25.532 -1.368 0.948  -0.178 N      DP2 4  
DP2 CA     CA     C 0  1 N N R N N N 7.863  1.637  24.782 -0.623 2.206  -0.089 CA     DP2 5  
DP2 C      C      C 0  1 N N N N N N 7.158  1.154  23.502 -1.436 3.218  0.677  C      DP2 6  
DP2 N2     N2     N 0  1 N N N N N N 6.707  2.023  22.580 -0.947 4.457  0.885  N2     DP2 7  
DP2 O      O      O 0  1 N N N N N N 6.970  -0.016 23.274 -2.530 2.918  1.107  O      DP2 8  
DP2 CB     CB     C 0  1 N N N N N N 9.198  2.289  24.423 0.703  1.964  0.635  CB     DP2 9  
DP2 CG     CG     C 0  1 N N N N N N 10.283 1.271  24.061 1.579  1.032  -0.206 CG     DP2 10 
DP2 CD     CD     C 0  1 N N N N N N 11.644 1.985  23.987 2.905  0.790  0.518  CD     DP2 11 
DP2 NE     NE     N 0  1 N N N N N N 12.703 0.971  24.079 3.745  -0.102 -0.286 NE     DP2 12 
DP2 CZ     CZ     C 0  1 N N N N N N 13.738 0.844  23.281 4.992  -0.464 0.165  CZ     DP2 13 
DP2 NH1    NH1    N 0  1 N N N N N N 13.890 1.698  22.266 5.779  -1.301 -0.590 NH1    DP2 14 
DP2 NH2    NH2    N 0  1 N N N N N N 14.609 -0.160 23.526 5.428  -0.014 1.308  NH2    DP2 15 
DP2 "N'"   "N'"   N 0  1 N N N N N N 4.400  2.643  28.100 -3.584 -0.679 -2.606 "N'"   DP2 16 
DP2 "CA'"  "CA'"  C 0  1 N N R N N N 5.025  3.289  26.892 -3.042 -0.525 -1.249 "CA'"  DP2 17 
DP2 "C'"   "C'"   C 0  1 N N N N N N 5.819  2.229  26.093 -2.276 0.770  -1.158 "C'"   DP2 18 
DP2 "O'"   "O'"   O 0  1 N N N N N N 5.420  1.038  25.982 -2.476 1.651  -1.967 "O'"   DP2 19 
DP2 "CB'"  "CB'"  C 0  1 N N N N N N 3.902  3.975  26.070 -4.192 -0.509 -0.240 "CB'"  DP2 20 
DP2 "CG'"  "CG'"  C 0  1 N N N N N N 3.051  5.028  26.841 -4.893 -1.868 -0.244 "CG'"  DP2 21 
DP2 "CD'"  "CD'"  C 0  1 N N N N N N 2.849  6.272  25.953 -6.043 -1.852 0.765  "CD'"  DP2 22 
DP2 "CE'"  "CE'"  C 0  1 N N N N N N 1.753  7.231  26.487 -6.745 -3.212 0.761  "CE'"  DP2 23 
DP2 "NZ'"  "NZ'"  N 0  1 N N N N N N 0.918  7.637  25.332 -7.849 -3.197 1.730  "NZ'"  DP2 24 
DP2 HN     HN     H 0  1 N N N N N N 7.327  3.552  25.630 -1.209 0.243  0.469  HN     DP2 25 
DP2 HA     HA     H 0  1 N N N N N N 8.061  0.763  25.421 -0.426 2.583  -1.093 HA     DP2 26 
DP2 HN21   1HN2   H 0  0 N N N N N N 6.244  1.686  21.760 -0.072 4.697  0.541  HN21   DP2 27 
DP2 HN22   2HN2   H 0  0 N N N N N N 6.834  3.006  22.715 -1.470 5.108  1.378  HN22   DP2 28 
DP2 HB1    1HB    H 0  1 N N N N N N 9.042  2.956  23.562 1.217  2.914  0.779  HB1    DP2 29 
DP2 HB2    2HB    H 0  1 N N N N N N 9.544  2.878  25.285 0.509  1.504  1.604  HB2    DP2 30 
DP2 HG1    1HG    H 0  1 N N N N N N 10.321 0.485  24.830 1.065  0.082  -0.350 HG1    DP2 31 
DP2 HG2    2HG    H 0  1 N N N N N N 10.052 0.818  23.085 1.773  1.492  -1.175 HG2    DP2 32 
DP2 HD1    1HD    H 0  1 N N N N N N 11.729 2.526  23.033 3.419  1.740  0.663  HD1    DP2 33 
DP2 HD2    2HD    H 0  1 N N N N N N 11.737 2.696  24.821 2.712  0.330  1.487  HD2    DP2 34 
DP2 HNE    HNE    H 0  1 N N N N N N 12.628 0.310  24.826 3.420  -0.436 -1.137 HNE    DP2 35 
DP2 HH1    HH1    H 0  1 N N N N N N 13.346 2.537  22.294 5.491  -1.569 -1.477 HH1    DP2 36 
DP2 HH2    HH2    H 0  1 N N N N N N 15.359 -0.175 22.864 6.349  -0.166 1.569  HH2    DP2 37 
DP2 "HN'1" "1HN'" H 0  0 N N N N N N 3.887  3.328  28.617 -4.205 0.082  -2.836 "HN'1" DP2 38 
DP2 "HN'2" "2HN'" H 0  0 N N N N N N 3.781  1.915  27.806 -2.841 -0.757 -3.285 "HN'2" DP2 39 
DP2 "HA'"  "HA'"  H 0  1 N N N N N N 5.728  4.065  27.229 -2.376 -1.358 -1.027 "HA'"  DP2 40 
DP2 "HB'1" "1HB'" H 0  0 N N N N N N 4.371  4.481  25.213 -3.799 -0.306 0.756  "HB'1" DP2 41 
DP2 "HB'2" "2HB'" H 0  0 N N N N N N 3.222  3.191  25.706 -4.905 0.269  -0.514 "HB'2" DP2 42 
DP2 "HG'1" "1HG'" H 0  0 N N N N N N 2.072  4.595  27.094 -5.287 -2.071 -1.240 "HG'1" DP2 43 
DP2 "HG'2" "2HG'" H 0  0 N N N N N N 3.574  5.317  27.765 -4.180 -2.646 0.030  "HG'2" DP2 44 
DP2 "HD'1" "1HD'" H 0  0 N N N N N N 3.800  6.822  25.900 -5.650 -1.650 1.761  "HD'1" DP2 45 
DP2 "HD'2" "2HD'" H 0  0 N N N N N N 2.562  5.939  24.945 -6.757 -1.075 0.491  "HD'2" DP2 46 
DP2 "HE'1" "1HE'" H 0  0 N N N N N N 1.134  6.715  27.235 -7.138 -3.415 -0.235 "HE'1" DP2 47 
DP2 "HE'2" "2HE'" H 0  0 N N N N N N 2.219  8.117  26.944 -6.031 -3.990 1.035  "HE'2" DP2 48 
DP2 "HZ'1" "1HZ'" H 0  0 N N N N N N 0.198  8.258  25.642 -8.328 -4.085 1.746  "HZ'1" DP2 49 
DP2 "HZ'2" "2HZ'" H 0  0 N N N N N N 1.489  8.101  24.655 -7.519 -2.947 2.650  "HZ'2" DP2 50 
# 
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 
DP2 N1    O2     DOUB N N 1  
DP2 N1    O3     SING N N 2  
DP2 N1    NH1    SING N N 3  
DP2 N     CA     SING N N 4  
DP2 N     "C'"   SING N N 5  
DP2 N     HN     SING N N 6  
DP2 CA    C      SING N N 7  
DP2 CA    CB     SING N N 8  
DP2 CA    HA     SING N N 9  
DP2 C     N2     SING N N 10 
DP2 C     O      DOUB N N 11 
DP2 N2    HN21   SING N N 12 
DP2 N2    HN22   SING N N 13 
DP2 CB    CG     SING N N 14 
DP2 CB    HB1    SING N N 15 
DP2 CB    HB2    SING N N 16 
DP2 CG    CD     SING N N 17 
DP2 CG    HG1    SING N N 18 
DP2 CG    HG2    SING N N 19 
DP2 CD    NE     SING N N 20 
DP2 CD    HD1    SING N N 21 
DP2 CD    HD2    SING N N 22 
DP2 NE    CZ     SING N N 23 
DP2 NE    HNE    SING N N 24 
DP2 CZ    NH1    SING N N 25 
DP2 CZ    NH2    DOUB N N 26 
DP2 NH1   HH1    SING N N 27 
DP2 NH2   HH2    SING N N 28 
DP2 "N'"  "CA'"  SING N N 29 
DP2 "N'"  "HN'1" SING N N 30 
DP2 "N'"  "HN'2" SING N N 31 
DP2 "CA'" "C'"   SING N N 32 
DP2 "CA'" "CB'"  SING N N 33 
DP2 "CA'" "HA'"  SING N N 34 
DP2 "C'"  "O'"   DOUB N N 35 
DP2 "CB'" "CG'"  SING N N 36 
DP2 "CB'" "HB'1" SING N N 37 
DP2 "CB'" "HB'2" SING N N 38 
DP2 "CG'" "CD'"  SING N N 39 
DP2 "CG'" "HG'1" SING N N 40 
DP2 "CG'" "HG'2" SING N N 41 
DP2 "CD'" "CE'"  SING N N 42 
DP2 "CD'" "HD'1" SING N N 43 
DP2 "CD'" "HD'2" SING N N 44 
DP2 "CE'" "NZ'"  SING N N 45 
DP2 "CE'" "HE'1" SING N N 46 
DP2 "CE'" "HE'2" SING N N 47 
DP2 "NZ'" "HZ'1" SING N N 48 
DP2 "NZ'" "HZ'2" SING N N 49 
# 
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 
DP2 SMILES           ACDLabs              14.52   "NCCCCC(N)C(=O)NC(CCCNC(=N)N[N+]([O-])=O)C(N)=O"                                                                                                      
DP2 InChI            InChI                1.06    "InChI=1S/C12H26N8O4/c13-6-2-1-4-8(14)11(22)18-9(10(15)21)5-3-7-17-12(16)19-20(23)24/h8-9H,1-7,13-14H2,(H2,15,21)(H,18,22)(H3,16,17,19)/t8-,9-/m1/s1" 
DP2 InChIKey         InChI                1.06    NRDGOJQPHWAEES-RKDXNWHRSA-N                                                                                                                           
DP2 SMILES_CANONICAL CACTVS               3.385   "NCCCC[C@@H](N)C(=O)N[C@H](CCCNC(=N)N[N+]([O-])=O)C(N)=O"                                                                                             
DP2 SMILES           CACTVS               3.385   "NCCCC[CH](N)C(=O)N[CH](CCCNC(=N)N[N+]([O-])=O)C(N)=O"                                                                                                
DP2 SMILES_CANONICAL "OpenEye OEToolkits" 3.1.0.0 "C(CCN)C[C@H](C(=O)N[C@H](CCCNC(=N)N[N+](=O)[O-])C(=O)N)N"                                                                                            
DP2 SMILES           "OpenEye OEToolkits" 3.1.0.0 "C(CCN)CC(C(=O)NC(CCCNC(=N)N[N+](=O)[O-])C(=O)N)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 
DP2 "SYSTEMATIC NAME" ACDLabs              14.52   "D-lysyl-N~5~-(N-nitrocarbamimidoyl)-D-ornithinamide"                                                                      
DP2 "SYSTEMATIC NAME" "OpenEye OEToolkits" 3.1.0.0 "(2~{R})-2,6-bis(azanyl)-~{N}-[(2~{R})-1-azanyl-5-[(~{N}-nitrocarbamimidoyl)amino]-1-oxidanylidene-pentan-2-yl]hexanamide" 
# 
_pdbx_chem_comp_synonyms.ordinal      1 
_pdbx_chem_comp_synonyms.comp_id      DP2 
_pdbx_chem_comp_synonyms.name         "D-LYSINE-D-NITROARGININE AMIDE" 
_pdbx_chem_comp_synonyms.provenance   ? 
_pdbx_chem_comp_synonyms.type         ? 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
DP2 "Create component"   2003-12-18 RCSB 
DP2 "Modify descriptor"  2011-06-04 RCSB 
DP2 "Modify synonyms"    2021-03-01 PDBE 
DP2 "Other modification" 2026-04-05 RCSB 
# 
