data_AXD
# 
_chem_comp.id                                    AXD 
_chem_comp.name                                  "2-[4-({2-[(2S,5R)-2-(AMINOMETHYL)-5-ETHYNYLPYRROLIDIN-1-YL]-2-OXOETHYL}AMINO)-4-METHYLPIPERIDIN-1-YL]ISONICOTINIC ACID" 
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C21 H29 N5 O3" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2006-08-23 
_chem_comp.pdbx_modified_date                    2024-09-27 
_chem_comp.pdbx_ambiguous_flag                   ? 
_chem_comp.pdbx_release_status                   REL 
_chem_comp.pdbx_replaced_by                      ? 
_chem_comp.pdbx_replaces                         ? 
_chem_comp.formula_weight                        399.487 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     AXD 
_chem_comp.pdbx_model_coordinates_details        ? 
_chem_comp.pdbx_model_coordinates_missing_flag   N 
_chem_comp.pdbx_ideal_coordinates_details        ? 
_chem_comp.pdbx_ideal_coordinates_missing_flag   N 
_chem_comp.pdbx_model_coordinates_db_code        2I03 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  PDBJ 
_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 
AXD N1   N1   N 0 1 N N N N N N 32.449 4.621  64.077 0.525  -1.566 2.975  N1   AXD 1  
AXD C2   C2   C 0 1 N N N N N N 33.532 4.800  63.072 -0.255 -1.196 1.787  C2   AXD 2  
AXD C3   C3   C 0 1 N N N N N N 34.347 3.498  63.016 0.622  -0.374 0.825  C3   AXD 3  
AXD C4   C4   C 0 1 N N N N N N 35.471 3.608  61.970 1.776  -1.186 0.230  C4   AXD 4  
AXD N5   N5   N 0 1 N N N N N N 34.924 4.011  60.613 1.275  -2.424 -0.382 N5   AXD 5  
AXD C6   C6   C 0 1 N N N N N N 34.050 5.227  60.573 0.430  -3.278 0.461  C6   AXD 6  
AXD C7   C7   C 0 1 N N N N N N 32.960 5.084  61.634 -0.725 -2.469 1.059  C7   AXD 7  
AXD C8   C8   C 0 1 N N R N N N 29.717 8.134  64.000 2.127  1.508  5.574  C8   AXD 8  
AXD N9   N9   N 0 1 N N N N N N 29.449 6.800  63.388 2.265  0.056  5.739  N9   AXD 9  
AXD C10  C10  C 0 1 N N S N N N 28.171 6.789  62.668 3.235  -0.267 6.795  C10  AXD 10 
AXD C11  C11  C 0 1 N N N N N N 27.407 7.868  63.444 3.650  1.091  7.373  C11  AXD 11 
AXD C12  C12  C 0 1 N N N N N N 28.464 8.947  63.638 3.393  2.062  6.227  C12  AXD 12 
AXD C13  C13  C 0 1 N N N N N N 28.272 7.194  61.165 2.672  -1.176 7.882  C13  AXD 13 
AXD N14  N14  N 0 1 N N N N N N 29.450 7.433  60.569 3.659  -1.402 8.884  N14  AXD 14 
AXD C15  C15  C 0 1 N N N N N N 30.228 5.660  63.478 1.738  -0.917 4.898  C15  AXD 15 
AXD O16  O16  O 0 1 N N N N N N 29.949 4.609  62.928 1.876  -2.130 5.070  O16  AXD 16 
AXD C17  C17  C 0 1 N N N N N N 31.507 5.703  64.353 0.964  -0.415 3.704  C17  AXD 17 
AXD C18  C18  C 0 1 Y N N N N N 35.217 3.284  59.447 2.054  -3.008 -1.388 C18  AXD 18 
AXD C19  C19  C 0 1 Y N N N N N 36.046 2.143  59.493 1.408  -3.738 -2.394 C19  AXD 19 
AXD C20  C20  C 0 1 Y N N N N N 36.332 1.421  58.323 2.170  -4.324 -3.400 C20  AXD 20 
AXD C21  C21  C 0 1 Y N N N N N 35.780 1.853  57.077 3.552  -4.178 -3.392 C21  AXD 21 
AXD C22  C22  C 0 1 Y N N N N N 34.957 3.009  57.079 4.121  -3.442 -2.364 C22  AXD 22 
AXD N23  N23  N 0 1 Y N N N N N 34.687 3.709  58.234 3.414  -2.858 -1.371 N23  AXD 23 
AXD C24  C24  C 0 1 N N N N N N 30.861 8.825  63.348 0.912  1.998  6.243  C24  AXD 24 
AXD C25  C25  C 0 1 N N N N N N 31.761 9.335  62.736 -0.080 2.398  6.789  C25  AXD 25 
AXD C26  C26  C 0 1 N N N N N N 34.465 5.974  63.535 -1.466 -0.367 2.237  C26  AXD 26 
AXD C27  C27  C 0 1 N N N N N N 37.210 0.241  58.429 1.523  -5.086 -4.456 C27  AXD 27 
AXD O28  O28  O 0 1 N N N N N N 37.677 -0.069 59.554 2.413  -5.587 -5.356 O28  AXD 28 
AXD O29  O29  O 0 1 N N N N N N 37.472 -0.419 57.409 0.307  -5.278 -4.559 O29  AXD 29 
AXD HN1  HN1  H 0 1 N N N N N N 31.897 3.853  63.753 1.330  -2.126 2.666  HN1  AXD 30 
AXD H31  1H3  H 0 1 N N N N N N 33.680 2.667  62.742 1.026  0.511  1.332  H31  AXD 31 
AXD H32  2H3  H 0 1 N N N N N N 34.797 3.317  64.003 -0.003 -0.000 0.002  H32  AXD 32 
AXD H41  1H4  H 0 1 N N N N N N 35.968 2.631  61.877 2.279  -0.568 -0.525 H41  AXD 33 
AXD H42  2H4  H 0 1 N N N N N N 36.181 4.379  62.302 2.520  -1.429 0.998  H42  AXD 34 
AXD H61  1H6  H 0 1 N N N N N N 34.653 6.124  60.779 1.039  -3.733 1.252  H61  AXD 35 
AXD H62  2H6  H 0 1 N N N N N N 33.592 5.326  59.578 0.009  -4.096 -0.136 H62  AXD 36 
AXD H71  1H7  H 0 1 N N N N N N 32.388 6.023  61.669 -1.408 -2.184 0.247  H71  AXD 37 
AXD H72  2H7  H 0 1 N N N N N N 32.335 4.224  61.352 -1.303 -3.110 1.737  H72  AXD 38 
AXD H8   H8   H 0 1 N N N N N N 29.940 8.036  65.073 2.092  1.763  4.510  H8   AXD 39 
AXD H10  H10  H 0 1 N N N N N N 27.719 5.787  62.633 4.088  -0.760 6.314  H10  AXD 40 
AXD H111 1H11 H 0 0 N N N N N N 26.540 8.241  62.880 4.693  1.099  7.702  H111 AXD 41 
AXD H112 2H11 H 0 0 N N N N N N 26.979 7.503  64.389 3.025  1.360  8.234  H112 AXD 42 
AXD H121 1H12 H 0 0 N N N N N N 28.613 9.541  62.724 3.301  3.098  6.567  H121 AXD 43 
AXD H122 2H12 H 0 0 N N N N N N 28.192 9.687  64.405 4.230  2.007  5.519  H122 AXD 44 
AXD H131 1H13 H 0 0 N N N N N N 27.702 8.131  61.075 2.392  -2.122 7.436  H131 AXD 45 
AXD H132 2H13 H 0 0 N N N N N N 27.924 6.287  60.650 1.811  -0.698 8.331  H132 AXD 46 
AXD H141 1H14 H 0 0 N N N N N N 29.318 7.492  59.580 3.980  -0.631 9.459  H141 AXD 47 
AXD H142 2H14 H 0 0 N N N N N N 29.826 8.296  60.907 4.184  -2.270 8.888  H142 AXD 48 
AXD H171 1H17 H 0 0 N N N N N N 32.019 6.657  64.161 1.627  0.201  3.105  H171 AXD 49 
AXD H172 2H17 H 0 0 N N N N N N 31.186 5.591  65.399 0.122  0.167  4.067  H172 AXD 50 
AXD H19  H19  H 0 1 N N N N N N 36.464 1.822  60.436 0.327  -3.841 -2.383 H19  AXD 51 
AXD H21  H21  H 0 1 N N N N N N 35.983 1.316  56.162 4.176  -4.621 -4.161 H21  AXD 52 
AXD H22  H22  H 0 1 N N N N N N 34.530 3.350  56.147 5.195  -3.298 -2.313 H22  AXD 53 
AXD H25  H25  H 0 1 N N N N N N 32.555 9.785  62.196 -0.959 2.752  7.274  H25  AXD 54 
AXD H261 1H26 H 0 0 N N N N N N 34.683 5.868  64.608 -1.791 -0.672 3.236  H261 AXD 55 
AXD H262 2H26 H 0 0 N N N N N N 35.405 5.942  62.965 -1.214 0.697  2.266  H262 AXD 56 
AXD H263 3H26 H 0 0 N N N N N N 33.960 6.935  63.357 -2.304 -0.504 1.546  H263 AXD 57 
AXD HO28 HO28 H 0 0 N N N N N N 38.222 -0.842 59.469 1.986  -6.103 -6.073 HO28 AXD 58 
# 
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 
AXD N1  C2   SING N N 1  
AXD N1  C17  SING N N 2  
AXD N1  HN1  SING N N 3  
AXD C2  C7   SING N N 4  
AXD C2  C3   SING N N 5  
AXD C2  C26  SING N N 6  
AXD C3  C4   SING N N 7  
AXD C3  H31  SING N N 8  
AXD C3  H32  SING N N 9  
AXD C4  N5   SING N N 10 
AXD C4  H41  SING N N 11 
AXD C4  H42  SING N N 12 
AXD N5  C18  SING N N 13 
AXD N5  C6   SING N N 14 
AXD C6  C7   SING N N 15 
AXD C6  H61  SING N N 16 
AXD C6  H62  SING N N 17 
AXD C7  H71  SING N N 18 
AXD C7  H72  SING N N 19 
AXD C8  C24  SING N N 20 
AXD C8  N9   SING N N 21 
AXD C8  C12  SING N N 22 
AXD C8  H8   SING N N 23 
AXD N9  C10  SING N N 24 
AXD N9  C15  SING N N 25 
AXD C10 C13  SING N N 26 
AXD C10 C11  SING N N 27 
AXD C10 H10  SING N N 28 
AXD C11 C12  SING N N 29 
AXD C11 H111 SING N N 30 
AXD C11 H112 SING N N 31 
AXD C12 H121 SING N N 32 
AXD C12 H122 SING N N 33 
AXD C13 N14  SING N N 34 
AXD C13 H131 SING N N 35 
AXD C13 H132 SING N N 36 
AXD N14 H141 SING N N 37 
AXD N14 H142 SING N N 38 
AXD C15 O16  DOUB N N 39 
AXD C15 C17  SING N N 40 
AXD C17 H171 SING N N 41 
AXD C17 H172 SING N N 42 
AXD C18 N23  DOUB Y N 43 
AXD C18 C19  SING Y N 44 
AXD C19 C20  DOUB Y N 45 
AXD C19 H19  SING N N 46 
AXD C20 C21  SING Y N 47 
AXD C20 C27  SING N N 48 
AXD C21 C22  DOUB Y N 49 
AXD C21 H21  SING N N 50 
AXD C22 N23  SING Y N 51 
AXD C22 H22  SING N N 52 
AXD C24 C25  TRIP N N 53 
AXD C25 H25  SING N N 54 
AXD C26 H261 SING N N 55 
AXD C26 H262 SING N N 56 
AXD C26 H263 SING N N 57 
AXD C27 O29  DOUB N N 58 
AXD C27 O28  SING N N 59 
AXD O28 HO28 SING N N 60 
# 
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 
AXD SMILES           ACDLabs              10.04 "O=C(O)c1cc(ncc1)N3CCC(NCC(=O)N2C(C#C)CCC2CN)(CC3)C"                                                                                                                                    
AXD SMILES_CANONICAL CACTVS               3.341 "CC1(CCN(CC1)c2cc(ccn2)C(O)=O)NCC(=O)N3[C@H](CN)CC[C@@H]3C#C"                                                                                                                           
AXD SMILES           CACTVS               3.341 "CC1(CCN(CC1)c2cc(ccn2)C(O)=O)NCC(=O)N3[CH](CN)CC[CH]3C#C"                                                                                                                              
AXD SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "CC1(CCN(CC1)c2cc(ccn2)C(=O)O)NCC(=O)N3[C@@H](CC[C@@H]3C#C)CN"                                                                                                                          
AXD SMILES           "OpenEye OEToolkits" 1.5.0 "CC1(CCN(CC1)c2cc(ccn2)C(=O)O)NCC(=O)N3C(CCC3C#C)CN"                                                                                                                                    
AXD InChI            InChI                1.03  "InChI=1S/C21H29N5O3/c1-3-16-4-5-17(13-22)26(16)19(27)14-24-21(2)7-10-25(11-8-21)18-12-15(20(28)29)6-9-23-18/h1,6,9,12,16-17,24H,4-5,7-8,10-11,13-14,22H2,2H3,(H,28,29)/t16-,17-/m0/s1" 
AXD InChIKey         InChI                1.03  SDLYKSXRUIHFDH-IRXDYDNUSA-N                                                                                                                                                             
# 
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 
AXD "SYSTEMATIC NAME" ACDLabs              10.04 "2-[4-({2-[(2S,5R)-2-(aminomethyl)-5-ethynylpyrrolidin-1-yl]-2-oxoethyl}amino)-4-methylpiperidin-1-yl]pyridine-4-carboxylic acid"    
AXD "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "2-[4-[[2-[(2S,5R)-2-(aminomethyl)-5-ethynyl-pyrrolidin-1-yl]-2-oxo-ethyl]amino]-4-methyl-piperidin-1-yl]pyridine-4-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 
AXD "Create component"  2006-08-23 PDBJ 
AXD "Modify descriptor" 2011-06-04 RCSB 
AXD "Modify PCM"        2024-09-27 PDBE 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            AXD 
_pdbx_chem_comp_pcm.modified_residue_id                SER 
_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               C13 
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom   OG 
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession     ? 
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession      ? 
# 
