data_I3B
# 
_chem_comp.id                                    I3B 
_chem_comp.name                                  "5-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)amino]pentanoic acid" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C13 H21 N2 O7 P" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2022-01-07 
_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                        348.289 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     I3B 
_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        7TA0 
_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 
I3B C02 C1  C 0 1 Y N N N N N 69.351 -25.260 47.516 1.223  -1.745 -0.463 C02 I3B 1  
I3B C03 C2  C 0 1 Y N N N N N 67.845 -25.041 47.260 2.181  -0.820 -0.082 C03 I3B 2  
I3B C05 C3  C 0 1 Y N N N N N 67.086 -24.578 48.260 3.340  -1.262 0.529  C05 I3B 3  
I3B C07 C4  C 0 1 Y N N N N N 68.940 -24.452 49.830 2.655  -3.458 0.404  C07 I3B 4  
I3B C09 C5  C 0 1 Y N N N N N 69.860 -24.985 48.719 1.468  -3.092 -0.214 C09 I3B 5  
I3B C27 C6  C 0 1 N N N N N N 72.467 -23.426 41.533 -5.718 0.379  0.847  C27 I3B 6  
I3B C29 C7  C 0 1 N N N N N N 72.161 -24.163 43.925 -3.369 -0.339 0.386  C29 I3B 7  
I3B O13 O1  O 0 1 N N N N N N 67.128 -26.680 45.637 3.089  1.387  0.151  O13 I3B 8  
I3B O32 O2  O 0 1 N N N N N N 70.223 -22.695 41.012 -8.070 1.115  0.997  O32 I3B 9  
I3B C01 C8  C 0 1 N N N N N N 70.312 -25.797 46.455 -0.056 -1.303 -1.126 C01 I3B 10 
I3B C04 C9  C 0 1 N N N N N N 67.198 -25.315 45.907 1.963  0.650  -0.331 C04 I3B 11 
I3B C08 C10 C 0 1 N N N N N N 69.513 -24.137 51.210 2.934  -4.913 0.680  C08 I3B 12 
I3B C26 C11 C 0 1 N N N N N N 71.277 -23.248 40.600 -7.014 0.824  0.221  C26 I3B 13 
I3B C28 C12 C 0 1 N N N N N N 72.156 -22.982 42.960 -4.685 0.113  -0.250 C28 I3B 14 
I3B C30 C13 C 0 1 N N N N N N 70.900 -24.230 44.777 -2.337 -0.604 -0.711 C30 I3B 15 
I3B N06 N1  N 0 1 Y N N N N N 67.629 -24.263 49.593 3.541  -2.546 0.751  N06 I3B 16 
I3B N33 N2  N 0 1 N N N N N N 71.232 -24.738 46.093 -1.074 -1.038 -0.100 N33 I3B 17 
I3B O10 O3  O 0 1 N N N N N N 71.221 -25.192 48.930 0.556  -4.036 -0.570 O10 I3B 18 
I3B O12 O4  O 0 1 N N N N N N 66.982 -28.544 43.858 3.262  3.426  -1.500 O12 I3B 19 
I3B O14 O5  O 0 1 N N N N N N 67.848 -26.314 43.208 2.011  3.605  0.685  O14 I3B 20 
I3B O15 O6  O 0 1 N N N N N N 65.456 -26.603 43.683 4.529  3.487  0.803  O15 I3B 21 
I3B O31 O7  O 0 1 N N N N N N 71.362 -23.660 39.417 -7.103 0.920  -0.981 O31 I3B 22 
I3B P11 P1  P 0 1 N N N N N N 66.846 -27.054 44.061 3.197  2.990  0.049  P11 I3B 23 
I3B H1  H1  H 0 1 N N N N N N 66.031 -24.429 48.083 4.091  -0.545 0.828  H1  I3B 24 
I3B H2  H2  H 0 1 N N N N N N 72.750 -24.489 41.547 -5.349 1.159  1.513  H2  I3B 25 
I3B H3  H3  H 0 1 N N N N N N 73.308 -22.828 41.152 -5.885 -0.535 1.417  H3  I3B 26 
I3B H4  H4  H 0 1 N N N N N N 72.243 -25.093 43.343 -3.000 0.442  1.051  H4  I3B 27 
I3B H5  H5  H 0 1 N N N N N N 73.031 -24.070 44.591 -3.537 -1.253 0.956  H5  I3B 28 
I3B H6  H6  H 0 1 N N N N N N 69.585 -22.665 40.309 -8.879 1.396  0.549  H6  I3B 29 
I3B H7  H7  H 0 1 N N N N N N 69.745 -26.116 45.568 0.127  -0.394 -1.699 H7  I3B 30 
I3B H8  H8  H 0 1 N N N N N N 70.872 -26.653 46.860 -0.409 -2.088 -1.794 H8  I3B 31 
I3B H9  H9  H 0 1 N N N N N N 67.793 -24.826 45.122 1.846  0.824  -1.401 H9  I3B 32 
I3B H10 H10 H 0 1 N N N N N N 66.180 -24.899 45.908 1.064  0.978  0.191  H10 I3B 33 
I3B H11 H11 H 0 1 N N N N N N 68.710 -23.771 51.866 3.452  -5.351 -0.172 H11 I3B 34 
I3B H12 H12 H 0 1 N N N N N N 69.952 -25.049 51.641 3.558  -5.000 1.569  H12 I3B 35 
I3B H13 H13 H 0 1 N N N N N N 70.290 -23.364 51.117 1.993  -5.438 0.843  H13 I3B 36 
I3B H14 H14 H 0 1 N N N N N N 72.915 -22.254 43.282 -5.054 -0.667 -0.915 H14 I3B 37 
I3B H15 H15 H 0 1 N N N N N N 71.163 -22.509 42.979 -4.518 1.027  -0.820 H15 I3B 38 
I3B H16 H16 H 0 1 N N N N N N 70.467 -23.223 44.871 -2.706 -1.385 -1.377 H16 I3B 39 
I3B H17 H17 H 0 1 N N N N N N 70.170 -24.900 44.299 -2.170 0.310  -1.281 H17 I3B 40 
I3B H18 H18 H 0 1 N N N N N N 72.165 -25.097 46.085 -0.744 -0.360 0.570  H18 I3B 41 
I3B H20 H20 H 0 1 N N N N N N 71.443 -24.956 49.823 0.680  -4.385 -1.463 H20 I3B 42 
I3B H21 H21 H 0 1 N N N N N N 67.674 -28.717 43.231 4.016  3.058  -1.981 H21 I3B 43 
I3B H22 H22 H 0 1 N N N N N N 65.510 -25.953 42.992 4.659  4.445  0.781  H22 I3B 44 
# 
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 
I3B O31 C26 DOUB N N 1  
I3B C26 O32 SING N N 2  
I3B C26 C27 SING N N 3  
I3B C27 C28 SING N N 4  
I3B C28 C29 SING N N 5  
I3B O14 P11 DOUB N N 6  
I3B O15 P11 SING N N 7  
I3B O12 P11 SING N N 8  
I3B C29 C30 SING N N 9  
I3B P11 O13 SING N N 10 
I3B C30 N33 SING N N 11 
I3B O13 C04 SING N N 12 
I3B C04 C03 SING N N 13 
I3B N33 C01 SING N N 14 
I3B C01 C02 SING N N 15 
I3B C03 C02 DOUB Y N 16 
I3B C03 C05 SING Y N 17 
I3B C02 C09 SING Y N 18 
I3B C05 N06 DOUB Y N 19 
I3B C09 O10 SING N N 20 
I3B C09 C07 DOUB Y N 21 
I3B N06 C07 SING Y N 22 
I3B C07 C08 SING N N 23 
I3B C05 H1  SING N N 24 
I3B C27 H2  SING N N 25 
I3B C27 H3  SING N N 26 
I3B C29 H4  SING N N 27 
I3B C29 H5  SING N N 28 
I3B O32 H6  SING N N 29 
I3B C01 H7  SING N N 30 
I3B C01 H8  SING N N 31 
I3B C04 H9  SING N N 32 
I3B C04 H10 SING N N 33 
I3B C08 H11 SING N N 34 
I3B C08 H12 SING N N 35 
I3B C08 H13 SING N N 36 
I3B C28 H14 SING N N 37 
I3B C28 H15 SING N N 38 
I3B C30 H16 SING N N 39 
I3B C30 H17 SING N N 40 
I3B N33 H18 SING N N 41 
I3B O10 H20 SING N N 42 
I3B O12 H21 SING N N 43 
I3B O15 H22 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 
I3B SMILES           ACDLabs              12.01 "Oc1c(CNCCCCC(=O)O)c(cnc1C)COP(=O)(O)O"                                                                                              
I3B InChI            InChI                1.03  "InChI=1S/C13H21N2O7P/c1-9-13(18)11(7-14-5-3-2-4-12(16)17)10(6-15-9)8-22-23(19,20)21/h6,14,18H,2-5,7-8H2,1H3,(H,16,17)(H2,19,20,21)" 
I3B InChIKey         InChI                1.03  JXMZQLZPXCDFBY-UHFFFAOYSA-N                                                                                                          
I3B SMILES_CANONICAL CACTVS               3.385 "Cc1ncc(CO[P](O)(O)=O)c(CNCCCCC(O)=O)c1O"                                                                                            
I3B SMILES           CACTVS               3.385 "Cc1ncc(CO[P](O)(O)=O)c(CNCCCCC(O)=O)c1O"                                                                                            
I3B SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "Cc1c(c(c(cn1)COP(=O)(O)O)CNCCCCC(=O)O)O"                                                                                            
I3B SMILES           "OpenEye OEToolkits" 2.0.7 "Cc1c(c(c(cn1)COP(=O)(O)O)CNCCCCC(=O)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 
I3B "SYSTEMATIC NAME" ACDLabs              12.01 "5-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)amino]pentanoic acid" 
I3B "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "5-[[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylamino]pentanoic 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 
I3B "Create component" 2022-01-07 RCSB 
I3B "Initial release"  2022-05-04 RCSB 
I3B "Modify PCM"       2024-09-27 PDBE 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            I3B 
_pdbx_chem_comp_pcm.modified_residue_id                LYS 
_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               C01 
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom   NZ 
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession     ? 
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession      ? 
# 
