data_DDE
#
_chem_comp.id DDE
_chem_comp.name "{3-[4-(2-AMINO-2-CARBOXY-ETHYL)-1H-IMIDAZOL-2-YL]-1-CARBAMOYL-PROPYL}-TRIMETHYL-AMMONIUM"
_chem_comp.type "L-PEPTIDE LINKING"
_chem_comp.pdbx_type ATOMP
_chem_comp.formula "C13 H24 N5 O3"
_chem_comp.mon_nstd_parent_comp_id HIS
_chem_comp.pdbx_synonyms "DIPHTHAMIDE; 2-(3-CARBOXYAMIDO-3-(TRIMETHYLAMMONIO)PROPYL)HISTIDINE"
_chem_comp.pdbx_formal_charge 1
_chem_comp.pdbx_initial_date 2004-07-29
_chem_comp.pdbx_modified_date 2024-09-27
_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 298.361
_chem_comp.one_letter_code H
_chem_comp.three_letter_code DDE
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag Y
_chem_comp.pdbx_ideal_coordinates_details ?
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code 1U2R
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site RCSB
_chem_comp.pdbx_pcm Y
#
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_backbone_atom_flag
_chem_comp_atom.pdbx_n_terminal_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
DDE N N N 0 1 N N N Y Y N 90.204 83.284 47.837 -0.602 5.138 -4.246 N DDE 1
DDE CA CA C 0 1 N N S Y N N 91.170 82.432 47.137 -0.992 3.753 -4.156 CA DDE 2
DDE C C C 0 1 N N N Y N Y 90.548 81.039 46.963 -0.305 2.920 -5.228 C DDE 3
DDE O O O 0 1 N N N Y N Y 91.162 80.145 46.392 -0.055 3.350 -6.349 O DDE 4
DDE CB CB C 0 1 N N N N N N 92.511 82.391 47.855 -2.534 3.615 -4.237 CB DDE 5
DDE CG CG C 0 1 Y N N N N N 93.196 83.707 48.037 -3.025 2.236 -4.091 CG DDE 6
DDE ND1 ND1 N 0 1 Y N N N N N 93.689 84.363 46.941 -3.184 1.431 -5.191 ND1 DDE 7
DDE CD2 CD2 C 0 1 Y N N N N N 93.417 84.444 49.117 -3.378 1.576 -2.938 CD2 DDE 8
DDE CE1 CE1 C 0 1 Y N N N N N 94.224 85.522 47.375 -3.621 0.319 -4.693 CE1 DDE 9
DDE NE2 NE2 N 0 1 Y N N N N N 94.049 85.593 48.762 -3.763 0.332 -3.350 NE2 DDE 10
DDE NAD NAD N 0 1 N N N N N N 95.993 88.572 42.645 -1.585 0.496 -7.967 NAD DDE 11
DDE CBI CBI C 0 1 N N N N N N 95.265 87.726 43.391 -1.861 -0.835 -7.741 CBI DDE 12
DDE OAG OAG O 0 1 N N N N N N 95.303 86.470 43.411 -2.321 -1.588 -8.596 OAG DDE 13
DDE CBW CBW C 0 1 N N R N N N 94.261 88.380 44.352 -1.533 -1.277 -6.325 CBW DDE 14
DDE NCB NCB N 1 1 N N N N N N 94.162 89.913 44.374 -0.437 -2.286 -6.353 NCB DDE 15
DDE CAB CAB C 0 1 N N N N N N 93.109 90.318 45.364 -0.090 -2.745 -4.933 CAB DDE 16
DDE CAC CAC C 0 1 N N N N N N 95.339 90.665 44.845 -0.857 -3.515 -7.168 CAC DDE 17
DDE CAA CAA C 0 1 N N N N N N 93.712 90.493 43.103 0.825 -1.694 -6.990 CAA DDE 18
DDE CAU CAU C 0 1 N N N N N N 94.649 87.912 45.733 -2.773 -1.876 -5.649 CAU DDE 19
DDE CAT CAT C 0 1 N N N N N N 94.938 86.657 46.607 -3.964 -0.922 -5.479 CAT DDE 20
DDE OXT OXT O 0 1 N Y N Y N Y ? ? ? 0.020 1.661 -4.849 OXT DDE 21
DDE H 1HN H 0 1 N N N Y Y N 90.617 84.209 47.952 -0.164 5.469 -5.089 H DDE 22
DDE H2 2HN H 0 1 N Y N Y Y N 89.892 82.880 48.720 -0.585 5.695 -3.408 H2 DDE 23
DDE HA HA H 0 1 N N N Y N N 91.390 82.857 46.130 -0.624 3.394 -3.188 HA DDE 24
DDE HB2 1HB H 0 1 N N N N N N 92.397 81.883 48.841 -2.989 4.264 -3.460 HB2 DDE 25
DDE HB3 2HB H 0 1 N N N N N N 93.194 81.676 47.340 -2.876 4.073 -5.191 HB3 DDE 26
DDE HD2 HD2 H 0 1 N N N N N N 93.124 84.150 50.139 -3.391 1.865 -1.897 HD2 DDE 27
DDE HE2 HE2 H 0 1 N N N N N N 94.329 86.341 49.395 -4.086 -0.420 -2.756 HE2 DDE 28
DDE HAD1 1HAD H 0 0 N N N N N N 96.659 88.137 42.006 -1.203 1.101 -7.247 HAD1 DDE 29
DDE HAD2 2HAD H 0 0 N N N N N N 95.962 89.591 42.628 -1.757 0.918 -8.873 HAD2 DDE 30
DDE HBW HBW H 0 1 N N N N N N 93.253 88.068 43.990 -1.140 -0.420 -5.769 HBW DDE 31
DDE HAB1 1HAB H 0 0 N N N N N N 93.037 91.430 45.380 0.865 -3.272 -4.976 HAB1 DDE 32
DDE HAB2 2HAB H 0 0 N N N N N N 92.126 89.831 45.162 -0.020 -1.857 -4.302 HAB2 DDE 33
DDE HAB3 3HAB H 0 0 N N N N N N 93.290 89.889 46.377 -0.889 -3.407 -4.591 HAB3 DDE 34
DDE HAC1 1HAC H 0 0 N N N N N N 95.267 91.777 44.861 0.051 -4.031 -7.486 HAC1 DDE 35
DDE HAC2 2HAC H 0 0 N N N N N N 95.628 90.299 45.858 -1.464 -4.152 -6.522 HAC2 DDE 36
DDE HAC3 3HAC H 0 0 N N N N N N 96.232 90.361 44.250 -1.431 -3.165 -8.028 HAC3 DDE 37
DDE HAA1 1HAA H 0 0 N N N N N N 93.640 91.605 43.119 1.382 -1.174 -6.208 HAA1 DDE 38
DDE HAA2 2HAA H 0 0 N N N N N N 94.361 90.152 42.263 1.408 -2.518 -7.405 HAA2 DDE 39
DDE HAA3 3HAA H 0 0 N N N N N N 92.743 90.040 42.784 0.511 -1.002 -7.774 HAA3 DDE 40
DDE HAU3 1HAU H 0 0 N N N N N N 95.590 88.488 45.886 -3.113 -2.745 -6.229 HAU3 DDE 41
DDE HAU2 2HAU H 0 0 N N N N N N 93.862 88.410 46.345 -2.491 -2.274 -4.665 HAU2 DDE 42
DDE HAT2 1HAT H 0 0 N N N N N N 95.581 87.091 47.407 -4.765 -1.458 -4.952 HAT2 DDE 43
DDE HAT3 2HAT H 0 0 N N N N N N 95.615 86.076 45.938 -4.385 -0.658 -6.456 HAT3 DDE 44
DDE HXT HXT H 0 1 N Y N Y N Y -0.384 -0.861 -0.107 0.467 1.126 -5.537 HXT DDE 45
#
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
DDE N CA SING N N 1
DDE N H SING N N 2
DDE N H2 SING N N 3
DDE CA C SING N N 4
DDE CA CB SING N N 5
DDE CA HA SING N N 6
DDE C O DOUB N N 7
DDE C OXT SING N N 8
DDE CB CG SING N N 9
DDE CB HB2 SING N N 10
DDE CB HB3 SING N N 11
DDE CG ND1 SING Y N 12
DDE CG CD2 DOUB Y N 13
DDE ND1 CE1 DOUB Y N 14
DDE CD2 NE2 SING Y N 15
DDE CD2 HD2 SING N N 16
DDE CE1 NE2 SING Y N 17
DDE CE1 CAT SING N N 18
DDE NE2 HE2 SING N N 19
DDE NAD CBI SING N N 20
DDE NAD HAD1 SING N N 21
DDE NAD HAD2 SING N N 22
DDE CBI OAG DOUB N N 23
DDE CBI CBW SING N N 24
DDE CBW NCB SING N N 25
DDE CBW CAU SING N N 26
DDE CBW HBW SING N N 27
DDE NCB CAB SING N N 28
DDE NCB CAC SING N N 29
DDE NCB CAA SING N N 30
DDE CAB HAB1 SING N N 31
DDE CAB HAB2 SING N N 32
DDE CAB HAB3 SING N N 33
DDE CAC HAC1 SING N N 34
DDE CAC HAC2 SING N N 35
DDE CAC HAC3 SING N N 36
DDE CAA HAA1 SING N N 37
DDE CAA HAA2 SING N N 38
DDE CAA HAA3 SING N N 39
DDE CAU CAT SING N N 40
DDE CAU HAU3 SING N N 41
DDE CAU HAU2 SING N N 42
DDE CAT HAT2 SING N N 43
DDE CAT HAT3 SING N N 44
DDE OXT HXT SING N N 45
#
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
DDE SMILES ACDLabs 10.04 "O=C(O)C(N)Cc1nc(nc1)CCC(C(=O)N)[N+](C)(C)C"
DDE SMILES_CANONICAL CACTVS 3.341 "C[N+](C)(C)[C@H](CCc1[nH]cc(C[C@H](N)C(O)=O)n1)C(N)=O"
DDE SMILES CACTVS 3.341 "C[N+](C)(C)[CH](CCc1[nH]cc(C[CH](N)C(O)=O)n1)C(N)=O"
DDE SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C[N+](C)(C)[C@H](CCc1[nH]cc(n1)C[C@@H](C(=O)O)N)C(=O)N"
DDE SMILES "OpenEye OEToolkits" 1.5.0 "C[N+](C)(C)C(CCc1[nH]cc(n1)CC(C(=O)O)N)C(=O)N"
DDE InChI InChI 1.03 "InChI=1S/C13H23N5O3/c1-18(2,3)10(12(15)19)4-5-11-16-7-8(17-11)6-9(14)13(20)21/h7,9-10H,4-6,14H2,1-3H3,(H3-,15,16,17,19,20,21)/p+1/t9-,10+/m0/s1"
DDE InChIKey InChI 1.03 FOOBQHKMWYGHCE-VHSXEESVSA-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
DDE "SYSTEMATIC NAME" ACDLabs 10.04 "(2R)-1-amino-4-{4-[(2S)-2-amino-2-carboxyethyl]-1H-imidazol-2-yl}-N,N,N-trimethyl-1-oxobutan-2-aminium"
DDE "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R)-1-amino-4-[4-[(2S)-2-amino-3-hydroxy-3-oxo-propyl]-1H-imidazol-2-yl]-1-oxo-butan-2-yl]-trimethyl-azanium"
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
DDE "Create component" 2004-07-29 RCSB
DDE "Modify descriptor" 2011-06-04 RCSB
DDE "Modify synonyms" 2020-06-05 PDBE
DDE "Modify backbone" 2023-11-03 PDBE
DDE "Modify PCM" 2024-09-27 PDBE
#
loop_
_pdbx_chem_comp_synonyms.ordinal
_pdbx_chem_comp_synonyms.comp_id
_pdbx_chem_comp_synonyms.name
_pdbx_chem_comp_synonyms.provenance
_pdbx_chem_comp_synonyms.type
1 DDE DIPHTHAMIDE ? ?
2 DDE "2-(3-CARBOXYAMIDO-3-(TRIMETHYLAMMONIO)PROPYL)HISTIDINE" ? ?
#
_pdbx_chem_comp_pcm.pcm_id 1
_pdbx_chem_comp_pcm.comp_id DDE
_pdbx_chem_comp_pcm.modified_residue_id HIS
_pdbx_chem_comp_pcm.type Diphthamide
_pdbx_chem_comp_pcm.category "Named protein modification"
_pdbx_chem_comp_pcm.position "Amino-acid side chain"
_pdbx_chem_comp_pcm.polypeptide_position "Any position"
_pdbx_chem_comp_pcm.comp_id_linking_atom ?
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom ?
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession PTM-0118
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession ?
#