data_DP2 # _chem_comp.id DP2 _chem_comp.name "L-LYSYL-N~5~-[(Z)-(2,2-DIHYDROXYHYDRAZINO)(IMINO)METHYL]-L-ORNITHINAMIDE" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C12 H28 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 2021-03-01 _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 348.402 _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 ? _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 # # 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 DP2 N1 N1 N 0 1 N N N 14.709 1.535 21.207 1.530 0.219 -6.996 N1 DP2 1 DP2 O2 O2 O 0 1 N N N 14.393 2.115 20.121 2.930 0.641 -7.009 O2 DP2 2 DP2 O3 O3 O 0 1 N N N 15.791 0.830 21.281 1.430 -0.932 -7.893 O3 DP2 3 DP2 N N N 0 1 N N N 7.017 2.606 25.532 -0.977 -0.098 1.356 N DP2 4 DP2 CA CA C 0 1 N N R 7.863 1.637 24.782 -2.266 -0.202 0.668 CA DP2 5 DP2 C C C 0 1 N N N 7.158 1.154 23.502 -3.335 0.452 1.504 C DP2 6 DP2 N2 N2 N 0 1 N N N 6.707 2.023 22.580 -3.021 1.485 2.311 N2 DP2 7 DP2 O O O 0 1 N N N 6.970 -0.016 23.274 -4.478 0.050 1.451 O DP2 8 DP2 CB CB C 0 1 N N N 9.198 2.289 24.423 -2.178 0.497 -0.688 CB DP2 9 DP2 CG CG C 0 1 N N N 10.283 1.271 24.061 -1.093 -0.167 -1.536 CG DP2 10 DP2 CD CD C 0 1 N N N 11.644 1.985 23.987 -1.005 0.532 -2.894 CD DP2 11 DP2 NE NE N 0 1 N N N 12.703 0.971 24.079 0.033 -0.104 -3.706 NE DP2 12 DP2 CZ CZ C 0 1 N N N 13.738 0.844 23.281 0.295 0.358 -4.974 CZ DP2 13 DP2 NH1 NH1 N 0 1 N N N 13.890 1.698 22.266 1.270 -0.240 -5.736 NH1 DP2 14 DP2 NH2 NH2 N 0 1 N N N 14.609 -0.160 23.526 -0.381 1.363 -5.453 NH2 DP2 15 DP2 "N'" "N'" N 0 1 N N N 4.400 2.643 28.100 1.265 -2.307 3.175 "N'" DP2 16 DP2 "CA'" "CA'" C 0 1 N N R 5.025 3.289 26.892 0.738 -0.960 2.916 "CA'" DP2 17 DP2 "C'" "C'" C 0 1 N N N 5.819 2.229 26.093 -0.588 -1.067 2.209 "C'" DP2 18 DP2 "O'" "O'" O 0 1 N N N 5.420 1.038 25.982 -1.305 -2.025 2.407 "O'" DP2 19 DP2 "CB'" "CB'" C 0 1 N N N 3.902 3.975 26.070 0.550 -0.222 4.243 "CB'" DP2 20 DP2 "CG'" "CG'" C 0 1 N N N 3.051 5.028 26.841 1.897 -0.113 4.961 "CG'" DP2 21 DP2 "CD'" "CD'" C 0 1 N N N 2.849 6.272 25.953 1.709 0.624 6.288 "CD'" DP2 22 DP2 "CE'" "CE'" C 0 1 N N N 1.753 7.231 26.487 3.056 0.732 7.006 "CE'" DP2 23 DP2 "NZ'" "NZ'" N 0 1 N N N 0.918 7.637 25.332 2.876 1.441 8.280 "NZ'" DP2 24 DP2 HO2 HO2 H 0 1 N N N 13.598 2.632 20.066 3.116 0.967 -7.901 HO2 DP2 25 DP2 HO3 HO3 H 0 1 N N N 16.027 0.396 22.092 1.613 -0.608 -8.785 HO3 DP2 26 DP2 HN HN H 0 1 N N N 7.272 3.583 25.669 -0.403 0.667 1.197 HN DP2 27 DP2 HA HA H 0 1 N N N 8.040 0.750 25.435 -2.515 -1.253 0.519 HA DP2 28 DP2 HN21 1HN2 H 0 0 N N N 6.865 3.011 22.772 -3.709 1.907 2.849 HN21 DP2 29 DP2 HN22 2HN2 H 0 0 N N N 6.239 1.702 21.731 -2.107 1.807 2.354 HN22 DP2 30 DP2 HB1 1HB H 0 1 N N N 9.068 3.039 23.608 -3.138 0.420 -1.199 HB1 DP2 31 DP2 HB2 2HB H 0 1 N N N 9.543 2.965 25.239 -1.930 1.548 -0.539 HB2 DP2 32 DP2 HG1 1HG H 0 1 N N N 10.298 0.402 24.760 -0.134 -0.090 -1.025 HG1 DP2 33 DP2 HG2 2HG H 0 1 N N N 10.045 0.715 23.124 -1.342 -1.218 -1.685 HG2 DP2 34 DP2 HD1 1HD H 0 1 N N N 11.742 2.627 23.081 -1.965 0.455 -3.405 HD1 DP2 35 DP2 HD2 2HD H 0 1 N N N 11.750 2.787 24.754 -0.757 1.583 -2.745 HD2 DP2 36 DP2 HNE HNE H 0 1 N N N 12.231 0.066 24.078 0.537 -0.852 -3.349 HNE DP2 37 DP2 HH1 HH1 H 0 1 N N N 12.957 1.861 21.885 1.774 -0.988 -5.380 HH1 DP2 38 DP2 HH2 HH2 H 0 1 N N N 14.281 -1.108 23.341 -0.197 1.689 -6.348 HH2 DP2 39 DP2 "HN'1" "1HN'" H 0 0 N N N 3.876 3.342 28.626 0.586 -2.777 3.754 "HN'1" DP2 40 DP2 "HN'2" "2HN'" H 0 0 N N N 5.087 2.160 28.678 1.274 -2.789 2.289 "HN'2" DP2 41 DP2 "HA'" "HA'" H 0 1 N N N 5.759 4.077 27.178 1.440 -0.409 2.290 "HA'" DP2 42 DP2 "HB'1" "1HB'" H 0 0 N N N 4.330 4.432 25.147 -0.151 -0.773 4.869 "HB'1" DP2 43 DP2 "HB'2" "2HB'" H 0 0 N N N 3.235 3.203 25.617 0.159 0.776 4.051 "HB'2" DP2 44 DP2 "HG'1" "1HG'" H 0 0 N N N 2.084 4.606 27.202 2.599 0.437 4.335 "HG'1" DP2 45 DP2 "HG'2" "2HG'" H 0 0 N N N 3.493 5.284 27.832 2.288 -1.113 5.153 "HG'2" DP2 46 DP2 "HD'1" "1HD'" H 0 0 N N N 3.812 6.813 25.803 1.007 0.073 6.914 "HD'1" DP2 47 DP2 "HD'2" "2HD'" H 0 0 N N N 2.639 5.977 24.898 1.318 1.623 6.096 "HD'2" DP2 48 DP2 "HE'1" "1HE'" H 0 0 N N N 1.158 6.790 27.320 3.447 -0.266 7.198 "HE'1" DP2 49 DP2 "HE'2" "2HE'" H 0 0 N N N 2.170 8.099 27.049 3.758 1.283 6.380 "HE'2" DP2 50 DP2 "HZ'1" "1HZ'" H 0 0 N N N 0.197 8.267 25.683 3.785 1.489 8.716 "HZ'1" DP2 51 DP2 "HZ'2" "2HZ'" H 0 0 N N N 0.536 6.843 24.817 2.614 2.388 8.051 "HZ'2" DP2 52 # # 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 SING N N 1 DP2 N1 O3 SING N N 2 DP2 N1 NH1 SING N N 3 DP2 O2 HO2 SING N N 4 DP2 O3 HO3 SING N N 5 DP2 N CA SING N N 6 DP2 N "C'" SING N N 7 DP2 N HN SING N N 8 DP2 CA C SING N N 9 DP2 CA CB SING N N 10 DP2 CA HA SING N N 11 DP2 C N2 SING N N 12 DP2 C O DOUB N N 13 DP2 N2 HN21 SING N N 14 DP2 N2 HN22 SING N N 15 DP2 CB CG SING N N 16 DP2 CB HB1 SING N N 17 DP2 CB HB2 SING N N 18 DP2 CG CD SING N N 19 DP2 CG HG1 SING N N 20 DP2 CG HG2 SING N N 21 DP2 CD NE SING N N 22 DP2 CD HD1 SING N N 23 DP2 CD HD2 SING N N 24 DP2 NE CZ SING N N 25 DP2 NE HNE SING N N 26 DP2 CZ NH1 SING N N 27 DP2 CZ NH2 DOUB N N 28 DP2 NH1 HH1 SING N N 29 DP2 NH2 HH2 SING N N 30 DP2 "N'" "CA'" SING N N 31 DP2 "N'" "HN'1" SING N N 32 DP2 "N'" "HN'2" SING N N 33 DP2 "CA'" "C'" SING N N 34 DP2 "CA'" "CB'" SING N N 35 DP2 "CA'" "HA'" SING N N 36 DP2 "C'" "O'" DOUB N N 37 DP2 "CB'" "CG'" SING N N 38 DP2 "CB'" "HB'1" SING N N 39 DP2 "CB'" "HB'2" SING N N 40 DP2 "CG'" "CD'" SING N N 41 DP2 "CG'" "HG'1" SING N N 42 DP2 "CG'" "HG'2" SING N N 43 DP2 "CD'" "CE'" SING N N 44 DP2 "CD'" "HD'1" SING N N 45 DP2 "CD'" "HD'2" SING N N 46 DP2 "CE'" "NZ'" SING N N 47 DP2 "CE'" "HE'1" SING N N 48 DP2 "CE'" "HE'2" SING N N 49 DP2 "NZ'" "HZ'1" SING N N 50 DP2 "NZ'" "HZ'2" 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 DP2 SMILES ACDLabs 10.04 "O=C(N)C(NC(=O)C(N)CCCCN)CCCNC(=[N@H])NN(O)O" DP2 SMILES_CANONICAL CACTVS 3.341 "NCCCC[C@@H](N)C(=O)N[C@H](CCCNC(=N)NN(O)O)C(N)=O" DP2 SMILES CACTVS 3.341 "NCCCC[CH](N)C(=O)N[CH](CCCNC(=N)NN(O)O)C(N)=O" DP2 SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C(CCN)C[C@H](C(=O)N[C@H](CCCNC(=N)NN(O)O)C(=O)N)N" DP2 SMILES "OpenEye OEToolkits" 1.5.0 "C(CCN)CC(C(=O)NC(CCCNC(=N)NN(O)O)C(=O)N)N" DP2 InChI InChI 1.03 "InChI=1S/C12H28N8O4/c13-6-2-1-4-8(14)11(22)18-9(10(15)21)5-3-7-17-12(16)19-20(23)24/h8-9,23-24H,1-7,13-14H2,(H2,15,21)(H,18,22)(H3,16,17,19)/t8-,9-/m1/s1" DP2 InChIKey InChI 1.03 VKBOUZQMRKGFCB-RKDXNWHRSA-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 10.04 "D-lysyl-N~5~-[(E)-(2,2-dihydroxyhydrazino)(imino)methyl]-D-ornithinamide" DP2 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "(2R)-2,6-diamino-N-[(2R)-1-amino-5-[[N-(dihydroxyamino)carbamimidoyl]amino]-1-oxo-pentan-2-yl]hexanamide" # # 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 # _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 ? ##