data_PVN # _chem_comp.id PVN _chem_comp.name PHYCOVIOLOBILIN _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C33 H40 N4 O6" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "Phycoviolobilin, bound form" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2006-11-02 _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 588.694 _chem_comp.one_letter_code ? _chem_comp.three_letter_code PVN _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 2J96 _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 PVN C31 C31 C 0 1 N N N N N N -24.875 15.221 -3.833 -5.821 2.758 -0.135 C31 PVN 1 PVN C32 C32 C 0 1 N N N N N N -24.306 14.331 -4.946 -6.085 1.568 0.789 C32 PVN 2 PVN C3 C3 C 0 1 N N N N N N -26.110 16.059 -4.362 -4.792 2.374 -1.167 C3 PVN 3 PVN C2 C2 C 0 1 N N N N N N -26.081 17.051 -5.300 -5.033 1.931 -2.397 C2 PVN 4 PVN C21 C21 C 0 1 N N N N N N -24.894 17.618 -6.084 -6.403 1.729 -2.992 C21 PVN 5 PVN C1 C1 C 0 1 N N N N N N -27.494 17.517 -5.444 -3.766 1.668 -3.088 C1 PVN 6 PVN O1 O1 O 0 1 N N N N N N -27.835 18.394 -6.196 -3.666 1.255 -4.227 O1 PVN 7 PVN N1 N1 N 0 1 N N N N N N -28.318 16.832 -4.629 -2.731 1.953 -2.275 N1 PVN 8 PVN C4 C4 C 0 1 N N R N N N -27.571 15.897 -3.896 -3.291 2.426 -1.002 C4 PVN 9 PVN C5 C5 C 0 1 N N N N N N -27.812 15.921 -2.400 -2.853 1.504 0.138 C5 PVN 10 PVN C6 C6 C 0 1 Y N N N N N -29.180 15.480 -1.920 -1.375 1.669 0.378 C6 PVN 11 PVN C7 C7 C 0 1 Y N N N N N -30.332 16.270 -1.856 -0.799 2.679 1.086 C7 PVN 12 PVN C41 C41 C 0 1 N N N N N N -30.502 17.696 -2.230 -1.525 3.815 1.760 C41 PVN 13 PVN N2 N2 N 0 1 Y N N N N N -29.481 14.215 -1.458 -0.414 0.837 -0.070 N2 PVN 14 PVN C9 C9 C 0 1 Y N N N N N -30.826 14.193 -1.103 0.814 1.314 0.348 C9 PVN 15 PVN C8 C8 C 0 1 Y N N N N N -31.366 15.464 -1.357 0.577 2.480 1.080 C8 PVN 16 PVN C51 C51 C 0 1 N N N N N N -32.776 16.001 -1.168 1.614 3.352 1.740 C51 PVN 17 PVN C52 C52 C 0 1 N N N N N N -32.981 16.702 0.183 1.857 2.864 3.169 C52 PVN 18 PVN C53 C53 C 0 1 N N N N N N -33.710 15.783 1.138 2.894 3.736 3.829 C53 PVN 19 PVN O54 O54 O 0 1 N N N N N N -34.682 15.095 0.708 3.268 3.493 5.095 O54 PVN 20 PVN O55 O55 O 0 1 N N N N N N -33.325 15.731 2.338 3.388 4.654 3.218 O55 PVN 21 PVN C10 C10 C 0 1 N N N N N N -31.554 13.075 -0.569 2.060 0.737 0.090 C10 PVN 22 PVN C11 C11 C 0 1 N N N N N N -31.147 11.720 -0.529 2.139 -0.596 -0.347 C11 PVN 23 PVN C12 C12 C 0 1 N N N N N N -31.970 10.640 -0.083 3.281 -1.219 -0.907 C12 PVN 24 PVN C61 C61 C 0 1 N N N N N N -33.389 10.746 0.434 4.626 -0.584 -1.145 C61 PVN 25 PVN C62 C62 C 0 1 N N N N N N -33.579 10.249 1.884 4.616 0.144 -2.491 C62 PVN 26 PVN C63 C63 C 0 1 N N N N N N -32.642 10.935 2.827 5.961 0.779 -2.729 C63 PVN 27 PVN O64 O64 O 0 1 N N N N N N -32.952 12.084 3.247 6.839 0.663 -1.906 O64 PVN 28 PVN O65 O65 O 0 1 N N N N N N -31.573 10.341 3.149 6.185 1.475 -3.855 O65 PVN 29 PVN N3 N3 N 0 1 N N N N N N -29.917 11.185 -0.922 1.149 -1.497 -0.299 N3 PVN 30 PVN C14 C14 C 0 1 N N N N N N -29.975 9.852 -0.745 1.578 -2.654 -0.795 C14 PVN 31 PVN C13 C13 C 0 1 N N N N N N -31.231 9.487 -0.227 2.929 -2.501 -1.188 C13 PVN 32 PVN C71 C71 C 0 1 N N N N N N -31.671 8.078 0.093 3.810 -3.560 -1.799 C71 PVN 33 PVN C15 C15 C 0 1 N N N N N N -28.917 8.933 -1.100 0.788 -3.877 -0.911 C15 PVN 34 PVN C16 C16 C 0 1 N N N N N N -28.563 8.516 -2.421 -0.049 -4.256 0.114 C16 PVN 35 PVN C17 C17 C 0 1 N N N N N N -29.381 8.562 -3.629 -0.981 -3.428 0.780 C17 PVN 36 PVN C81 C81 C 0 1 N N N N N N -30.773 9.061 -3.785 -1.240 -1.970 0.499 C81 PVN 37 PVN N4 N4 N 0 1 N N N N N N -27.308 7.963 -2.727 -0.137 -5.525 0.678 N4 PVN 38 PVN C19 C19 C 0 1 N N N N N N -27.346 7.677 -4.065 -1.069 -5.492 1.650 C19 PVN 39 PVN O19 O19 O 0 1 N N N N N N -26.411 7.175 -4.688 -1.400 -6.434 2.350 O19 PVN 40 PVN C18 C18 C 0 1 N N N N N N -28.593 8.029 -4.656 -1.601 -4.188 1.720 C18 PVN 41 PVN C91 C91 C 0 1 N N N N N N -28.984 7.853 -6.128 -2.673 -3.720 2.671 C91 PVN 42 PVN C92 C92 C 0 1 N N N N N N -29.121 6.370 -6.503 -4.049 -4.015 2.072 C92 PVN 43 PVN H321 H321 H 0 0 N N N N N N -25.084 13.636 -5.293 -5.159 1.283 1.288 H321 PVN 44 PVN H322 H322 H 0 0 N N N N N N -23.975 14.960 -5.785 -6.829 1.846 1.536 H322 PVN 45 PVN HC4 HC4 H 0 1 N N N N N N -27.880 14.897 -4.234 -2.969 3.448 -0.805 HC4 PVN 46 PVN H211 H211 H 0 0 N N N N N N -24.429 16.816 -6.676 -7.109 1.475 -2.201 H211 PVN 47 PVN H212 H212 H 0 0 N N N N N N -25.245 18.414 -6.757 -6.723 2.646 -3.486 H212 PVN 48 PVN H213 H213 H 0 0 N N N N N N -24.155 18.031 -5.382 -6.366 0.918 -3.720 H213 PVN 49 PVN HN1 HN1 H 0 1 N N N N N N -29.306 16.968 -4.557 -1.790 1.865 -2.492 HN1 PVN 50 PVN H5C1 H5C1 H 0 0 N N N N N N -27.655 16.953 -2.054 -3.400 1.764 1.045 H5C1 PVN 51 PVN H5C2 H5C2 H 0 0 N N N N N N -27.067 15.261 -1.932 -3.065 0.469 -0.130 H5C2 PVN 52 PVN HN2 HN2 H 0 1 N N N N N N -28.843 13.448 -1.390 -0.559 0.036 -0.597 HN2 PVN 53 PVN H411 H411 H 0 0 N N N N N N -30.791 17.766 -3.289 -1.778 3.530 2.781 H411 PVN 54 PVN H412 H412 H 0 0 N N N N N N -31.287 18.148 -1.605 -0.885 4.697 1.777 H412 PVN 55 PVN H413 H413 H 0 0 N N N N N N -29.554 18.232 -2.072 -2.439 4.039 1.209 H413 PVN 56 PVN H101 H101 H 0 0 N N N N N N -32.525 13.294 -0.149 2.962 1.315 0.225 H101 PVN 57 PVN H511 H511 H 0 0 N N N N N N -32.986 16.722 -1.971 2.545 3.300 1.175 H511 PVN 58 PVN H512 H512 H 0 0 N N N N N N -33.482 15.160 -1.236 1.260 4.383 1.763 H512 PVN 59 PVN H521 H521 H 0 0 N N N N N N -33.574 17.616 0.033 0.926 2.915 3.734 H521 PVN 60 PVN H522 H522 H 0 0 N N N N N N -32.002 16.967 0.608 2.211 1.833 3.146 H522 PVN 61 PVN H54 H54 H 0 1 N N N N N N -35.037 14.571 1.416 3.936 4.079 5.475 H54 PVN 62 PVN H611 H611 H 0 0 N N N N N N -33.693 11.802 0.390 4.837 0.130 -0.348 H611 PVN 63 PVN H612 H612 H 0 0 N N N N N N -34.040 10.149 -0.222 5.396 -1.355 -1.155 H612 PVN 64 PVN H621 H621 H 0 0 N N N N N N -34.614 10.451 2.198 4.405 -0.570 -3.288 H621 PVN 65 PVN H622 H622 H 0 0 N N N N N N -33.390 9.166 1.918 3.846 0.915 -2.481 H622 PVN 66 PVN H65 H65 H 0 1 N N N N N N -31.069 10.891 3.737 7.064 1.865 -3.963 H65 PVN 67 PVN H151 H151 H 0 0 N N N N N N -28.337 8.521 -0.287 0.861 -4.485 -1.801 H151 PVN 68 PVN H711 H711 H 0 0 N N N N N N -31.931 8.009 1.160 3.199 -4.253 -2.377 H711 PVN 69 PVN H712 H712 H 0 0 N N N N N N -32.550 7.821 -0.516 4.544 -3.089 -2.454 H712 PVN 70 PVN H713 H713 H 0 0 N N N N N N -30.853 7.378 -0.131 4.326 -4.104 -1.008 H713 PVN 71 PVN HN4 HN4 H 0 1 N N N N N N -26.546 7.810 -2.098 0.384 -6.300 0.417 HN4 PVN 72 PVN H811 H811 H 0 0 N N N N N N -31.088 8.950 -4.833 -0.619 -1.645 -0.336 H811 PVN 73 PVN H812 H812 H 0 0 N N N N N N -31.445 8.480 -3.137 -2.291 -1.830 0.246 H812 PVN 74 PVN H813 H813 H 0 0 N N N N N N -30.816 10.123 -3.500 -0.997 -1.381 1.383 H813 PVN 75 PVN H911 H911 H 0 0 N N N N N N -29.946 8.356 -6.304 -2.570 -4.244 3.621 H911 PVN 76 PVN H912 H912 H 0 0 N N N N N N -28.209 8.311 -6.760 -2.570 -2.647 2.834 H912 PVN 77 PVN H921 H921 H 0 0 N N N N N N -29.402 6.284 -7.563 -4.187 -5.093 1.990 H921 PVN 78 PVN H922 H922 H 0 0 N N N N N N -28.161 5.859 -6.335 -4.823 -3.598 2.717 H922 PVN 79 PVN H923 H923 H 0 0 N N N N N N -29.898 5.904 -5.879 -4.120 -3.563 1.082 H923 PVN 80 PVN H31 H31 H 0 1 N N N N N N -25.201 14.587 -2.995 -6.747 3.043 -0.634 H31 PVN 81 PVN H323 H323 H 0 0 N N N N N N -23.451 13.759 -4.557 -6.455 0.728 0.203 H323 PVN 82 PVN HXT HXT H 0 1 N Y N N N N -24.092 15.912 -3.487 -5.450 3.599 0.451 HXT PVN 83 # 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 PVN C31 C32 SING N N 1 PVN C31 C3 SING N N 2 PVN C31 H31 SING N N 3 PVN C31 HXT SING N N 4 PVN C32 H323 SING N N 5 PVN C32 H321 SING N N 6 PVN C32 H322 SING N N 7 PVN C3 C4 SING N N 8 PVN C3 C2 DOUB N N 9 PVN C2 C21 SING N N 10 PVN C2 C1 SING N N 11 PVN C21 H212 SING N N 12 PVN C21 H213 SING N N 13 PVN C21 H211 SING N N 14 PVN C1 O1 DOUB N N 15 PVN C1 N1 SING N N 16 PVN N1 C4 SING N N 17 PVN N1 HN1 SING N N 18 PVN C4 C5 SING N N 19 PVN C4 HC4 SING N N 20 PVN C5 C6 SING N N 21 PVN C5 H5C2 SING N N 22 PVN C5 H5C1 SING N N 23 PVN C6 C7 DOUB Y N 24 PVN C6 N2 SING Y N 25 PVN C7 C41 SING N N 26 PVN C7 C8 SING Y N 27 PVN C41 H411 SING N N 28 PVN C41 H412 SING N N 29 PVN C41 H413 SING N N 30 PVN N2 C9 SING Y N 31 PVN N2 HN2 SING N N 32 PVN C9 C8 DOUB Y N 33 PVN C9 C10 SING N N 34 PVN C8 C51 SING N N 35 PVN C51 C52 SING N N 36 PVN C51 H511 SING N N 37 PVN C51 H512 SING N N 38 PVN C52 C53 SING N N 39 PVN C52 H522 SING N N 40 PVN C52 H521 SING N N 41 PVN C53 O54 SING N N 42 PVN C53 O55 DOUB N N 43 PVN O54 H54 SING N N 44 PVN C10 C11 DOUB N Z 45 PVN C10 H101 SING N N 46 PVN C11 C12 SING N N 47 PVN C11 N3 SING N N 48 PVN C12 C61 SING N N 49 PVN C12 C13 DOUB N N 50 PVN C61 H611 SING N N 51 PVN C61 H612 SING N N 52 PVN C61 C62 SING N N 53 PVN C62 H621 SING N N 54 PVN C62 H622 SING N N 55 PVN C62 C63 SING N N 56 PVN C63 O65 SING N N 57 PVN C63 O64 DOUB N N 58 PVN O65 H65 SING N N 59 PVN N3 C14 DOUB N N 60 PVN C14 C13 SING N N 61 PVN C14 C15 SING N N 62 PVN C13 C71 SING N N 63 PVN C71 H713 SING N N 64 PVN C71 H711 SING N N 65 PVN C71 H712 SING N N 66 PVN C15 H151 SING N N 67 PVN C15 C16 DOUB N E 68 PVN C16 C17 SING N N 69 PVN C16 N4 SING N N 70 PVN C17 C81 SING N N 71 PVN C17 C18 DOUB N N 72 PVN C81 H811 SING N N 73 PVN C81 H812 SING N N 74 PVN C81 H813 SING N N 75 PVN N4 HN4 SING N N 76 PVN N4 C19 SING N N 77 PVN C19 O19 DOUB N N 78 PVN C19 C18 SING N N 79 PVN C18 C91 SING N N 80 PVN C91 H911 SING N N 81 PVN C91 H912 SING N N 82 PVN C91 C92 SING N N 83 PVN C92 H921 SING N N 84 PVN C92 H922 SING N N 85 PVN C92 H923 SING N N 86 # 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 PVN InChI InChI 1.03 "InChI=1S/C33H40N4O7/c1-7-20-15(2)25(36-33(20)44)12-23-16(3)21(8-10-29(39)40)26(34-23)14-27-22(9-11-30(41)42)17(4)24(35-27)13-28-31(19(6)38)18(5)32(43)37-28/h12,14,19,28,35,38H,7-11,13H2,1-6H3,(H,36,44)(H,37,43)(H,39,40)(H,41,42)/b25-12+,26-14-/t19?,28-/m1/s1" PVN InChIKey InChI 1.03 SYEAKBPGLNVPDH-HVONXEAXSA-N PVN SMILES_CANONICAL CACTVS 3.370 "CCC1=C(C)C(=O)N[C@@H]1Cc2[nH]c(\C=C\3N=C(\C=C/4NC(=O)C(=C/4C)CC)C(=C\3CCC(O)=O)C)c(CCC(O)=O)c2C" PVN SMILES CACTVS 3.370 "CCC1=C(C)C(=O)N[CH]1Cc2[nH]c(C=C3N=C(C=C4NC(=O)C(=C4C)CC)C(=C3CCC(O)=O)C)c(CCC(O)=O)c2C" PVN SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "CCC1=C(C(=O)N[C@@H]1Cc2c(c(c([nH]2)/C=C\3/C(=C(C(=N3)/C=C/4\C(=C(C(=O)N4)CC)C)C)CCC(=O)O)CCC(=O)O)C)C" PVN SMILES "OpenEye OEToolkits" 1.7.6 "CCC1=C(C(=O)NC1Cc2c(c(c([nH]2)C=C3C(=C(C(=N3)C=C4C(=C(C(=O)N4)CC)C)C)CCC(=O)O)CCC(=O)O)C)C" # _pdbx_chem_comp_identifier.comp_id PVN _pdbx_chem_comp_identifier.type "SYSTEMATIC NAME" _pdbx_chem_comp_identifier.program "OpenEye OEToolkits" _pdbx_chem_comp_identifier.program_version 1.7.6 _pdbx_chem_comp_identifier.identifier "3-[5-[[(2R)-3-ethyl-4-methyl-5-oxidanylidene-1,2-dihydropyrrol-2-yl]methyl]-2-[(Z)-[5-[(E)-(4-ethyl-3-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-3-(3-hydroxy-3-oxopropyl)-4-methyl-pyrrol-2-ylidene]methyl]-4-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 PVN "Create component" 2006-11-02 RCSB PVN "Modify descriptor" 2011-06-04 RCSB PVN "Modify synonyms" 2012-07-17 EBI PVN "Modify value order" 2012-07-17 EBI PVN "Modify synonyms" 2020-06-05 PDBE PVN "Modify PCM" 2024-09-27 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id PVN _pdbx_chem_comp_synonyms.name "Phycoviolobilin, bound form" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? # _pdbx_chem_comp_pcm.pcm_id 1 _pdbx_chem_comp_pcm.comp_id PVN _pdbx_chem_comp_pcm.modified_residue_id CYS _pdbx_chem_comp_pcm.type None _pdbx_chem_comp_pcm.category "Covalent chemical 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 C31 _pdbx_chem_comp_pcm.modified_residue_id_linking_atom SG _pdbx_chem_comp_pcm.uniprot_specific_ptm_accession ? _pdbx_chem_comp_pcm.uniprot_generic_ptm_accession ? #