data_Y5C
# 
_chem_comp.id                                    Y5C 
_chem_comp.name                                  "4-[4-(2-amino-4-oxo-3,4-dihydro-5H-pyrrolo[3,2-d]pyrimidin-5-yl)butyl]-2-fluorobenzoic acid" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C17 H17 F N4 O3" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2023-06-12 
_chem_comp.pdbx_modified_date                    2024-02-16 
_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                        344.340 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     Y5C 
_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        8T4O 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  RCSB 
# 
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 
Y5C C12 C1  C 0 1 Y N N N N N -39.121 72.434 2.690 -5.486 0.060  0.061  C12 Y5C 1  
Y5C C13 C2  C 0 1 Y N N N N N -37.879 73.001 2.924 -4.647 -1.055 0.163  C13 Y5C 2  
Y5C C14 C3  C 0 1 Y N N N N N -39.409 71.171 3.184 -4.977 1.334  0.325  C14 Y5C 3  
Y5C C15 C4  C 0 1 Y N N N N N -36.924 72.306 3.653 -3.323 -0.887 0.524  C15 Y5C 4  
Y5C C16 C5  C 0 1 Y N N N N N -38.453 70.474 3.913 -3.654 1.485  0.684  C16 Y5C 5  
Y5C C17 C6  C 0 1 N N N N N N -40.171 73.210 1.885 -6.899 -0.108 -0.329 C17 Y5C 6  
Y5C C2  C7  C 0 1 N N N N N N -39.131 63.936 3.610 6.274  -1.212 0.247  C2  Y5C 7  
Y5C C20 C8  C 0 1 N N N N N N -35.264 66.829 5.317 1.781  1.135  -0.938 C20 Y5C 8  
Y5C C21 C9  C 0 1 N N N N N N -35.519 68.108 6.117 0.931  0.932  0.319  C21 Y5C 9  
Y5C C22 C10 C 0 1 N N N N N N -36.652 68.954 5.527 -0.535 0.755  -0.080 C22 Y5C 10 
Y5C C23 C11 C 0 1 N N N N N N -36.149 70.281 4.951 -1.385 0.552  1.176  C23 Y5C 11 
Y5C C24 C12 C 0 1 Y N N N N N -37.210 71.041 4.148 -2.829 0.377  0.783  C24 Y5C 12 
Y5C C4  C13 C 0 1 N N N N N N -37.095 65.020 3.445 4.001  -1.119 -0.368 C4  Y5C 13 
Y5C C5  C14 C 0 1 Y N N N N N -37.883 65.009 6.945 5.103  2.274  -0.027 C5  Y5C 14 
Y5C C6  C15 C 0 1 Y N N N N N -36.661 65.672 6.949 3.817  2.496  -0.368 C6  Y5C 15 
Y5C C8  C16 C 0 1 Y N N N N N -37.080 65.195 4.860 4.084  0.285  -0.326 C8  Y5C 16 
Y5C C9  C17 C 0 1 Y N N N N N -38.144 64.705 5.578 5.308  0.877  0.008  C9  Y5C 17 
Y5C F25 F1  F 0 1 N N N N N N -37.598 74.246 2.437 -5.130 -2.291 -0.090 F25 Y5C 18 
Y5C N1  N1  N 0 1 N N N N N N -39.157 64.079 4.926 6.369  0.096  0.290  N1  Y5C 19 
Y5C N11 N2  N 0 1 N N N N N N -40.229 63.262 2.942 7.380  -1.971 0.542  N11 Y5C 20 
Y5C N3  N3  N 0 1 N N N N N N -38.120 64.396 2.883 5.107  -1.839 -0.078 N3  Y5C 21 
Y5C N7  N4  N 0 1 Y N N N N N -36.196 65.782 5.714 3.185  1.305  -0.555 N7  Y5C 22 
Y5C O10 O1  O 0 1 N N N N N N -36.050 65.490 2.642 2.953  -1.674 -0.654 O10 Y5C 23 
Y5C O18 O2  O 0 1 N N N N N N -39.877 74.237 1.370 -7.337 -1.217 -0.563 O18 Y5C 24 
Y5C O19 O3  O 0 1 N N N N N N -41.527 72.693 1.758 -7.703 0.969  -0.426 O19 Y5C 25 
Y5C H1  H1  H 0 1 N N N N N N -40.377 70.728 3.002 -5.618 2.200  0.248  H1  Y5C 26 
Y5C H2  H2  H 0 1 N N N N N N -35.957 72.750 3.835 -2.673 -1.746 0.604  H2  Y5C 27 
Y5C H3  H3  H 0 1 N N N N N N -38.679 69.490 4.297 -3.261 2.469  0.888  H3  Y5C 28 
Y5C H4  H4  H 0 1 N N N N N N -34.235 66.486 5.501 1.684  0.265  -1.586 H4  Y5C 29 
Y5C H5  H5  H 0 1 N N N N N N -35.393 67.041 4.245 1.439  2.024  -1.468 H5  Y5C 30 
Y5C H6  H6  H 0 1 N N N N N N -35.785 67.832 7.148 1.273  0.044  0.849  H6  Y5C 31 
Y5C H7  H7  H 0 1 N N N N N N -34.598 68.709 6.125 1.028  1.803  0.968  H7  Y5C 32 
Y5C H8  H8  H 0 1 N N N N N N -37.384 69.168 6.320 -0.877 1.644  -0.611 H8  Y5C 33 
Y5C H9  H9  H 0 1 N N N N N N -37.139 68.382 4.724 -0.632 -0.116 -0.729 H9  Y5C 34 
Y5C H10 H10 H 0 1 N N N N N N -35.295 70.072 4.289 -1.042 -0.337 1.706  H10 Y5C 35 
Y5C H11 H11 H 0 1 N N N N N N -35.820 70.919 5.784 -1.287 1.422  1.825  H11 Y5C 36 
Y5C H12 H12 H 0 1 N N N N N N -38.503 64.774 7.798 5.844  3.030  0.183  H12 Y5C 37 
Y5C H13 H13 H 0 1 N N N N N N -36.163 66.044 7.832 3.360  3.468  -0.475 H13 Y5C 38 
Y5C H14 H14 H 0 1 N N N N N N -40.998 62.909 3.475 8.216  -1.539 0.779  H14 Y5C 39 
Y5C H15 H15 H 0 1 N N N N N N -40.217 63.150 1.948 7.326  -2.939 0.515  H15 Y5C 40 
Y5C H16 H16 H 0 1 N N N N N N -38.132 64.269 1.891 5.071  -2.808 -0.101 H16 Y5C 41 
Y5C H17 H17 H 0 1 N N N N N N -42.047 73.292 1.236 -8.621 0.809  -0.685 H17 Y5C 42 
# 
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 
Y5C O18 C17 DOUB N N 1  
Y5C O19 C17 SING N N 2  
Y5C C17 C12 SING N N 3  
Y5C F25 C13 SING N N 4  
Y5C O10 C4  DOUB N N 5  
Y5C C12 C13 DOUB Y N 6  
Y5C C12 C14 SING Y N 7  
Y5C N3  C4  SING N N 8  
Y5C N3  C2  SING N N 9  
Y5C C13 C15 SING Y N 10 
Y5C N11 C2  SING N N 11 
Y5C C14 C16 DOUB Y N 12 
Y5C C4  C8  SING N N 13 
Y5C C2  N1  DOUB N N 14 
Y5C C15 C24 DOUB Y N 15 
Y5C C16 C24 SING Y N 16 
Y5C C24 C23 SING N N 17 
Y5C C8  C9  DOUB Y N 18 
Y5C C8  N7  SING Y N 19 
Y5C N1  C9  SING N N 20 
Y5C C23 C22 SING N N 21 
Y5C C20 N7  SING N N 22 
Y5C C20 C21 SING N N 23 
Y5C C22 C21 SING N N 24 
Y5C C9  C5  SING Y N 25 
Y5C N7  C6  SING Y N 26 
Y5C C5  C6  DOUB Y N 27 
Y5C C14 H1  SING N N 28 
Y5C C15 H2  SING N N 29 
Y5C C16 H3  SING N N 30 
Y5C C20 H4  SING N N 31 
Y5C C20 H5  SING N N 32 
Y5C C21 H6  SING N N 33 
Y5C C21 H7  SING N N 34 
Y5C C22 H8  SING N N 35 
Y5C C22 H9  SING N N 36 
Y5C C23 H10 SING N N 37 
Y5C C23 H11 SING N N 38 
Y5C C5  H12 SING N N 39 
Y5C C6  H13 SING N N 40 
Y5C N11 H14 SING N N 41 
Y5C N11 H15 SING N N 42 
Y5C N3  H16 SING N N 43 
Y5C O19 H17 SING N N 44 
# 
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 
Y5C SMILES           ACDLabs              12.01 "O=C(O)c1ccc(cc1F)CCCCn1ccc2N=C(N)NC(=O)c21"                                                                                                   
Y5C InChI            InChI                1.06  "InChI=1S/C17H17FN4O3/c18-12-9-10(4-5-11(12)16(24)25)3-1-2-7-22-8-6-13-14(22)15(23)21-17(19)20-13/h4-6,8-9H,1-3,7H2,(H,24,25)(H3,19,20,21,23)" 
Y5C InChIKey         InChI                1.06  MKEZEFIAXUENAX-UHFFFAOYSA-N                                                                                                                    
Y5C SMILES_CANONICAL CACTVS               3.385 "NC1=Nc2ccn(CCCCc3ccc(C(O)=O)c(F)c3)c2C(=O)N1"                                                                                                 
Y5C SMILES           CACTVS               3.385 "NC1=Nc2ccn(CCCCc3ccc(C(O)=O)c(F)c3)c2C(=O)N1"                                                                                                 
Y5C SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1cc(c(cc1CCCCn2ccc3c2C(=O)NC(=N3)N)F)C(=O)O"                                                                                                 
Y5C SMILES           "OpenEye OEToolkits" 2.0.7 "c1cc(c(cc1CCCCn2ccc3c2C(=O)NC(=N3)N)F)C(=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 
Y5C "SYSTEMATIC NAME" ACDLabs              12.01 "4-[4-(2-amino-4-oxo-3,4-dihydro-5H-pyrrolo[3,2-d]pyrimidin-5-yl)butyl]-2-fluorobenzoic acid"       
Y5C "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "4-[4-(2-azanyl-4-oxidanylidene-3~{H}-pyrrolo[3,2-d]pyrimidin-5-yl)butyl]-2-fluoranyl-benzoic 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 
Y5C "Create component" 2023-06-12 RCSB 
Y5C "Initial release"  2024-02-21 RCSB 
# 
