data_BJM
#
_chem_comp.id BJM
_chem_comp.name
;(2~{S})-2-azanyl-1-[(1~{S},3~{S},5~{S})-3-(iminomethyl)-2-azabicyclo[3.1.0]hexan-2-yl]-2-[(5~{R},7~{S})-3-oxidanyl-1-ad
amantyl]ethanone
;
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C18 H27 N3 O2"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms "Saxagliptin, bound form"
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2007-12-13
_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 317.426
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code BJM
_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 3BJM
_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
BJM C1 C1 C 0 1 N N N N N N 46.780 50.851 35.045 -0.915 0.345 0.397 C1 BJM 1
BJM C2 C2 C 0 1 N N S N N N 46.417 51.403 36.461 0.276 0.517 1.342 C2 BJM 2
BJM C3 C3 C 0 1 N N N N N N 47.285 49.386 35.253 -2.057 -0.352 1.139 C3 BJM 3
BJM C8 C4 C 0 1 N N N N N N 47.454 48.652 33.913 -3.249 -0.524 0.194 C8 BJM 4
BJM C9 C5 C 0 1 N N R N N N 45.788 50.190 32.767 -2.576 1.547 -1.031 C9 BJM 5
BJM C10 C6 C 0 1 N N S N N N 48.277 50.883 32.887 -1.686 -0.675 -1.750 C10 BJM 6
BJM C13 C7 C 0 1 N N N N N N 46.143 48.736 33.099 -3.718 0.849 -0.290 C13 BJM 7
BJM C14 C8 C 0 1 N N N N N N 48.642 49.361 33.142 -2.828 -1.372 -1.008 C14 BJM 8
BJM C16 C9 C 0 1 N N N N N N 46.977 50.904 32.003 -2.155 0.699 -2.234 C16 BJM 9
BJM C19 C10 C 0 1 N N S N N N 47.223 49.007 40.090 4.346 -0.499 -1.088 C19 BJM 10
BJM C20 C11 C 0 1 N N N N N N 47.564 48.194 38.886 4.784 0.812 -0.433 C20 BJM 11
BJM C21 C12 C 0 1 N N N N N N 48.181 50.020 40.690 3.731 -1.595 -0.188 C21 BJM 12
BJM C22 C13 C 0 1 N N N N N N 50.139 50.241 39.110 1.564 -1.772 1.069 C22 BJM 13
BJM N23 N1 N 0 1 N N N N N N 50.300 49.757 37.842 0.585 -2.588 0.959 N23 BJM 14
BJM C4 C14 C 0 1 N N N N N N 45.510 50.832 34.152 -1.385 1.719 -0.087 C4 BJM 15
BJM C5 C15 C 0 1 N N N N N N 47.888 51.615 34.247 -0.495 -0.503 -0.805 C5 BJM 16
BJM C6 C16 C 0 1 N N N N N N 47.652 51.445 37.398 1.444 1.087 0.579 C6 BJM 17
BJM N7 N2 N 0 1 N N N N N N 45.883 52.757 36.426 -0.091 1.433 2.431 N7 BJM 18
BJM N11 N3 N 0 1 N N N N N N 47.703 50.527 38.375 2.246 0.271 -0.133 N11 BJM 19
BJM O12 O1 O 0 1 N N N N N N 48.539 52.284 37.257 1.662 2.280 0.605 O12 BJM 20
BJM O15 O2 O 0 1 N N N N N N 47.547 47.289 34.222 -4.315 -1.176 0.887 O15 BJM 21
BJM C17 C17 C 0 1 N N S N N N 46.735 49.442 38.775 3.342 0.669 -1.037 C17 BJM 22
BJM C18 C18 C 0 1 N N S N N N 48.686 50.700 39.480 2.227 -1.220 -0.167 C18 BJM 23
BJM H1 H1 H 0 1 N N N N N N 45.671 50.729 36.908 0.552 -0.451 1.759 H1 BJM 24
BJM H2 H2 H 0 1 N N N N N N 46.555 48.841 35.870 -1.723 -1.331 1.483 H2 BJM 25
BJM H3 H3 H 0 1 N N N N N N 48.255 49.413 35.771 -2.357 0.252 1.995 H3 BJM 26
BJM H4 H4 H 0 1 N N N N N N 44.879 50.227 32.148 -2.911 2.525 -1.376 H4 BJM 27
BJM H5 H5 H 0 1 N N N N N N 49.105 51.406 32.385 -1.386 -1.279 -2.606 H5 BJM 28
BJM H6 H6 H 0 1 N N N N N N 45.326 48.293 33.688 -4.567 0.727 -0.963 H6 BJM 29
BJM H7 H7 H 0 1 N N N N N N 46.266 48.174 32.162 -4.018 1.453 0.566 H7 BJM 30
BJM H8 H8 H 0 1 N N N N N N 48.805 48.857 32.178 -2.493 -2.351 -0.663 H8 BJM 31
BJM H9 H9 H 0 1 N N N N N N 49.559 49.301 33.747 -3.677 -1.495 -1.681 H9 BJM 32
BJM H10 H10 H 0 1 N N N N N N 47.171 50.376 31.058 -3.004 0.576 -2.907 H10 BJM 33
BJM H11 H11 H 0 1 N N N N N N 46.699 51.947 31.790 -1.342 1.196 -2.762 H11 BJM 34
BJM H12 H12 H 0 1 N N N N N N 46.482 48.576 40.780 4.812 -0.815 -2.021 H12 BJM 35
BJM H13 H13 H 0 1 N N N N N N 47.102 47.207 38.735 4.894 0.820 0.651 H13 BJM 36
BJM H14 H14 H 0 1 N N N N N N 48.595 48.178 38.503 5.490 1.436 -0.982 H14 BJM 37
BJM H15 H15 H 0 1 N N N N N N 48.994 49.526 41.242 3.877 -2.582 -0.627 H15 BJM 38
BJM H16 H16 H 0 1 N N N N N N 47.658 50.722 41.357 4.156 -1.554 0.815 H16 BJM 39
BJM H17 H17 H 0 1 N N N N N N 50.958 50.303 39.811 1.915 -1.478 2.047 H17 BJM 40
BJM H19 H19 H 0 1 N Y N N N N 51.244 49.481 37.664 0.157 -2.942 1.755 H19 BJM 41
BJM H22 H22 H 0 1 N N N N N N 45.165 51.866 34.002 -1.684 2.323 0.770 H22 BJM 42
BJM H23 H23 H 0 1 N N N N N N 44.725 50.253 34.661 -0.571 2.216 -0.615 H23 BJM 43
BJM H24 H24 H 0 1 N N N N N N 48.787 51.690 34.876 0.319 -0.006 -1.333 H24 BJM 44
BJM H25 H25 H 0 1 N N N N N N 47.520 52.624 34.011 -0.160 -1.481 -0.460 H25 BJM 45
BJM H26 H26 H 0 1 N N N N N N 45.670 53.056 37.356 0.657 1.513 3.103 H26 BJM 46
BJM H27 H27 H 0 1 N N N N N N 46.562 53.373 36.025 -0.351 2.338 2.069 H27 BJM 47
BJM H29 H29 H 0 1 N N N N N N 48.334 47.132 34.730 -5.106 -1.318 0.347 H29 BJM 48
BJM H30 H30 H 0 1 N N N N N N 45.676 49.440 38.477 3.076 1.236 -1.929 H30 BJM 49
BJM H31 H31 H 0 1 N N N N N N 48.745 51.775 39.703 1.724 -1.579 -1.064 H31 BJM 50
#
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
BJM C16 C9 SING N N 1
BJM C16 C10 SING N N 2
BJM C9 C13 SING N N 3
BJM C9 C4 SING N N 4
BJM C10 C14 SING N N 5
BJM C10 C5 SING N N 6
BJM C13 C8 SING N N 7
BJM C14 C8 SING N N 8
BJM C8 O15 SING N N 9
BJM C8 C3 SING N N 10
BJM C4 C1 SING N N 11
BJM C5 C1 SING N N 12
BJM C1 C3 SING N N 13
BJM C1 C2 SING N N 14
BJM N7 C2 SING N N 15
BJM C2 C6 SING N N 16
BJM O12 C6 DOUB N N 17
BJM C6 N11 SING N N 18
BJM N23 C22 DOUB N N 19
BJM N11 C17 SING N N 20
BJM N11 C18 SING N N 21
BJM C17 C20 SING N N 22
BJM C17 C19 SING N N 23
BJM C20 C19 SING N N 24
BJM C22 C18 SING N N 25
BJM C18 C21 SING N N 26
BJM C19 C21 SING N N 27
BJM C2 H1 SING N N 28
BJM C3 H2 SING N N 29
BJM C3 H3 SING N N 30
BJM C9 H4 SING N N 31
BJM C10 H5 SING N N 32
BJM C13 H6 SING N N 33
BJM C13 H7 SING N N 34
BJM C14 H8 SING N N 35
BJM C14 H9 SING N N 36
BJM C16 H10 SING N N 37
BJM C16 H11 SING N N 38
BJM C19 H12 SING N N 39
BJM C20 H13 SING N N 40
BJM C20 H14 SING N N 41
BJM C21 H15 SING N N 42
BJM C21 H16 SING N N 43
BJM C22 H17 SING N N 44
BJM N23 H19 SING N N 45
BJM C4 H22 SING N N 46
BJM C4 H23 SING N N 47
BJM C5 H24 SING N N 48
BJM C5 H25 SING N N 49
BJM N7 H26 SING N N 50
BJM N7 H27 SING N N 51
BJM O15 H29 SING N N 52
BJM C17 H30 SING N N 53
BJM C18 H31 SING N N 54
#
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
BJM InChI InChI 1.03 "InChI=1S/C18H27N3O2/c19-8-13-2-12-3-14(12)21(13)16(22)15(20)17-4-10-1-11(5-17)7-18(23,6-10)9-17/h8,10-15,19,23H,1-7,9,20H2/t10-,11+,12-,13+,14+,15-,17+,18-/m1/s1"
BJM InChIKey InChI 1.03 KMSQNYQXZPWGMJ-YQBUGCKMSA-N
BJM SMILES_CANONICAL CACTVS 3.385 "N[C@H](C(=O)N1[C@@H](C[C@@H]2C[C@H]12)C=N)C34C[C@H]5C[C@H](CC(O)(C5)C3)C4"
BJM SMILES CACTVS 3.385 "N[CH](C(=O)N1[CH](C[CH]2C[CH]12)C=N)C34C[CH]5C[CH](CC(O)(C5)C3)C4"
BJM SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "C1[C@@H]2C[C@@H]2N([C@@H]1C=N)C(=O)[C@H](C34C[C@H]5C[C@@H](C3)CC(C5)(C4)O)N"
BJM SMILES "OpenEye OEToolkits" 2.0.6 "C1C2CC2N(C1C=N)C(=O)C(C34CC5CC(C3)CC(C5)(C4)O)N"
#
_pdbx_chem_comp_identifier.comp_id BJM
_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 "(2~{S})-2-azanyl-1-[(1~{S},3~{S},5~{S})-3-(iminomethyl)-2-azabicyclo[3.1.0]hexan-2-yl]-2-[(5~{R},7~{S})-3-oxidanyl-1-adamantyl]ethanone"
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
BJM "Create component" 2007-12-13 RCSB
BJM "Modify descriptor" 2011-06-04 RCSB
BJM "Modify synonyms" 2016-04-12 RCSB
BJM "Modify synonyms" 2018-02-05 RCSB
BJM "Modify synonyms" 2020-06-05 PDBE
BJM "Modify PCM" 2024-09-27 PDBE
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id BJM
_pdbx_chem_comp_synonyms.name "Saxagliptin, bound form"
_pdbx_chem_comp_synonyms.provenance ?
_pdbx_chem_comp_synonyms.type ?
#
_pdbx_chem_comp_pcm.pcm_id 1
_pdbx_chem_comp_pcm.comp_id BJM
_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 C22
_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 ?
#