data_DPM
#
_chem_comp.id DPM
_chem_comp.name "3-[5-{[3-(2-carboxyethyl)-4-(carboxymethyl)-5-methyl-1H-pyrrol-2-yl]methyl}-4-(carboxymethyl)-1H-pyrrol-3-yl]propanoic acid"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C20 H24 N2 O8"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms "DIPYRROMETHANE COFACTOR"
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 1999-07-08
_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 420.413
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code DPM
_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 1PDA
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site RCSB
_chem_comp.pdbx_pcm N
#
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
DPM C1A C1A C 0 1 Y N N N N N 15.792 0.736 27.331 2.559 2.585 0.185 C1A DPM 1
DPM C2A C2A C 0 1 Y N N N N N 16.421 0.239 28.504 3.285 1.469 -0.030 C2A DPM 2
DPM C3A C3A C 0 1 Y N N N N N 17.111 1.296 29.086 2.520 0.620 -0.854 C3A DPM 3
DPM C4A C4A C 0 1 Y N N N N N 16.943 2.443 28.270 1.355 1.249 -1.111 C4A DPM 4
DPM C5A C5A C 0 1 N N N N N N 16.368 -1.176 29.040 4.662 1.183 0.512 C5A DPM 5
DPM C6A C6A C 0 1 N N N N N N 17.493 -2.086 28.490 4.544 0.489 1.844 C6A DPM 6
DPM C7A C7A C 0 1 N N N N N N 17.808 1.354 30.454 2.928 -0.742 -1.355 C7A DPM 7
DPM C8A C8A C 0 1 N N N N N N 19.263 1.110 30.370 2.480 -1.809 -0.355 C8A DPM 8
DPM C9A C9A C 0 1 N N N N N N 19.768 1.034 31.862 2.888 -3.170 -0.857 C9A DPM 9
DPM CHA CHA C 0 1 N N N N N N 14.851 0.062 26.378 2.985 3.770 1.012 CHA DPM 10
DPM NA NA N 0 1 Y N N N N N 16.097 2.128 27.198 1.376 2.458 -0.481 NA DPM 11
DPM O1A O1A O 0 1 N N N N N N 18.420 -1.704 27.801 3.453 0.252 2.307 O1A DPM 12
DPM O2A O2A O 0 1 N N N N N N 17.442 -3.320 28.800 5.650 0.136 2.517 O2A DPM 13
DPM O3A O3A O 0 1 N N N N N N 20.775 0.293 32.051 3.477 -3.276 -1.906 O3A DPM 14
DPM O4A O4A O 0 1 N N N N N N 19.403 1.733 32.855 2.597 -4.266 -0.137 O4A DPM 15
DPM C1B C1B C 0 1 Y N N N N N 17.394 4.882 27.828 -0.658 -0.166 -1.109 C1B DPM 16
DPM C2B C2B C 0 1 Y N N N N N 17.994 6.154 28.228 -1.674 0.254 -0.330 C2B DPM 17
DPM C3B C3B C 0 1 Y N N N N N 17.861 7.031 27.137 -2.235 -0.884 0.283 C3B DPM 18
DPM C4B C4B C 0 1 Y N N N N N 17.165 6.391 26.066 -1.539 -1.957 -0.146 C4B DPM 19
DPM C5B C5B C 0 1 N N N N N N 18.627 6.407 29.585 -2.128 1.680 -0.146 C5B DPM 20
DPM C6B C6B C 0 1 N N N N N N 17.646 7.023 30.642 -3.176 2.010 -1.177 C6B DPM 21
DPM C7B C7B C 0 1 N N N N N N 18.504 8.432 27.100 -3.398 -0.900 1.241 C7B DPM 22
DPM C8B C8B C 0 1 N N N N N N 19.901 8.193 26.498 -4.708 -0.928 0.452 C8B DPM 23
DPM C9B C9B C 0 1 N N N N N N 20.599 9.530 26.032 -5.871 -0.943 1.411 C9B DPM 24
DPM CHB CHB C 0 1 N N N N N N 17.382 3.753 28.664 0.229 0.712 -1.955 CHB DPM 25
DPM NB NB N 0 1 Y N N N N N 16.896 5.048 26.511 -0.566 -1.522 -0.996 NB DPM 26
DPM O1B O1B O 0 1 N N N N N N 17.637 6.711 31.856 -3.520 1.173 -1.979 O1B DPM 27
DPM O2B O2B O 0 1 N N N N N N 16.841 7.959 30.344 -3.728 3.233 -1.205 O2B DPM 28
DPM O3B O3B O 0 1 N N N N N N 19.967 10.172 25.198 -5.672 -0.934 2.603 O3B DPM 29
DPM O4B O4B O 0 1 N N N N N N 21.751 9.845 26.347 -7.128 -0.968 0.941 O4B DPM 30
DPM H5A1 H5A1 H 0 0 N N N N N N 16.456 -1.137 30.136 5.200 0.540 -0.185 H5A1 DPM 31
DPM H5A2 H5A2 H 0 0 N N N N N N 15.398 -1.616 28.765 5.206 2.119 0.636 H5A2 DPM 32
DPM H7A1 H7A1 H 0 0 N N N N N N 17.644 2.351 30.889 2.459 -0.929 -2.321 H7A1 DPM 33
DPM H7A2 H7A2 H 0 0 N N N N N N 17.361 0.590 31.108 4.012 -0.779 -1.464 H7A2 DPM 34
DPM H8A1 H8A1 H 0 0 N N N N N N 19.464 0.163 29.848 2.949 -1.622 0.611 H8A1 DPM 35
DPM H8A2 H8A2 H 0 0 N N N N N N 19.760 1.934 29.838 1.396 -1.772 -0.246 H8A2 DPM 36
DPM HCA1 HCA1 H 0 0 N N N N N N 13.819 0.167 26.745 3.505 4.488 0.378 HCA1 DPM 37
DPM HCA2 HCA2 H 0 0 N N N N N N 14.937 0.529 25.386 2.105 4.242 1.450 HCA2 DPM 38
DPM HCA3 HCA3 H 0 0 N N N N N N 15.106 -1.005 26.304 3.652 3.437 1.808 HCA3 DPM 39
DPM H10 H10 H 0 1 N N N N N N 15.772 2.750 26.485 0.664 3.117 -0.498 ? ? 40
DPM HOA2 HOA2 H 0 0 N N N N N N 18.184 -3.774 28.419 5.524 -0.306 3.368 HOA2 DPM 41
DPM HOA4 HOA4 H 0 0 N N N N N N 19.979 1.564 33.591 2.879 -5.117 -0.500 HOA4 DPM 42
DPM H4B1 H4B1 H 0 0 N N N N N N 16.895 6.826 25.115 -1.719 -2.983 0.138 H4B1 DPM 43
DPM H5B1 H5B1 H 0 0 N N N N N N 19.000 5.449 29.977 -2.548 1.802 0.852 H5B1 DPM 44
DPM H5B2 H5B2 H 0 0 N N N N N N 19.470 7.101 29.450 -1.276 2.350 -0.266 H5B2 DPM 45
DPM H7B1 H7B1 H 0 0 N N N N N N 17.918 9.113 26.466 -3.335 -1.786 1.873 H7B1 DPM 46
DPM H7B2 H7B2 H 0 0 N N N N N N 18.583 8.851 28.114 -3.367 -0.007 1.864 H7B2 DPM 47
DPM H8B1 H8B1 H 0 0 N N N N N N 20.534 7.711 27.258 -4.771 -0.041 -0.179 H8B1 DPM 48
DPM H8B2 H8B2 H 0 0 N N N N N N 19.800 7.527 25.629 -4.739 -1.821 -0.171 H8B2 DPM 49
DPM HCB1 HCB1 H 0 0 N N N N N N 16.750 4.029 29.521 -0.355 1.542 -2.353 HCB1 DPM 50
DPM HCB2 HCB2 H 0 0 N N N N N N 18.422 3.626 29.000 0.638 0.128 -2.779 HCB2 DPM 51
DPM H22 H22 H 0 1 N N N N N N 16.431 4.343 25.975 0.080 -2.085 -1.451 ? ? 52
DPM HOB2 HOB2 H 0 0 N N N N N N 16.381 8.242 31.125 -4.396 3.398 -1.885 HOB2 DPM 53
DPM HOB4 HOB4 H 0 0 N N N N N N 22.016 10.613 25.855 -7.841 -0.978 1.594 HOB4 DPM 54
#
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
DPM C1A C2A DOUB Y N 1
DPM C1A CHA SING N N 2
DPM C1A NA SING Y N 3
DPM C2A C3A SING Y N 4
DPM C2A C5A SING N N 5
DPM C3A C4A DOUB Y N 6
DPM C3A C7A SING N N 7
DPM C4A NA SING Y N 8
DPM C4A CHB SING N N 9
DPM C5A C6A SING N N 10
DPM C6A O1A DOUB N N 11
DPM C6A O2A SING N N 12
DPM C7A C8A SING N N 13
DPM C8A C9A SING N N 14
DPM C9A O3A DOUB N N 15
DPM C9A O4A SING N N 16
DPM C1B C2B DOUB Y N 17
DPM C1B CHB SING N N 18
DPM C1B NB SING Y N 19
DPM C2B C3B SING Y N 20
DPM C2B C5B SING N N 21
DPM C3B C4B DOUB Y N 22
DPM C3B C7B SING N N 23
DPM C4B NB SING Y N 24
DPM C5B C6B SING N N 25
DPM C6B O1B DOUB N N 26
DPM C6B O2B SING N N 27
DPM C7B C8B SING N N 28
DPM C8B C9B SING N N 29
DPM C9B O3B DOUB N N 30
DPM C9B O4B SING N N 31
DPM C5A H5A1 SING N N 32
DPM C5A H5A2 SING N N 33
DPM C7A H7A1 SING N N 34
DPM C7A H7A2 SING N N 35
DPM C8A H8A1 SING N N 36
DPM C8A H8A2 SING N N 37
DPM CHA HCA1 SING N N 38
DPM CHA HCA2 SING N N 39
DPM CHA HCA3 SING N N 40
DPM NA H10 SING N N 41
DPM O2A HOA2 SING N N 42
DPM O4A HOA4 SING N N 43
DPM C4B H4B1 SING N N 44
DPM C5B H5B1 SING N N 45
DPM C5B H5B2 SING N N 46
DPM C7B H7B1 SING N N 47
DPM C7B H7B2 SING N N 48
DPM C8B H8B1 SING N N 49
DPM C8B H8B2 SING N N 50
DPM CHB HCB1 SING N N 51
DPM CHB HCB2 SING N N 52
DPM NB H22 SING N N 53
DPM O2B HOB2 SING N N 54
DPM O4B HOB4 SING N N 55
#
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
DPM SMILES ACDLabs 12.01 "O=C(O)Cc1c(ncc1CCC(=O)O)Cc2c(c(c(n2)C)CC(=O)O)CCC(=O)O"
DPM InChI InChI 1.03 "InChI=1S/C20H24N2O8/c1-10-13(6-19(27)28)12(3-5-18(25)26)16(22-10)8-15-14(7-20(29)30)11(9-21-15)2-4-17(23)24/h9,21-22H,2-8H2,1H3,(H,23,24)(H,25,26)(H,27,28)(H,29,30)"
DPM InChIKey InChI 1.03 LCAXMKQKEYTFDM-UHFFFAOYSA-N
DPM SMILES_CANONICAL CACTVS 3.385 "Cc1[nH]c(Cc2[nH]cc(CCC(O)=O)c2CC(O)=O)c(CCC(O)=O)c1CC(O)=O"
DPM SMILES CACTVS 3.385 "Cc1[nH]c(Cc2[nH]cc(CCC(O)=O)c2CC(O)=O)c(CCC(O)=O)c1CC(O)=O"
DPM SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "Cc1c(c(c([nH]1)Cc2c(c(c[nH]2)CCC(=O)O)CC(=O)O)CCC(=O)O)CC(=O)O"
DPM SMILES "OpenEye OEToolkits" 1.7.6 "Cc1c(c(c([nH]1)Cc2c(c(c[nH]2)CCC(=O)O)CC(=O)O)CCC(=O)O)CC(=O)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
DPM "SYSTEMATIC NAME" ACDLabs 12.01 "3-[5-{[3-(2-carboxyethyl)-4-(carboxymethyl)-5-methyl-1H-pyrrol-2-yl]methyl}-4-(carboxymethyl)-1H-pyrrol-3-yl]propanoic acid"
DPM "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "3-[4-(2-hydroxy-2-oxoethyl)-5-[[4-(2-hydroxy-2-oxoethyl)-3-(3-hydroxy-3-oxopropyl)-5-methyl-1H-pyrrol-2-yl]methyl]-1H-pyrrol-3-yl]propanoic acid"
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
DPM "Create component" 1999-07-08 RCSB
DPM "Other modification" 2013-09-12 RCSB
DPM "Modify synonyms" 2021-03-01 PDBE
DPM "Modify PCM" 2024-09-27 PDBE
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id DPM
_pdbx_chem_comp_synonyms.name "DIPYRROMETHANE COFACTOR"
_pdbx_chem_comp_synonyms.provenance ?
_pdbx_chem_comp_synonyms.type ?
#