data_YMF
# 
_chem_comp.id                                    YMF 
_chem_comp.name                                  "7-[(1~{S})-1-[(5~{R})-5-[(2~{R})-3-azanyl-2-methyl-propyl]-2-oxidanylidene-1,3-oxazolidin-3-yl]ethyl]-3-(1~{H}-pyrazol-4-yl)-1~{H}-indole-2-carboxylic acid" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C21 H25 N5 O4" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2023-06-19 
_chem_comp.pdbx_modified_date                    2024-07-05 
_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                        411.454 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     YMF 
_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        8PH1 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  PDBE 
# 
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 
YMF C10  C1  C 0 1 Y N N N N N -21.367 -13.249 7.632  5.321  0.297  -0.429 C10  YMF 1  
YMF C13  C2  C 0 1 Y N N N N N -20.389 -11.207 7.581  4.068  1.983  -1.224 C13  YMF 2  
YMF C14  C3  C 0 1 Y N N N N N -22.183 -10.750 10.291 1.985  0.691  1.051  C14  YMF 3  
YMF C15  C4  C 0 1 N N N N N N -22.433 -9.363  9.717  2.199  1.959  1.748  C15  YMF 4  
YMF C19  C5  C 0 1 Y N N N N N -22.364 -12.236 11.980 1.055  -1.282 0.458  C19  YMF 5  
YMF C01  C6  C 0 1 N N N N N N -22.574 -12.432 15.677 -1.370 -4.109 1.073  C01  YMF 6  
YMF C02  C7  C 0 1 N N S N N N -23.197 -12.060 14.317 -0.941 -2.643 1.152  C02  YMF 7  
YMF C03  C8  C 0 1 Y N N N N N -22.600 -12.887 13.172 0.282  -2.430 0.298  C03  YMF 8  
YMF C04  C9  C 0 1 Y N N N N N -22.257 -14.254 13.179 0.639  -3.371 -0.642 C04  YMF 9  
YMF C05  C10 C 0 1 Y N N N N N -21.709 -14.820 12.015 1.763  -3.188 -1.436 C05  YMF 10 
YMF C06  C11 C 0 1 Y N N N N N -21.464 -14.182 10.859 2.536  -2.070 -1.297 C06  YMF 11 
YMF C07  C12 C 0 1 Y N N N N N -21.756 -12.884 10.690 2.193  -1.102 -0.350 C07  YMF 12 
YMF C08  C13 C 0 1 Y N N N N N -21.744 -11.787 9.788  2.788  0.179  0.047  C08  YMF 13 
YMF C09  C14 C 0 1 Y N N N N N -21.209 -12.040 8.380  4.006  0.802  -0.517 C09  YMF 14 
YMF C21  C15 C 0 1 N N N N N N -25.308 -13.442 14.728 -2.734 -0.771 1.462  C21  YMF 15 
YMF C22  C16 C 0 1 N N R N N N -26.715 -13.071 14.463 -3.762 -0.184 0.476  C22  YMF 16 
YMF C23  C17 C 0 1 N N N N N N -27.742 -12.772 15.746 -3.507 1.309  0.261  C23  YMF 17 
YMF C24  C18 C 0 1 N N R N N N -28.697 -13.601 15.077 -4.612 1.893  -0.622 C24  YMF 18 
YMF C25  C19 C 0 1 N N N N N N -29.387 -14.638 16.129 -4.292 3.355  -0.939 C25  YMF 19 
YMF C27  C20 C 0 1 N N N N N N -27.918 -14.187 14.012 -5.950 1.813  0.116  C27  YMF 20 
YMF C29  C21 C 0 1 N N N N N N -25.434 -11.458 13.425 -2.542 -1.806 -0.569 C29  YMF 21 
YMF N11  N1  N 0 1 Y N N N N N -20.758 -13.082 6.422  6.117  1.127  -1.047 N11  YMF 22 
YMF N12  N2  N 0 1 Y N N N N N -20.139 -11.866 6.375  5.358  2.189  -1.552 N12  YMF 23 
YMF N18  N3  N 0 1 Y N N N N N -22.529 -10.865 11.511 0.950  -0.194 1.293  N18  YMF 24 
YMF N20  N4  N 0 1 N N N N N N -24.604 -12.281 14.254 -2.028 -1.788 0.669  N20  YMF 25 
YMF N26  N5  N 0 1 N N N N N N -30.533 -15.275 15.470 -5.287 3.881  -1.883 N26  YMF 26 
YMF O16  O1  O 0 1 N N N N N N -22.765 -9.325  8.523  3.150  2.659  1.457  O16  YMF 27 
YMF O17  O2  O 0 1 N N N N N N -22.357 -8.315  10.478 1.342  2.351  2.714  O17  YMF 28 
YMF O28  O3  O 0 1 N N N N N N -26.732 -11.985 13.525 -3.530 -0.924 -0.758 O28  YMF 29 
YMF O30  O4  O 0 1 N N N N N N -25.130 -10.509 12.770 -2.146 -2.555 -1.440 O30  YMF 30 
YMF H101 H1  H 0 0 N N N N N N -21.879 -14.139 7.967  5.617  -0.616 0.067  H101 YMF 31 
YMF H131 H2  H 0 0 N N N N N N -20.020 -10.230 7.857  3.235  2.625  -1.469 H131 YMF 32 
YMF H011 H3  H 0 0 N N N N N N -23.028 -11.818 16.469 -0.561 -4.745 1.433  H011 YMF 33 
YMF H013 H4  H 0 0 N N N N N N -22.759 -13.496 15.886 -2.255 -4.262 1.691  H013 YMF 34 
YMF H012 H5  H 0 0 N N N N N N -21.490 -12.248 15.646 -1.601 -4.365 0.038  H012 YMF 35 
YMF H021 H6  H 0 0 N N N N N N -22.981 -10.999 14.122 -0.711 -2.387 2.187  H021 YMF 36 
YMF H041 H7  H 0 0 N N N N N N -22.412 -14.855 14.062 0.038  -4.260 -0.763 H041 YMF 37 
YMF H051 H8  H 0 0 N N N N N N -21.461 -15.870 12.054 2.029  -3.936 -2.169 H051 YMF 38 
YMF H061 H9  H 0 0 N N N N N N -21.019 -14.730 10.042 3.409  -1.935 -1.918 H061 YMF 39 
YMF H211 H10 H 0 0 N N N N N N -25.132 -13.607 15.801 -2.042 0.001  1.798  H211 YMF 40 
YMF H212 H11 H 0 0 N N N N N N -25.019 -14.343 14.167 -3.239 -1.230 2.312  H212 YMF 41 
YMF H1   H12 H 0 1 N N N N N N -27.166 -13.934 13.952 -4.777 -0.349 0.837  H1   YMF 42 
YMF H232 H13 H 0 0 N N N N N N -27.394 -13.160 16.715 -3.504 1.820  1.224  H232 YMF 43 
YMF H231 H14 H 0 0 N N N N N N -28.044 -11.720 15.859 -2.542 1.447  -0.227 H231 YMF 44 
YMF H241 H15 H 0 0 N N N N N N -29.500 -12.980 14.652 -4.674 1.325  -1.550 H241 YMF 45 
YMF H251 H16 H 0 0 N N N N N N -28.657 -15.405 16.427 -4.317 3.941  -0.020 H251 YMF 46 
YMF H252 H17 H 0 0 N N N N N N -29.728 -14.091 17.020 -3.299 3.421  -1.385 H252 YMF 47 
YMF H271 H18 H 0 0 N N N N N N -28.556 -14.857 13.417 -5.888 2.382  1.044  H271 YMF 48 
YMF H272 H19 H 0 0 N N N N N N -27.521 -13.390 13.367 -6.737 2.230  -0.513 H272 YMF 49 
YMF H2   H20 H 0 1 N N N N N N -27.083 -14.761 14.441 -6.178 0.772  0.342  H2   YMF 50 
YMF H121 H21 H 0 0 N N N N N N -19.601 -11.510 5.611  5.702  2.944  -2.054 H121 YMF 51 
YMF H181 H22 H 0 0 N N N N N N -22.870 -10.113 12.075 0.252  -0.067 1.955  H181 YMF 52 
YMF H262 H23 H 0 0 N N N N N N -30.968 -15.915 16.103 -6.222 3.772  -1.520 H262 YMF 53 
YMF H3   H24 H 0 1 N N N N N N -31.193 -14.574 15.198 -5.097 4.846  -2.108 H3   YMF 54 
YMF H4   H26 H 0 1 N N N N N N -22.592 -7.542  9.978  1.566  3.201  3.116  H4   YMF 55 
# 
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 
YMF C10 C09  SING Y N 1  
YMF C10 N11  DOUB Y N 2  
YMF C13 C09  DOUB Y N 3  
YMF C13 N12  SING Y N 4  
YMF C14 C15  SING N N 5  
YMF C14 C08  DOUB Y N 6  
YMF C14 N18  SING Y N 7  
YMF C15 O16  DOUB N N 8  
YMF C15 O17  SING N N 9  
YMF C19 C03  DOUB Y N 10 
YMF C19 C07  SING Y N 11 
YMF C19 N18  SING Y N 12 
YMF C01 C02  SING N N 13 
YMF C02 C03  SING N N 14 
YMF C02 N20  SING N N 15 
YMF C03 C04  SING Y N 16 
YMF C04 C05  DOUB Y N 17 
YMF C05 C06  SING Y N 18 
YMF C06 C07  DOUB Y N 19 
YMF C07 C08  SING Y N 20 
YMF C08 C09  SING N N 21 
YMF C21 C22  SING N N 22 
YMF C21 N20  SING N N 23 
YMF C22 C23  SING N N 24 
YMF C22 O28  SING N N 25 
YMF C23 C24  SING N N 26 
YMF C24 C25  SING N N 27 
YMF C24 C27  SING N N 28 
YMF C25 N26  SING N N 29 
YMF C29 N20  SING N N 30 
YMF C29 O28  SING N N 31 
YMF C29 O30  DOUB N N 32 
YMF N11 N12  SING Y N 33 
YMF C10 H101 SING N N 34 
YMF C13 H131 SING N N 35 
YMF C01 H011 SING N N 36 
YMF C01 H013 SING N N 37 
YMF C01 H012 SING N N 38 
YMF C02 H021 SING N N 39 
YMF C04 H041 SING N N 40 
YMF C05 H051 SING N N 41 
YMF C06 H061 SING N N 42 
YMF C21 H211 SING N N 43 
YMF C21 H212 SING N N 44 
YMF C22 H1   SING N N 45 
YMF C23 H232 SING N N 46 
YMF C23 H231 SING N N 47 
YMF C24 H241 SING N N 48 
YMF C25 H251 SING N N 49 
YMF C25 H252 SING N N 50 
YMF C27 H271 SING N N 51 
YMF C27 H272 SING N N 52 
YMF C27 H2   SING N N 53 
YMF N12 H121 SING N N 54 
YMF N18 H181 SING N N 55 
YMF N26 H262 SING N N 56 
YMF N26 H3   SING N N 57 
YMF O17 H4   SING N N 58 
# 
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 
YMF InChI            InChI                1.06  "InChI=1S/C21H25N5O4/c1-11(7-22)6-14-10-26(21(29)30-14)12(2)15-4-3-5-16-17(13-8-23-24-9-13)19(20(27)28)25-18(15)16/h3-5,8-9,11-12,14,25H,6-7,10,22H2,1-2H3,(H,23,24)(H,27,28)/t11-,12+,14-/m1/s1" 
YMF InChIKey         InChI                1.06  OJYBICGUZCKJGO-MBNYWOFBSA-N                                                                                                                                                                       
YMF SMILES_CANONICAL CACTVS               3.385 "C[C@@H](CN)C[C@@H]1CN([C@@H](C)c2cccc3c2[nH]c(C(O)=O)c3c4c[nH]nc4)C(=O)O1"                                                                                                                       
YMF SMILES           CACTVS               3.385 "C[CH](CN)C[CH]1CN([CH](C)c2cccc3c2[nH]c(C(O)=O)c3c4c[nH]nc4)C(=O)O1"                                                                                                                             
YMF SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C[C@H](C[C@@H]1CN(C(=O)O1)[C@@H](C)c2cccc3c2[nH]c(c3c4c[nH]nc4)C(=O)O)CN"                                                                                                                        
YMF SMILES           "OpenEye OEToolkits" 2.0.7 "CC(CC1CN(C(=O)O1)C(C)c2cccc3c2[nH]c(c3c4c[nH]nc4)C(=O)O)CN"                                                                                                                                      
# 
_pdbx_chem_comp_identifier.comp_id           YMF 
_pdbx_chem_comp_identifier.type              "SYSTEMATIC NAME" 
_pdbx_chem_comp_identifier.program           "OpenEye OEToolkits" 
_pdbx_chem_comp_identifier.program_version   2.0.7 
_pdbx_chem_comp_identifier.identifier        "7-[(1~{S})-1-[(5~{R})-5-[(2~{R})-3-azanyl-2-methyl-propyl]-2-oxidanylidene-1,3-oxazolidin-3-yl]ethyl]-3-(1~{H}-pyrazol-4-yl)-1~{H}-indole-2-carboxylic 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 
YMF "Create component" 2023-06-19 PDBE 
YMF "Initial release"  2024-07-10 RCSB 
# 
