data_A1EMP
# 
_chem_comp.id                                    A1EMP 
_chem_comp.name                                  "(2~{S})-2-azanyl-6-[(1~{S})-7-[6-(3,5-dimethyl-1,2-oxazol-4-yl)-1-[(1~{S})-1-pyridin-2-ylethyl]pyrrolo[3,2-b]pyridin-3-yl]-3-methylidene-1-oxidanyl-1~{H}-isoindol-2-yl]hexanoic acid" 
_chem_comp.type                                  "L-peptide linking" 
_chem_comp.pdbx_type                             ATOMP 
_chem_comp.formula                               "C34 H36 N6 O4" 
_chem_comp.mon_nstd_parent_comp_id               LYS 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2025-03-05 
_chem_comp.pdbx_modified_date                    2025-11-28 
_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                        592.687 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     A1EMP 
_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        9KT2 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  PDBC 
_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_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 
A1EMP N   N1  N 0 1 N N N Y Y N 1.539   -6.063  25.942 -8.747 0.539  -1.137 N   A1EMP 1  
A1EMP CA  C1  C 0 1 N N S N Y N 0.343   -5.314  26.306 -7.861 -0.623 -0.989 CA  A1EMP 2  
A1EMP C   C2  C 0 1 N N N N Y Y -0.869  -6.237  26.517 -8.588 -1.718 -0.252 C   A1EMP 3  
A1EMP O   O1  O 0 1 N N N N Y Y -1.635  -6.073  27.471 -9.557 -1.454 0.420  O   A1EMP 4  
A1EMP CB  C3  C 0 1 N N N N N N 0.037   -4.297  25.204 -6.615 -0.217 -0.200 CB  A1EMP 5  
A1EMP CG  C4  C 0 1 N N N N N N -1.148  -3.395  25.481 -5.811 0.804  -1.006 CG  A1EMP 6  
A1EMP CD  C5  C 0 1 N N N N N N -1.511  -2.644  24.222 -4.565 1.210  -0.217 CD  A1EMP 7  
A1EMP CE  C6  C 0 1 N N N N N N -2.761  -1.810  24.409 -3.760 2.232  -1.023 CE  A1EMP 8  
A1EMP NZ  N2  N 0 1 N N N N N N -3.548  -1.775  23.152 -2.567 2.620  -0.267 NZ  A1EMP 9  
A1EMP CAX C7  C 0 1 Y N N N N N -10.235 -8.169  21.693 5.961  2.129  -1.355 CAX A1EMP 10 
A1EMP CAW C8  C 0 1 Y N N N N N -11.424 -8.351  21.020 7.094  2.712  -0.807 CAW A1EMP 11 
A1EMP CAV C9  C 0 1 Y N N N N N -11.887 -7.401  20.147 7.933  1.924  -0.033 CAV A1EMP 12 
A1EMP CAU C10 C 0 1 Y N N N N N -11.146 -6.235  19.944 7.614  0.595  0.166  CAU A1EMP 13 
A1EMP NAT N3  N 0 1 Y N N N N N -9.953  -6.056  20.611 6.527  0.074  -0.370 NAT A1EMP 14 
A1EMP CAS C11 C 0 1 Y N N N N N -9.490  -7.009  21.484 5.704  0.794  -1.108 CAS A1EMP 15 
A1EMP CAR C12 C 0 1 N N S N N N -8.181  -6.820  22.237 4.476  0.150  -1.698 CAR A1EMP 16 
A1EMP CAY C13 C 0 1 N N N N N N -8.432  -6.162  23.577 4.191  0.760  -3.072 CAY A1EMP 17 
A1EMP NAD N4  N 0 1 Y N N N N N -7.279  -6.024  21.455 3.331  0.381  -0.813 NAD A1EMP 18 
A1EMP CAC C14 C 0 1 Y N N N N N -6.985  -4.701  21.571 2.847  1.608  -0.465 CAC A1EMP 19 
A1EMP CAE C15 C 0 1 Y N N N N N -6.505  -6.641  20.350 2.582  -0.609 -0.217 CAE A1EMP 20 
A1EMP CAG C16 C 0 1 Y N N N N N -6.431  -7.882  19.837 2.644  -1.998 -0.238 CAG A1EMP 21 
A1EMP CAH C17 C 0 1 Y N N N N N -5.551  -8.080  18.762 1.702  -2.711 0.501  CAH A1EMP 22 
A1EMP CAK C18 C 0 1 Y N N N N N -5.446  -9.446  18.164 1.725  -4.195 0.512  CAK A1EMP 23 
A1EMP CAO C19 C 0 1 Y N N N N N -5.301  -9.754  16.704 1.511  -5.050 -0.531 CAO A1EMP 24 
A1EMP CAQ C20 C 0 1 N N N N N N -5.635  -8.796  15.576 1.196  -4.677 -1.957 CAQ A1EMP 25 
A1EMP OAN O2  O 0 1 Y N N N N N -5.332  -11.297 16.540 1.637  -6.288 -0.034 OAN A1EMP 26 
A1EMP NAM N5  N 0 1 Y N N N N N -5.299  -11.910 17.964 1.894  -6.274 1.147  NAM A1EMP 27 
A1EMP CAL C21 C 0 1 Y N N N N N -5.511  -10.797 18.970 1.983  -5.063 1.611  CAL A1EMP 28 
A1EMP CAP C22 C 0 1 N N N N N N -5.022  -10.923 20.416 2.294  -4.658 3.029  CAP A1EMP 29 
A1EMP CAI C23 C 0 1 Y N N N N N -4.782  -6.964  18.236 0.735  -2.016 1.232  CAI A1EMP 30 
A1EMP NAJ N6  N 0 1 Y N N N N N -4.911  -5.705  18.791 0.700  -0.703 1.234  NAJ A1EMP 31 
A1EMP CAF C24 C 0 1 Y N N N N N -5.729  -5.531  19.817 1.578  0.018  0.544  CAF A1EMP 32 
A1EMP CAB C25 C 0 1 Y N N N N N -6.116  -4.483  20.640 1.784  1.464  0.364  CAB A1EMP 33 
A1EMP CAA C26 C 0 1 Y N N N N N -5.516  -3.068  20.389 0.981  2.553  0.970  CAA A1EMP 34 
A1EMP CBD C27 C 0 1 Y N N N N N -5.929  -2.395  19.244 1.563  3.419  1.898  CBD A1EMP 35 
A1EMP CBC C28 C 0 1 Y N N N N N -5.425  -1.130  18.986 0.814  4.433  2.461  CBC A1EMP 36 
A1EMP CBB C29 C 0 1 Y N N N N N -4.518  -0.555  19.879 -0.511 4.599  2.112  CBB A1EMP 37 
A1EMP CBA C30 C 0 1 Y N N N N N -4.115  -1.250  21.039 -1.106 3.740  1.186  CBA A1EMP 38 
A1EMP CAZ C31 C 0 1 Y N N N N N -4.606  -2.491  21.304 -0.352 2.716  0.617  CAZ A1EMP 39 
A1EMP CBE C32 C 0 1 N N S N N N -3.986  -2.987  22.606 -1.255 1.967  -0.331 CBE A1EMP 40 
A1EMP OBI O3  O 0 1 N N N N N N -4.831  -3.726  23.378 -0.736 2.041  -1.661 OBI A1EMP 41 
A1EMP CBG C33 C 0 1 N N N N N N -3.214  -0.892  22.113 -2.477 3.679  0.635  CBG A1EMP 42 
A1EMP CBH C34 C 0 1 N N N N N N -1.906  -0.176  21.798 -3.473 4.507  0.953  CBH A1EMP 43 
A1EMP H   H1  H 0 1 N N N Y Y N 1.746   -6.730  26.658 -9.035 0.891  -0.237 H   A1EMP 44 
A1EMP H2  H2  H 0 1 N N N Y Y N 1.383   -6.540  25.077 -8.306 1.263  -1.684 H2  A1EMP 45 
A1EMP HA  H4  H 0 1 N N N N Y N 0.527   -4.766  27.242 -7.566 -0.983 -1.975 HA  A1EMP 46 
A1EMP OXT O4  O 0 1 N Y N N Y Y -1.045  -7.005  25.851 -8.159 -2.987 -0.342 OXT A1EMP 47 
A1EMP HB2 H6  H 0 1 N N N N N N -0.164  -4.850  24.275 -6.915 0.225  0.751  HB2 A1EMP 48 
A1EMP HB3 H7  H 0 1 N N N N N N 0.925   -3.663  25.068 -6.000 -1.098 -0.013 HB3 A1EMP 49 
A1EMP HG2 H8  H 0 1 N N N N N N -0.887  -2.678  26.273 -5.511 0.362  -1.956 HG2 A1EMP 50 
A1EMP HG3 H9  H 0 1 N N N N N N -2.005  -4.004  25.805 -6.425 1.685  -1.193 HG3 A1EMP 51 
A1EMP HD2 H10 H 0 1 N N N N N N -1.683  -3.368  23.412 -4.864 1.652  0.734  HD2 A1EMP 52 
A1EMP HD3 H11 H 0 1 N N N N N N -0.677  -1.980  23.950 -3.950 0.329  -0.030 HD3 A1EMP 53 
A1EMP HE2 H12 H 0 1 N N N N N N -2.475  -0.785  24.687 -3.461 1.790  -1.973 HE2 A1EMP 54 
A1EMP HE3 H13 H 0 1 N N N N N N -3.374  -2.250  25.209 -4.375 3.112  -1.210 HE3 A1EMP 55 
A1EMP H15 H15 H 0 1 N N N N N N -9.881  -8.923  22.381 5.286  2.713  -1.962 H15 A1EMP 56 
A1EMP H16 H16 H 0 1 N N N N N N -11.997 -9.252  21.182 7.319  3.754  -0.980 H16 A1EMP 57 
A1EMP H17 H17 H 0 1 N N N N N N -12.818 -7.553  19.620 8.824  2.345  0.409  H17 A1EMP 58 
A1EMP H18 H18 H 0 1 N N N N N N -11.507 -5.475  19.266 8.261  -0.026 0.768  H18 A1EMP 59 
A1EMP H19 H19 H 0 1 N N N N N N -7.737  -7.811  22.414 4.643  -0.922 -1.804 H19 A1EMP 60 
A1EMP H20 H20 H 0 1 N N N N N N -9.124  -6.781  24.166 4.024  1.832  -2.965 H20 A1EMP 61 
A1EMP H21 H21 H 0 1 N N N N N N -7.480  -6.059  24.119 5.043  0.589  -3.729 H21 A1EMP 62 
A1EMP H22 H22 H 0 1 N N N N N N -8.874  -5.167  23.420 3.302  0.295  -3.498 H22 A1EMP 63 
A1EMP H23 H23 H 0 1 N N N N N N -7.387  -3.993  22.281 3.251  2.553  -0.799 H23 A1EMP 64 
A1EMP H24 H24 H 0 1 N N N N N N -7.024  -8.692  20.236 3.402  -2.510 -0.812 H24 A1EMP 65 
A1EMP H25 H25 H 0 1 N N N N N N -5.889  -9.368  14.671 2.124  -4.572 -2.519 H25 A1EMP 66 
A1EMP H26 H26 H 0 1 N N N N N N -6.492  -8.171  15.867 0.583  -5.456 -2.410 H26 A1EMP 67 
A1EMP H27 H27 H 0 1 N N N N N N -4.766  -8.153  15.371 0.653  -3.732 -1.973 H27 A1EMP 68 
A1EMP H28 H28 H 0 1 N N N N N N -4.532  -11.898 20.554 1.366  -4.575 3.595  H28 A1EMP 69 
A1EMP H29 H29 H 0 1 N N N N N N -4.304  -10.118 20.631 2.934  -5.410 3.489  H29 A1EMP 70 
A1EMP H30 H30 H 0 1 N N N N N N -5.879  -10.843 21.101 2.806  -3.696 3.028  H30 A1EMP 71 
A1EMP H31 H31 H 0 1 N N N N N N -4.107  -7.120  17.408 0.004  -2.568 1.805  H31 A1EMP 72 
A1EMP H32 H32 H 0 1 N N N N N N -6.633  -2.852  18.565 2.600  3.296  2.175  H32 A1EMP 73 
A1EMP H33 H33 H 0 1 N N N N N N -5.731  -0.593  18.101 1.268  5.100  3.179  H33 A1EMP 74 
A1EMP H34 H34 H 0 1 N N N N N N -4.122  0.430   19.680 -1.090 5.394  2.558  H34 A1EMP 75 
A1EMP H35 H35 H 0 1 N N N N N N -3.109  -3.595  22.339 -1.341 0.926  -0.021 H35 A1EMP 76 
A1EMP H36 H36 H 0 1 N N N N N N -4.381  -4.000  24.168 0.110  1.588  -1.778 H36 A1EMP 77 
A1EMP H38 H38 H 0 1 N N N N N N -1.045  -0.320  22.434 -3.309 5.299  1.668  H38 A1EMP 78 
A1EMP H39 H39 H 0 1 N N N N N N -1.840  0.476   20.939 -4.444 4.384  0.496  H39 A1EMP 79 
A1EMP HXT H3  H 0 1 N Y N N Y Y -1.824  -7.481  26.115 -8.658 -3.655 0.149  HXT A1EMP 80 
# 
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 
A1EMP CAQ CAO SING N N 1  
A1EMP OAN CAO SING Y N 2  
A1EMP OAN NAM SING Y N 3  
A1EMP CAO CAK DOUB Y N 4  
A1EMP NAM CAL DOUB Y N 5  
A1EMP CAK CAH SING N N 6  
A1EMP CAK CAL SING Y N 7  
A1EMP CAI CAH DOUB Y N 8  
A1EMP CAI NAJ SING Y N 9  
A1EMP CAH CAG SING Y N 10 
A1EMP NAJ CAF DOUB Y N 11 
A1EMP CAL CAP SING N N 12 
A1EMP CBC CBD DOUB Y N 13 
A1EMP CBC CBB SING Y N 14 
A1EMP CBD CAA SING Y N 15 
A1EMP CAF CAE SING Y N 16 
A1EMP CAF CAB SING Y N 17 
A1EMP CAG CAE DOUB Y N 18 
A1EMP CBB CBA DOUB Y N 19 
A1EMP CAU CAV DOUB Y N 20 
A1EMP CAU NAT SING Y N 21 
A1EMP CAV CAW SING Y N 22 
A1EMP CAE NAD SING Y N 23 
A1EMP CAA CAB SING N N 24 
A1EMP CAA CAZ DOUB Y N 25 
A1EMP NAT CAS DOUB Y N 26 
A1EMP CAB CAC DOUB Y N 27 
A1EMP CAW CAX DOUB Y N 28 
A1EMP CBA CAZ SING Y N 29 
A1EMP CBA CBG SING N N 30 
A1EMP CAZ CBE SING N N 31 
A1EMP NAD CAC SING Y N 32 
A1EMP NAD CAR SING N N 33 
A1EMP CAS CAX SING Y N 34 
A1EMP CAS CAR SING N N 35 
A1EMP CBH CBG DOUB N N 36 
A1EMP CBG NZ  SING N N 37 
A1EMP CAR CAY SING N N 38 
A1EMP CBE NZ  SING N N 39 
A1EMP CBE OBI SING N N 40 
A1EMP NZ  CE  SING N N 41 
A1EMP CD  CE  SING N N 42 
A1EMP CD  CG  SING N N 43 
A1EMP CB  CG  SING N N 44 
A1EMP CB  CA  SING N N 45 
A1EMP N   CA  SING N N 46 
A1EMP CA  C   SING N N 47 
A1EMP C   O   DOUB N N 48 
A1EMP N   H   SING N N 49 
A1EMP N   H2  SING N N 50 
A1EMP CA  HA  SING N N 51 
A1EMP C   OXT SING N N 52 
A1EMP CB  HB2 SING N N 53 
A1EMP CB  HB3 SING N N 54 
A1EMP CG  HG2 SING N N 55 
A1EMP CG  HG3 SING N N 56 
A1EMP CD  HD2 SING N N 57 
A1EMP CD  HD3 SING N N 58 
A1EMP CE  HE2 SING N N 59 
A1EMP CE  HE3 SING N N 60 
A1EMP CAX H15 SING N N 61 
A1EMP CAW H16 SING N N 62 
A1EMP CAV H17 SING N N 63 
A1EMP CAU H18 SING N N 64 
A1EMP CAR H19 SING N N 65 
A1EMP CAY H20 SING N N 66 
A1EMP CAY H21 SING N N 67 
A1EMP CAY H22 SING N N 68 
A1EMP CAC H23 SING N N 69 
A1EMP CAG H24 SING N N 70 
A1EMP CAQ H25 SING N N 71 
A1EMP CAQ H26 SING N N 72 
A1EMP CAQ H27 SING N N 73 
A1EMP CAP H28 SING N N 74 
A1EMP CAP H29 SING N N 75 
A1EMP CAP H30 SING N N 76 
A1EMP CAI H31 SING N N 77 
A1EMP CBD H32 SING N N 78 
A1EMP CBC H33 SING N N 79 
A1EMP CBB H34 SING N N 80 
A1EMP CBE H35 SING N N 81 
A1EMP OBI H36 SING N N 82 
A1EMP CBH H38 SING N N 83 
A1EMP CBH H39 SING N N 84 
A1EMP OXT HXT SING N N 85 
# 
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 
A1EMP InChI            InChI                1.06  "InChI=1S/C34H36N6O4/c1-19-30(22(4)44-38-19)23-16-29-32(37-17-23)26(18-40(29)21(3)28-13-5-7-14-36-28)25-11-9-10-24-20(2)39(33(41)31(24)25)15-8-6-12-27(35)34(42)43/h5,7,9-11,13-14,16-18,21,27,33,41H,2,6,8,12,15,35H2,1,3-4H3,(H,42,43)/t21-,27-,33-/m0/s1" 
A1EMP InChIKey         InChI                1.06  MJITZWMKYRGSCH-NNZMHCESSA-N                                                                                                                                                                                                                                  
A1EMP SMILES_CANONICAL CACTVS               3.385 "C[C@H](n1cc(c2cccc3C(=C)N(CCCC[C@H](N)C(O)=O)[C@@H](O)c23)c4ncc(cc14)c5c(C)onc5C)c6ccccn6"                                                                                                                                                                  
A1EMP SMILES           CACTVS               3.385 "C[CH](n1cc(c2cccc3C(=C)N(CCCC[CH](N)C(O)=O)[CH](O)c23)c4ncc(cc14)c5c(C)onc5C)c6ccccn6"                                                                                                                                                                      
A1EMP SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "Cc1c(c(on1)C)c2cc3c(c(cn3[C@@H](C)c4ccccn4)c5cccc6c5[C@@H](N(C6=C)CCCC[C@@H](C(=O)O)N)O)nc2"                                                                                                                                                                
A1EMP SMILES           "OpenEye OEToolkits" 2.0.7 "Cc1c(c(on1)C)c2cc3c(c(cn3C(C)c4ccccn4)c5cccc6c5C(N(C6=C)CCCCC(C(=O)O)N)O)nc2"                                                                                                                                                                               
# 
_pdbx_chem_comp_identifier.comp_id           A1EMP 
_pdbx_chem_comp_identifier.type              "SYSTEMATIC NAME" 
_pdbx_chem_comp_identifier.program           "OpenEye OEToolkits" 
_pdbx_chem_comp_identifier.program_version   2.0.7 
_pdbx_chem_comp_identifier.identifier        "(2~{S})-2-azanyl-6-[(1~{S})-7-[6-(3,5-dimethyl-1,2-oxazol-4-yl)-1-[(1~{S})-1-pyridin-2-ylethyl]pyrrolo[3,2-b]pyridin-3-yl]-3-methylidene-1-oxidanyl-1~{H}-isoindol-2-yl]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 
A1EMP "Create component" 2025-03-05 PDBC 
A1EMP "Initial release"  2025-12-03 RCSB 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            A1EMP 
_pdbx_chem_comp_pcm.modified_residue_id                LYS 
_pdbx_chem_comp_pcm.type                               None 
_pdbx_chem_comp_pcm.category                           "Non-standard residue" 
_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               ? 
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom   ? 
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession     ? 
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession      ? 
# 
