data_9V1 # _chem_comp.id 9V1 _chem_comp.name ;3-[2-[[5-[(4-ethenyl-3-methyl-5-oxidanylidene-pyrrol-2-yl)methyl]-3-(3-hydroxy-3-oxopropyl)-4-methyl-1~{H}-pyrrol-2-yl] methyl]-5-[[(3~{R},4~{R})-3-ethyl-4-methyl-5-oxidanylidene-3,4-dihydropyrrol-2-yl]methyl]-4-methyl-1~{H}-pyrrol-3-yl]pro panoic acid ; _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 "Billeverdin IXa, bound form" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2017-06-13 _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 9V1 _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 5VIV _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 9V1 O2D O1 O 0 1 N N N N N N 7.650 3.652 -10.160 -2.154 4.779 -0.706 O2D 9V1 1 9V1 CGD C1 C 0 1 N N N N N N 7.065 2.611 -10.302 -1.179 4.323 0.096 CGD 9V1 2 9V1 O1D O2 O 0 1 N N N N N N 7.309 1.792 -11.181 -0.988 4.842 1.171 O1D 9V1 3 9V1 CBD C2 C 0 1 N N N N N N 5.969 2.275 -9.308 -0.324 3.163 -0.343 CBD 9V1 4 9V1 CAD C3 C 0 1 N N N N N N 4.592 2.463 -9.944 0.703 2.845 0.746 CAD 9V1 5 9V1 C3D C4 C 0 1 Y N N N N N 3.502 2.415 -8.909 1.559 1.685 0.306 C3D 9V1 6 9V1 C2D C5 C 0 1 Y N N N N N 2.682 3.518 -8.411 2.766 1.766 -0.416 C2D 9V1 7 9V1 CMD C6 C 0 1 N N N N N N 2.728 4.958 -8.797 3.438 3.028 -0.891 CMD 9V1 8 9V1 C1D C7 C 0 1 Y N N N N N 1.784 2.888 -7.439 3.209 0.506 -0.604 C1D 9V1 9 9V1 CHD C8 C 0 1 N N N N N N 0.794 3.692 -6.683 4.469 0.112 -1.330 CHD 9V1 10 9V1 C4C C9 C 0 1 N N N N N N 0.158 3.430 -5.529 5.636 0.173 -0.379 C4C 9V1 11 9V1 C3C C10 C 0 1 N N R N N N -0.847 4.386 -4.988 7.058 -0.219 -0.720 C3C 9V1 12 9V1 CAC C11 C 0 1 N N N N N N -0.066 5.663 -4.660 7.132 -1.697 -1.109 CAC 9V1 13 9V1 CBC C12 C 0 1 N N N N N N -1.091 6.766 -4.334 8.550 -2.029 -1.579 CBC 9V1 14 9V1 C2C C13 C 0 1 N N R N N N -1.358 3.669 -3.758 7.820 0.037 0.598 C2C 9V1 15 9V1 CMC C14 C 0 1 N N N N N N -2.839 3.339 -3.752 8.901 1.102 0.400 CMC 9V1 16 9V1 C1C C15 C 0 1 N N N N N N -0.527 2.439 -3.727 6.730 0.543 1.520 C1C 9V1 17 9V1 OC O3 O 0 1 N N N N N N -0.616 1.605 -2.891 6.880 0.873 2.678 OC 9V1 18 9V1 NC N1 N 0 1 N N N N N N 0.313 2.401 -4.734 5.573 0.570 0.844 NC 9V1 19 9V1 C4D C16 C 0 1 Y N N N N N 2.991 1.256 -8.184 1.313 0.379 0.537 C4D 9V1 20 9V1 ND N2 N 0 1 Y N N N N N 1.985 1.566 -7.317 2.319 -0.350 -0.025 ND 9V1 21 9V1 CHA C17 C 0 1 N N N N N N 3.554 -0.087 -8.418 0.129 -0.179 1.283 CHA 9V1 22 9V1 C1A C18 C 0 1 Y N N N N N 3.212 -1.402 -7.857 -1.036 -0.327 0.339 C1A 9V1 23 9V1 C2A C19 C 0 1 Y N N N N N 3.797 -2.653 -8.333 -1.272 -1.384 -0.465 C2A 9V1 24 9V1 CAA C20 C 0 1 N N N N N N 4.804 -2.905 -9.411 -0.424 -2.624 -0.580 CAA 9V1 25 9V1 CBA C21 C 0 1 N N N N N N 6.137 -2.923 -8.686 -0.908 -3.668 0.429 CBA 9V1 26 9V1 CGA C22 C 0 1 N N N N N N 7.346 -3.233 -9.504 -0.059 -4.909 0.314 CGA 9V1 27 9V1 O2A O4 O 0 1 N N N N N N 7.196 -3.343 -10.725 0.840 -4.953 -0.492 O2A 9V1 28 9V1 O1A O5 O 0 1 N N N N N N 8.387 -3.303 -8.970 -0.303 -5.964 1.107 O1A 9V1 29 9V1 C3A C23 C 0 1 Y N N N N N 3.216 -3.664 -7.493 -2.458 -1.116 -1.176 C3A 9V1 30 9V1 CMA C24 C 0 1 N N N N N N 3.443 -5.130 -7.559 -3.111 -2.016 -2.193 CMA 9V1 31 9V1 C4A C25 C 0 1 Y N N N N N 2.353 -2.883 -6.603 -2.901 0.095 -0.781 C4A 9V1 32 9V1 NA N3 N 0 1 Y N N N N N 2.361 -1.579 -6.837 -2.036 0.581 0.154 NA 9V1 33 9V1 CHB C26 C 0 1 N N N N N N 1.487 -3.416 -5.539 -4.142 0.788 -1.281 CHB 9V1 34 9V1 C1B C27 C 0 1 N N N N N N 1.848 -4.571 -4.667 -5.336 0.310 -0.494 C1B 9V1 35 9V1 C2B C28 C 0 1 N N N N N N 0.861 -5.274 -3.832 -6.663 0.750 -0.703 C2B 9V1 36 9V1 CMB C29 C 0 1 N N N N N N -0.591 -4.949 -3.724 -7.120 1.755 -1.729 CMB 9V1 37 9V1 C3B C30 C 0 1 N N N N N N 1.647 -6.315 -3.209 -7.456 0.094 0.197 C3B 9V1 38 9V1 CAB C31 C 0 1 N N N N N N 1.112 -7.269 -2.219 -8.858 0.215 0.359 CAB 9V1 39 9V1 CBB C32 C 0 1 N N N N N N 1.686 -8.339 -1.790 -9.490 -0.506 1.299 CBB 9V1 40 9V1 C4B C33 C 0 1 N N N N N N 2.989 -6.080 -3.736 -6.516 -0.784 0.978 C4B 9V1 41 9V1 OB O6 O 0 1 N N N N N N 3.961 -6.764 -3.423 -6.811 -1.538 1.882 OB 9V1 42 9V1 NB N4 N 0 1 N N N N N N 3.083 -5.063 -4.590 -5.285 -0.574 0.473 NB 9V1 43 9V1 H1 H1 H 0 1 N N N N N N 8.320 3.733 -10.829 -2.677 5.525 -0.380 H1 9V1 44 9V1 H2 H2 H 0 1 N N N N N N 6.080 1.229 -8.987 -0.954 2.290 -0.515 H2 9V1 45 9V1 H3 H3 H 0 1 N N N N N N 6.057 2.937 -8.434 0.195 3.423 -1.266 H3 9V1 46 9V1 H4 H4 H 0 1 N N N N N N 4.562 3.438 -10.452 1.333 3.717 0.917 H4 9V1 47 9V1 H5 H5 H 0 1 N N N N N N 4.424 1.662 -10.679 0.184 2.584 1.669 H5 9V1 48 9V1 H6 H6 H 0 1 N N N N N N 2.047 5.133 -9.643 4.124 3.385 -0.124 H6 9V1 49 9V1 H7 H7 H 0 1 N N N N N N 2.417 5.577 -7.942 3.992 2.822 -1.807 H7 9V1 50 9V1 H8 H8 H 0 1 N N N N N N 3.754 5.226 -9.090 2.683 3.790 -1.087 H8 9V1 51 9V1 H9 H9 H 0 1 N N N N N N 1.314 4.642 -6.491 4.365 -0.903 -1.714 H9 9V1 52 9V1 H10 H10 H 0 1 N N N N N N -0.020 3.858 -7.404 4.641 0.798 -2.159 H10 9V1 53 9V1 H11 H11 H 0 1 N N N N N N -1.656 4.585 -5.707 7.447 0.409 -1.522 H11 9V1 54 9V1 H12 H12 H 0 1 N N N N N N 0.588 5.490 -3.792 6.882 -2.313 -0.245 H12 9V1 55 9V1 H13 H13 H 0 1 N N N N N N 0.544 5.962 -5.525 6.426 -1.896 -1.915 H13 9V1 56 9V1 H14 H14 H 0 1 N N N N N N -0.562 7.700 -4.093 9.243 -1.926 -0.744 H14 9V1 57 9V1 H15 H15 H 0 1 N N N N N N -1.744 6.929 -5.204 8.578 -3.053 -1.951 H15 9V1 58 9V1 H16 H16 H 0 1 N N N N N N -1.700 6.457 -3.472 8.838 -1.345 -2.377 H16 9V1 59 9V1 H17 H17 H 0 1 N N N N N N -1.130 4.280 -2.872 8.255 -0.887 0.978 H17 9V1 60 9V1 H18 H18 H 0 1 N N N N N N -3.096 2.822 -2.816 8.438 2.034 0.075 H18 9V1 61 9V1 H19 H19 H 0 1 N N N N N N -3.422 4.269 -3.830 9.425 1.266 1.342 H19 9V1 62 9V1 H20 H20 H 0 1 N N N N N N -3.073 2.687 -4.607 9.610 0.765 -0.356 H20 9V1 63 9V1 H21 H21 H 0 1 N N N N N N 1.496 0.937 -6.713 2.392 -1.317 -0.011 H21 9V1 64 9V1 H22 H22 H 0 1 N N N N N N 3.442 -0.230 -9.503 0.387 -1.153 1.698 H22 9V1 65 9V1 H23 H23 H 0 1 N N N N N N 4.620 0.031 -8.172 -0.143 0.500 2.092 H23 9V1 66 9V1 H24 H24 H 0 1 N N N N N N 4.780 -2.101 -10.162 -0.506 -3.029 -1.589 H24 9V1 67 9V1 H25 H25 H 0 1 N N N N N N 4.615 -3.871 -9.902 0.616 -2.374 -0.373 H25 9V1 68 9V1 H26 H26 H 0 1 N N N N N N 6.072 -3.679 -7.889 -0.825 -3.264 1.438 H26 9V1 69 9V1 H27 H27 H 0 1 N N N N N N 6.285 -1.929 -8.238 -1.948 -3.919 0.222 H27 9V1 70 9V1 H28 H28 H 0 1 N N N N N N 9.066 -3.453 -9.617 0.268 -6.737 0.996 H28 9V1 71 9V1 H29 H29 H 0 1 N N N N N N 4.286 -5.401 -6.907 -3.818 -2.678 -1.691 H29 9V1 72 9V1 H30 H30 H 0 1 N N N N N N 2.537 -5.657 -7.224 -3.641 -1.410 -2.928 H30 9V1 73 9V1 H31 H31 H 0 1 N N N N N N 3.674 -5.419 -8.595 -2.349 -2.612 -2.694 H31 9V1 74 9V1 H32 H32 H 0 1 N N N N N N 1.841 -0.875 -6.354 -2.116 1.434 0.609 H32 9V1 75 9V1 H33 H33 H 0 1 N N N N N N 1.302 -2.574 -4.856 -4.032 1.865 -1.156 H33 9V1 76 9V1 H34 H34 H 0 1 N N N N N N 0.547 -3.700 -6.035 -4.287 0.558 -2.336 H34 9V1 77 9V1 H35 H35 H 0 1 N N N N N N -1.072 -5.647 -3.024 -7.374 1.240 -2.655 H35 9V1 78 9V1 H36 H36 H 0 1 N N N N N N -0.710 -3.920 -3.355 -7.997 2.283 -1.354 H36 9V1 79 9V1 H37 H37 H 0 1 N N N N N N -1.062 -5.040 -4.714 -6.319 2.470 -1.918 H37 9V1 80 9V1 H38 H38 H 0 1 N N N N N N 0.137 -7.047 -1.811 -9.419 0.888 -0.273 H38 9V1 81 9V1 H39 H39 H 0 1 N N N N N N 1.191 -8.962 -1.059 -8.930 -1.179 1.931 H39 9V1 82 9V1 H40 H40 H 0 1 N N N N N N 2.662 -8.614 -2.161 -10.559 -0.414 1.422 H40 9V1 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 9V1 O1D CGD DOUB N N 1 9V1 O2A CGA DOUB N N 2 9V1 CGD O2D SING N N 3 9V1 CGD CBD SING N N 4 9V1 CAD CBD SING N N 5 9V1 CAD C3D SING N N 6 9V1 CGA O1A SING N N 7 9V1 CGA CBA SING N N 8 9V1 CAA CBA SING N N 9 9V1 CAA C2A SING N N 10 9V1 C3D C2D SING Y N 11 9V1 C3D C4D DOUB Y N 12 9V1 CMD C2D SING N N 13 9V1 CHA C4D SING N N 14 9V1 CHA C1A SING N N 15 9V1 C2D C1D DOUB Y N 16 9V1 C2A C1A DOUB Y N 17 9V1 C2A C3A SING Y N 18 9V1 C4D ND SING Y N 19 9V1 C1A NA SING Y N 20 9V1 CMA C3A SING N N 21 9V1 C3A C4A DOUB Y N 22 9V1 C1D ND SING Y N 23 9V1 C1D CHD SING N N 24 9V1 NA C4A SING Y N 25 9V1 CHD C4C SING N N 26 9V1 C4A CHB SING N N 27 9V1 CHB C1B SING N N 28 9V1 C4C C3C SING N N 29 9V1 C4C NC DOUB N N 30 9V1 C3C CAC SING N N 31 9V1 C3C C2C SING N N 32 9V1 NC C1C SING N N 33 9V1 C1B NB DOUB N N 34 9V1 C1B C2B SING N N 35 9V1 CAC CBC SING N N 36 9V1 NB C4B SING N N 37 9V1 C2B CMB SING N N 38 9V1 C2B C3B DOUB N N 39 9V1 C2C CMC SING N N 40 9V1 C2C C1C SING N N 41 9V1 C4B OB DOUB N N 42 9V1 C4B C3B SING N N 43 9V1 C1C OC DOUB N N 44 9V1 C3B CAB SING N N 45 9V1 CAB CBB DOUB N N 46 9V1 O2D H1 SING N N 47 9V1 CBD H2 SING N N 48 9V1 CBD H3 SING N N 49 9V1 CAD H4 SING N N 50 9V1 CAD H5 SING N N 51 9V1 CMD H6 SING N N 52 9V1 CMD H7 SING N N 53 9V1 CMD H8 SING N N 54 9V1 CHD H9 SING N N 55 9V1 CHD H10 SING N N 56 9V1 C3C H11 SING N N 57 9V1 CAC H12 SING N N 58 9V1 CAC H13 SING N N 59 9V1 CBC H14 SING N N 60 9V1 CBC H15 SING N N 61 9V1 CBC H16 SING N N 62 9V1 C2C H17 SING N N 63 9V1 CMC H18 SING N N 64 9V1 CMC H19 SING N N 65 9V1 CMC H20 SING N N 66 9V1 ND H21 SING N N 67 9V1 CHA H22 SING N N 68 9V1 CHA H23 SING N N 69 9V1 CAA H24 SING N N 70 9V1 CAA H25 SING N N 71 9V1 CBA H26 SING N N 72 9V1 CBA H27 SING N N 73 9V1 O1A H28 SING N N 74 9V1 CMA H29 SING N N 75 9V1 CMA H30 SING N N 76 9V1 CMA H31 SING N N 77 9V1 NA H32 SING N N 78 9V1 CHB H33 SING N N 79 9V1 CHB H34 SING N N 80 9V1 CMB H35 SING N N 81 9V1 CMB H36 SING N N 82 9V1 CMB H37 SING N N 83 9V1 CAB H38 SING N N 84 9V1 CBB H39 SING N N 85 9V1 CBB H40 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 9V1 InChI InChI 1.03 "InChI=1S/C33H40N4O6/c1-7-20-19(6)32(42)37-27(20)14-25-18(5)23(10-12-31(40)41)29(35-25)15-28-22(9-11-30(38)39)17(4)24(34-28)13-26-16(3)21(8-2)33(43)36-26/h8,19-20,34-35H,2,7,9-15H2,1,3-6H3,(H,38,39)(H,40,41)/t19-,20-/m1/s1" 9V1 InChIKey InChI 1.03 FCSIENOPZMSJPT-WOJBJXKFSA-N 9V1 SMILES_CANONICAL CACTVS 3.385 "CC[C@@H]1[C@@H](C)C(=O)N=C1Cc2[nH]c(Cc3[nH]c(CC4=NC(=O)C(=C4C)C=C)c(C)c3CCC(O)=O)c(CCC(O)=O)c2C" 9V1 SMILES CACTVS 3.385 "CC[CH]1[CH](C)C(=O)N=C1Cc2[nH]c(Cc3[nH]c(CC4=NC(=O)C(=C4C)C=C)c(C)c3CCC(O)=O)c(CCC(O)=O)c2C" 9V1 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "CC[C@@H]1[C@H](C(=O)N=C1Cc2c(c(c([nH]2)Cc3c(c(c([nH]3)CC4=NC(=O)C(=C4C)C=C)C)CCC(=O)O)CCC(=O)O)C)C" 9V1 SMILES "OpenEye OEToolkits" 2.0.6 "CCC1C(C(=O)N=C1Cc2c(c(c([nH]2)Cc3c(c(c([nH]3)CC4=NC(=O)C(=C4C)C=C)C)CCC(=O)O)CCC(=O)O)C)C" # _pdbx_chem_comp_identifier.comp_id 9V1 _pdbx_chem_comp_identifier.type "SYSTEMATIC NAME" _pdbx_chem_comp_identifier.program "OpenEye OEToolkits" _pdbx_chem_comp_identifier.program_version 2.0.6 _pdbx_chem_comp_identifier.identifier "3-[2-[[5-[(4-ethenyl-3-methyl-5-oxidanylidene-pyrrol-2-yl)methyl]-3-(3-hydroxy-3-oxopropyl)-4-methyl-1~{H}-pyrrol-2-yl]methyl]-5-[[(3~{R},4~{R})-3-ethyl-4-methyl-5-oxidanylidene-3,4-dihydropyrrol-2-yl]methyl]-4-methyl-1~{H}-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 9V1 "Create component" 2017-06-13 RCSB 9V1 "Initial release" 2017-06-21 RCSB 9V1 "Modify synonyms" 2020-06-05 PDBE 9V1 "Modify PCM" 2024-09-27 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id 9V1 _pdbx_chem_comp_synonyms.name "Billeverdin IXa, bound form" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? # loop_ _pdbx_chem_comp_pcm.pcm_id _pdbx_chem_comp_pcm.comp_id _pdbx_chem_comp_pcm.modified_residue_id _pdbx_chem_comp_pcm.type _pdbx_chem_comp_pcm.category _pdbx_chem_comp_pcm.position _pdbx_chem_comp_pcm.polypeptide_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 _pdbx_chem_comp_pcm.uniprot_generic_ptm_accession 1 9V1 CYS None "Covalent chemical modification" "Amino-acid side chain" "Any position" CAC SG ? ? 2 9V1 CYS None "Covalent chemical modification" "Amino-acid side chain" "Any position" CBC SG ? ? #