data_EXA
# 
_chem_comp.id                                    EXA 
_chem_comp.name                                  "N~6~-[(R)-[(E)-(1-carboxyethylidene)amino]{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl]-L-lysine" 
_chem_comp.type                                  "peptide linking" 
_chem_comp.pdbx_type                             ATOMP 
_chem_comp.formula                               "C17 H27 N4 O9 P" 
_chem_comp.mon_nstd_parent_comp_id               LYS 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2017-03-01 
_chem_comp.pdbx_modified_date                    2023-11-27 
_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                        462.391 
_chem_comp.one_letter_code                       K 
_chem_comp.three_letter_code                     EXA 
_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        5V12 
_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_n_terminal_atom_flag 
_chem_comp_atom.pdbx_backbone_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 
EXA N     N1  N 0 1 N N N N N N 32.591 -74.266 5.087  7.255  -0.035 1.745  N     EXA 1  
EXA CA    C1  C 0 1 N N S N N N 32.244 -75.644 4.640  7.132  -0.832 0.517  CA    EXA 2  
EXA CB    C2  C 0 1 N N N N N N 33.372 -76.627 4.951  5.988  -0.280 -0.336 CB    EXA 3  
EXA CG    C3  C 0 1 N N N N N N 34.390 -76.703 3.815  4.662  -0.470 0.405  CG    EXA 4  
EXA CD    C4  C 0 1 N N N N N N 35.360 -77.868 4.012  3.518  0.082  -0.448 CD    EXA 5  
EXA CE    C5  C 0 1 N N N N N N 36.517 -77.820 3.016  2.193  -0.108 0.292  CE    EXA 6  
EXA NZ    N2  N 0 1 N N N N N N 37.370 -79.016 3.153  1.094  0.422  -0.526 NZ    EXA 7  
EXA "C4'" C6  C 0 1 N N S N N N 38.744 -78.747 2.668  -0.197 0.257  0.154  "C4'" EXA 8  
EXA C4    C7  C 0 1 Y N N N N N 39.719 -79.391 3.592  -0.992 1.532  0.040  C4    EXA 9  
EXA C3    C8  C 0 1 Y N N N N N 39.385 -80.661 4.280  -0.353 2.765  -0.047 C3    EXA 10 
EXA O3    O1  O 0 1 N N N N N N 38.187 -81.275 4.083  1.004  2.840  -0.032 O3    EXA 11 
EXA C2    C9  C 0 1 Y N N N N N 40.398 -81.252 5.192  -1.120 3.915  -0.152 C2    EXA 12 
EXA "C2'" C10 C 0 1 N N N N N N 40.101 -82.539 5.915  -0.442 5.258  -0.247 "C2'" EXA 13 
EXA C5    C11 C 0 1 Y N N N N N 41.065 -78.823 3.888  -2.377 1.505  0.014  C5    EXA 14 
EXA C6    C12 C 0 1 Y N N N N N 41.915 -79.484 4.772  -3.073 2.694  -0.092 C6    EXA 15 
EXA N1    N3  N 0 1 Y N N N N N 41.588 -80.635 5.381  -2.437 3.847  -0.168 N1    EXA 16 
EXA "C5'" C13 C 0 1 N N N N N N 41.547 -77.536 3.264  -3.115 0.194  0.099  "C5'" EXA 17 
EXA OP4   O2  O 0 1 N N N N N N 40.607 -76.492 3.478  -4.523 0.436  0.052  OP4   EXA 18 
EXA P     P1  P 0 1 N N N N N N 40.804 -75.106 2.701  -5.618 -0.742 0.119  P     EXA 19 
EXA OP1   O3  O 0 1 N N N N N N 40.881 -75.379 1.219  -5.344 -1.732 -0.946 OP1   EXA 20 
EXA OP2   O4  O 0 1 N N N N N N 39.625 -74.218 3.018  -5.542 -1.464 1.556  OP2   EXA 21 
EXA OP3   O5  O 0 1 N N N N N N 42.102 -74.502 3.179  -7.089 -0.120 -0.091 OP3   EXA 22 
EXA C     C14 C 0 1 N N N N N N 30.960 -76.139 5.244  8.420  -0.758 -0.262 C     EXA 23 
EXA O     O6  O 0 1 N N N N N N 29.977 -76.302 4.492  9.199  0.143  -0.056 O     EXA 24 
EXA N3    N4  N 0 1 N N N N N N 38.919 -79.207 1.295  -0.941 -0.840 -0.469 N3    EXA 25 
EXA C7    C15 C 0 1 N N N N N N 38.854 -78.380 0.246  -1.163 -1.918 0.186  C7    EXA 26 
EXA C8    C16 C 0 1 N N N N N N 39.094 -78.865 -1.112 -1.987 -2.994 -0.413 C8    EXA 27 
EXA C9    C17 C 0 1 N N N N N N 38.563 -77.104 0.416  -0.585 -2.092 1.567  C9    EXA 28 
EXA O10   O7  O 0 1 N N N N N N 40.010 -78.345 -1.786 -2.197 -4.015 0.208  O10   EXA 29 
EXA O11   O8  O 0 1 N N N N N N 38.372 -79.778 -1.570 -2.504 -2.838 -1.647 O11   EXA 30 
EXA OXT   O9  O 0 1 N Y N N N N 30.694 -75.795 6.502  8.701  -1.692 -1.184 OXT   EXA 31 
EXA H     H1  H 0 1 N N N N N N 31.837 -73.645 4.872  7.962  -0.418 2.355  H     EXA 32 
EXA H2    H2  H 0 1 N N N N N N 32.751 -74.266 6.074  7.449  0.932  1.531  H2    EXA 33 
EXA HA    H4  H 0 1 N N N N N N 32.115 -75.624 3.548  6.924  -1.870 0.777  HA    EXA 34 
EXA HB2   H5  H 0 1 N N N N N N 32.940 -77.626 5.109  6.152  0.781  -0.521 HB2   EXA 35 
EXA HB3   H6  H 0 1 N N N N N N 33.885 -76.301 5.868  5.953  -0.814 -1.286 HB3   EXA 36 
EXA HG2   H7  H 0 1 N N N N N N 34.961 -75.763 3.783  4.498  -1.531 0.590  HG2   EXA 37 
EXA HG3   H8  H 0 1 N N N N N N 33.855 -76.840 2.864  4.697  0.064  1.355  HG3   EXA 38 
EXA HD2   H9  H 0 1 N N N N N N 34.813 -78.813 3.877  3.682  1.143  -0.634 HD2   EXA 39 
EXA HD3   H10 H 0 1 N N N N N N 35.767 -77.823 5.033  3.483  -0.452 -1.398 HD3   EXA 40 
EXA HE2   H11 H 0 1 N N N N N N 37.121 -76.921 3.207  2.029  -1.169 0.478  HE2   EXA 41 
EXA HE3   H12 H 0 1 N N N N N N 36.113 -77.780 1.994  2.228  0.426  1.242  HE3   EXA 42 
EXA HZ1   H13 H 0 1 N N N N N N 36.975 -79.763 2.618  1.081  -0.012 -1.438 HZ1   EXA 43 
EXA H15   H15 H 0 1 N N N N N N 38.912 -77.660 2.696  -0.026 0.028  1.206  H15   EXA 44 
EXA H16   H16 H 0 1 N N N N N N 38.149 -82.070 4.601  1.411  2.792  -0.908 H16   EXA 45 
EXA H17   H17 H 0 1 N N N N N N 40.961 -82.815 6.542  -0.262 5.500  -1.294 H17   EXA 46 
EXA H18   H18 H 0 1 N N N N N N 39.212 -82.406 6.550  -1.082 6.020  0.197  H18   EXA 47 
EXA H19   H19 H 0 1 N N N N N N 39.912 -83.336 5.181  0.507  5.224  0.287  H19   EXA 48 
EXA H20   H20 H 0 1 N N N N N N 42.883 -79.050 4.977  -4.153 2.680  -0.113 H20   EXA 49 
EXA H21   H21 H 0 1 N N N N N N 41.680 -77.686 2.182  -2.828 -0.440 -0.739 H21   EXA 50 
EXA H22   H22 H 0 1 N N N N N N 42.509 -77.254 3.716  -2.864 -0.305 1.035  H22   EXA 51 
EXA H23   H23 H 0 1 N N N N N N 39.163 -74.006 2.216  -5.711 -0.873 2.303  H23   EXA 52 
EXA H24   H24 H 0 1 N N N N N N 42.701 -74.418 2.447  -7.800 -0.774 -0.062 H24   EXA 53 
EXA H25   H25 H 0 1 N N N N N N 38.412 -76.901 1.487  -1.249 -1.632 2.299  H25   EXA 54 
EXA H26   H26 H 0 1 N N N N N N 39.391 -76.486 0.039  -0.482 -3.155 1.787  H26   EXA 55 
EXA H27   H27 H 0 1 N N N N N N 37.643 -76.861 -0.136 0.394  -1.615 1.614  H27   EXA 56 
EXA H28   H28 H 0 1 N N N N N N 38.640 -79.978 -2.459 -3.035 -3.567 -1.996 H28   EXA 57 
EXA HXT   H29 H 0 1 N Y N N N N 29.754 -75.728 6.621  9.540  -1.602 -1.658 HXT   EXA 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 
EXA O10   C8    DOUB N N 1  
EXA O11   C8    SING N N 2  
EXA C8    C7    SING N N 3  
EXA C7    C9    SING N N 4  
EXA C7    N3    DOUB N N 5  
EXA OP1   P     DOUB N N 6  
EXA N3    "C4'" SING N N 7  
EXA "C4'" NZ    SING N N 8  
EXA "C4'" C4    SING N N 9  
EXA P     OP2   SING N N 10 
EXA P     OP3   SING N N 11 
EXA P     OP4   SING N N 12 
EXA CE    NZ    SING N N 13 
EXA CE    CD    SING N N 14 
EXA "C5'" OP4   SING N N 15 
EXA "C5'" C5    SING N N 16 
EXA C4    C5    DOUB Y N 17 
EXA C4    C3    SING Y N 18 
EXA CG    CD    SING N N 19 
EXA CG    CB    SING N N 20 
EXA C5    C6    SING Y N 21 
EXA O3    C3    SING N N 22 
EXA C3    C2    DOUB Y N 23 
EXA O     C     DOUB N N 24 
EXA CA    CB    SING N N 25 
EXA CA    N     SING N N 26 
EXA CA    C     SING N N 27 
EXA C6    N1    DOUB Y N 28 
EXA C2    N1    SING Y N 29 
EXA C2    "C2'" SING N N 30 
EXA C     OXT   SING N N 31 
EXA N     H     SING N N 32 
EXA N     H2    SING N N 33 
EXA CA    HA    SING N N 34 
EXA CB    HB2   SING N N 35 
EXA CB    HB3   SING N N 36 
EXA CG    HG2   SING N N 37 
EXA CG    HG3   SING N N 38 
EXA CD    HD2   SING N N 39 
EXA CD    HD3   SING N N 40 
EXA CE    HE2   SING N N 41 
EXA CE    HE3   SING N N 42 
EXA NZ    HZ1   SING N N 43 
EXA "C4'" H15   SING N N 44 
EXA O3    H16   SING N N 45 
EXA "C2'" H17   SING N N 46 
EXA "C2'" H18   SING N N 47 
EXA "C2'" H19   SING N N 48 
EXA C6    H20   SING N N 49 
EXA "C5'" H21   SING N N 50 
EXA "C5'" H22   SING N N 51 
EXA OP2   H23   SING N N 52 
EXA OP3   H24   SING N N 53 
EXA C9    H25   SING N N 54 
EXA C9    H26   SING N N 55 
EXA C9    H27   SING N N 56 
EXA O11   H28   SING N N 57 
EXA OXT   HXT   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 
EXA SMILES           ACDLabs              12.01 "Oc1c(C(\N=C(/C)C(=O)O)NCCCCC(N)C(=O)O)c(cnc1C)COP(=O)(O)O"                                                                                                                                           
EXA InChI            InChI                1.06  "InChI=1S/C17H27N4O9P/c1-9-14(22)13(11(7-20-9)8-30-31(27,28)29)15(21-10(2)16(23)24)19-6-4-3-5-12(18)17(25)26/h7,12,15,19,22H,3-6,8,18H2,1-2H3,(H,23,24)(H,25,26)(H2,27,28,29)/b21-10+/t12-,15+/m0/s1" 
EXA InChIKey         InChI                1.06  AIKQXQJRQAGCPQ-GRNKCENMSA-N                                                                                                                                                                           
EXA SMILES_CANONICAL CACTVS               3.385 "Cc1ncc(CO[P](O)(O)=O)c([C@H](NCCCC[C@H](N)C(O)=O)N=C(C)C(O)=O)c1O"                                                                                                                                   
EXA SMILES           CACTVS               3.385 "Cc1ncc(CO[P](O)(O)=O)c([CH](NCCCC[CH](N)C(O)=O)N=C(C)C(O)=O)c1O"                                                                                                                                     
EXA SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "Cc1c(c(c(cn1)COP(=O)(O)O)[C@H](NCCCC[C@@H](C(=O)O)N)/N=C(\C)/C(=O)O)O"                                                                                                                               
EXA SMILES           "OpenEye OEToolkits" 2.0.7 "Cc1c(c(c(cn1)COP(=O)(O)O)C(NCCCCC(C(=O)O)N)N=C(C)C(=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 
EXA "SYSTEMATIC NAME" ACDLabs              12.01 "N~6~-[(R)-[(E)-(1-carboxyethylidene)amino]{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl]-L-lysine"                                                        
EXA "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "(2~{S})-2-azanyl-6-[[(~{R})-[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]-[(~{E})-(1-oxidanyl-1-oxidanylidene-propan-2-ylidene)amino]methyl]amino]hexanoic 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 
EXA "Create component" 2017-03-01 RCSB 
EXA "Initial release"  2018-03-07 RCSB 
EXA "Modify atom id"   2023-02-02 PDBJ 
EXA "Modify atom id"   2023-02-07 RCSB 
EXA "Modify atom id"   2023-11-27 RCSB 
# 
