data_3CY
#
_chem_comp.id 3CY
_chem_comp.name "(3S)-3-[({(2S)-5-[(N-ACETYL-L-ALPHA-ASPARTYL)AMINO]-4-OXO-1,2,4,5,6,7-HEXAHYDROAZEPINO[3,2,1-HI]INDOL-2-YL}CARBONYL)AMINO]-5-(BENZYLSULFANYL)-4-OXOPENTANOIC ACID"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C31 H34 N4 O9 S"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2003-11-24
_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 638.688
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code 3CY
_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 Y
_chem_comp.pdbx_model_coordinates_db_code 1RHU
_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
3CY C1 C1 C 0 1 Y N N N N N 73.744 -15.472 90.453 -5.848 3.824 0.839 C1 3CY 1
3CY C2 C2 C 0 1 Y N N N N N 73.365 -14.738 89.295 -6.526 4.653 1.714 C2 3CY 2
3CY C3 C3 C 0 1 Y N N N N N 72.027 -14.277 89.153 -7.806 4.328 2.122 C3 3CY 3
3CY C4 C4 C 0 1 Y N N N N N 71.067 -14.554 90.161 -8.409 3.175 1.656 C4 3CY 4
3CY C5 C5 C 0 1 Y N N N N N 71.452 -15.285 91.311 -7.733 2.348 0.778 C5 3CY 5
3CY C6 C6 C 0 1 Y N N N N N 72.796 -15.756 91.475 -6.451 2.670 0.373 C6 3CY 6
3CY C7 C7 C 0 1 N N N N N N 73.170 -16.548 92.727 -5.712 1.767 -0.580 C7 3CY 7
3CY S1 S1 S 0 1 N N N N N N 72.207 -16.031 94.156 -4.772 0.534 0.361 S1 3CY 8
3CY C8 C8 C 0 1 N N N N N N 72.744 -17.196 95.422 -4.007 -0.387 -1.002 C8 3CY 9
3CY C9 C9 C 0 1 N N N N N N 71.990 -16.980 96.754 -3.153 -1.496 -0.443 C9 3CY 10
3CY C10 C10 C 0 1 N N S N N N 72.374 -18.013 97.845 -2.404 -2.413 -1.375 C10 3CY 11
3CY O1 O1 O 0 1 N N N N N N 70.748 -17.050 96.440 -3.069 -1.649 0.752 O1 3CY 12
3CY N1 N1 N 0 1 N N N N N N 73.783 -18.142 98.093 -1.390 -3.154 -0.620 N1 3CY 13
3CY C11 C11 C 0 1 N N N N N N 71.672 -17.707 99.213 -3.383 -3.398 -2.016 C11 3CY 14
3CY C12 C12 C 0 1 N N N N N N 70.641 -18.741 99.663 -2.657 -4.234 -3.039 C12 3CY 15
3CY O2 O2 O 0 1 N N N N N N 70.255 -18.753 100.812 -3.337 -5.110 -3.795 O2 3CY 16
3CY O3 O3 O 0 1 N N N N N N 70.209 -19.543 98.881 -1.463 -4.115 -3.179 O3 3CY 17
3CY C13 C13 C 0 1 N N N N N N 74.353 -19.307 97.824 -0.196 -2.587 -0.360 C13 3CY 18
3CY O4 O4 O 0 1 N N N N N N 73.750 -20.315 97.349 0.008 -1.433 -0.672 O4 3CY 19
3CY C21 C21 C 0 1 Y N N N N N 76.800 -21.077 96.944 2.339 -2.450 1.919 C21 3CY 20
3CY N2 N2 N 0 1 N N N N N N 76.250 -20.824 98.176 2.081 -2.543 0.550 N2 3CY 21
3CY C14 C14 C 0 1 N N S N N N 75.842 -19.409 98.170 0.887 -3.387 0.317 C14 3CY 22
3CY C15 C15 C 0 1 N N N N N N 76.872 -18.742 97.167 0.425 -3.833 1.705 C15 3CY 23
3CY C16 C16 C 0 1 Y N N N N N 77.193 -19.920 96.325 1.410 -3.185 2.652 C16 3CY 24
3CY C17 C17 C 0 1 Y N N N N N 77.808 -19.954 95.056 1.455 -3.256 4.031 C17 3CY 25
3CY C18 C18 C 0 1 Y N N N N N 78.000 -21.207 94.423 2.440 -2.583 4.726 C18 3CY 26
3CY C19 C19 C 0 1 Y N N N N N 77.574 -22.413 95.056 3.365 -1.847 4.021 C19 3CY 27
3CY C20 C20 C 0 1 Y N N N N N 76.954 -22.379 96.340 3.326 -1.772 2.635 C20 3CY 28
3CY C22 C22 C 0 1 N N N N N N 76.430 -23.643 97.053 4.386 -0.939 1.991 C22 3CY 29
3CY C23 C23 C 0 1 N N N N N N 76.662 -23.933 98.553 4.859 -1.431 0.658 C23 3CY 30
3CY C24 C24 C 0 1 N N S N N N 77.236 -22.790 99.368 3.905 -1.121 -0.465 C24 3CY 31
3CY C25 C25 C 0 1 N N N N N N 76.349 -21.531 99.355 2.731 -2.017 -0.497 C25 3CY 32
3CY O5 O5 O 0 1 N N N N N N 75.782 -21.193 100.433 2.309 -2.309 -1.596 O5 3CY 33
3CY N3 N3 N 0 1 N N N N N N 77.438 -23.166 100.770 3.438 0.260 -0.317 N3 3CY 34
3CY C26 C26 C 0 1 N N N N N N 78.535 -23.826 101.154 4.144 1.272 -0.859 C26 3CY 35
3CY C27 C27 C 0 1 N N S N N N 78.619 -24.106 102.662 3.664 2.692 -0.707 C27 3CY 36
3CY O6 O6 O 0 1 N N N N N N 79.484 -24.197 100.392 5.166 1.039 -1.469 O6 3CY 37
3CY N4 N4 N 0 1 N N N N N N 79.048 -25.500 102.889 4.598 3.598 -1.380 N4 3CY 38
3CY C30 C30 C 0 1 N N N N N N 78.169 -26.537 102.922 5.717 4.004 -0.747 C30 3CY 39
3CY C31 C31 C 0 1 N N N N N N 78.840 -27.894 103.173 6.733 4.844 -1.477 C31 3CY 40
3CY O9 O9 O 0 1 N N N N N N 76.906 -26.438 102.766 5.905 3.693 0.410 O9 3CY 41
3CY C28 C28 C 0 1 N N N N N N 79.616 -23.097 103.283 2.276 2.831 -1.336 C28 3CY 42
3CY C29 C29 C 0 1 N N N N N N 79.812 -23.242 104.786 1.732 4.208 -1.054 C29 3CY 43
3CY O8 O8 O 0 1 N N N N N N 80.934 -23.308 105.241 0.573 4.598 -1.606 O8 3CY 44
3CY O7 O7 O 0 1 N N N N N N 78.849 -23.280 105.526 2.340 4.960 -0.330 O7 3CY 45
3CY H1 H1 H 0 1 N N N N N N 74.784 -15.825 90.560 -4.848 4.078 0.520 H1 3CY 46
3CY H2 H2 H 0 1 N N N N N N 74.108 -14.526 88.508 -6.055 5.554 2.078 H2 3CY 47
3CY H3 H3 H 0 1 N N N N N N 71.733 -13.703 88.258 -8.335 4.975 2.806 H3 3CY 48
3CY H4 H4 H 0 1 N N N N N N 70.027 -14.203 90.051 -9.409 2.921 1.975 H4 3CY 49
3CY H5 H5 H 0 1 N N N N N N 70.696 -15.490 92.088 -8.204 1.447 0.413 H5 3CY 50
3CY H71 1H7 H 0 1 N N N N N N 74.264 -16.490 92.932 -5.028 2.360 -1.187 H71 3CY 51
3CY H72 2H7 H 0 1 N N N N N N 73.083 -17.646 92.554 -6.427 1.261 -1.229 H72 3CY 52
3CY H81 1H8 H 0 1 N N N N N N 73.849 -17.156 95.569 -3.387 0.287 -1.593 H81 3CY 53
3CY H82 2H8 H 0 1 N N N N N N 72.653 -18.250 95.070 -4.786 -0.812 -1.635 H82 3CY 54
3CY H10 H10 H 0 1 N N N N N N 72.017 -18.979 97.417 -1.919 -1.824 -2.153 H10 3CY 55
3CY HN1 HN1 H 0 1 N N N N N N 74.382 -17.403 98.462 -1.579 -4.053 -0.307 HN1 3CY 56
3CY H111 1H11 H 0 0 N N N N N N 71.211 -16.692 99.188 -3.802 -4.048 -1.248 H111 3CY 57
3CY H112 2H11 H 0 0 N N N N N N 72.436 -17.556 100.011 -4.188 -2.846 -2.503 H112 3CY 58
3CY HO3 HO3 H 0 1 N N N N N N 69.568 -20.186 99.161 ? ? ? HO3 3CY 59
3CY H14 H14 H 0 1 N N N N N N 75.893 -18.869 99.144 1.150 -4.254 -0.290 H14 3CY 60
3CY H151 1H15 H 0 0 N N N N N N 77.741 -18.222 97.633 0.472 -4.919 1.791 H151 3CY 61
3CY H152 2H15 H 0 0 N N N N N N 76.511 -17.837 96.625 -0.585 -3.477 1.903 H152 3CY 62
3CY H17 H17 H 0 1 N N N N N N 78.132 -19.019 94.568 0.719 -3.838 4.566 H17 3CY 63
3CY H18 H18 H 0 1 N N N N N N 78.484 -21.244 93.432 2.484 -2.633 5.804 H18 3CY 64
3CY H19 H19 H 0 1 N N N N N N 77.725 -23.380 94.548 4.137 -1.317 4.557 H19 3CY 65
3CY H221 1H22 H 0 0 N N N N N N 76.807 -24.524 96.484 5.243 -0.894 2.663 H221 3CY 66
3CY H222 2H22 H 0 0 N N N N N N 75.331 -23.692 96.873 4.000 0.072 1.866 H222 3CY 67
3CY H231 1H23 H 0 0 N N N N N N 77.301 -24.839 98.669 4.997 -2.510 0.712 H231 3CY 68
3CY H232 2H23 H 0 0 N N N N N N 75.716 -24.294 99.020 5.821 -0.969 0.436 H232 3CY 69
3CY H24 H24 H 0 1 N N N N N N 78.211 -22.560 98.878 4.438 -1.209 -1.411 H24 3CY 70
3CY HN3 HN3 H 0 1 N N N N N N 76.779 -22.957 101.520 2.621 0.446 0.171 HN3 3CY 71
3CY H27 H27 H 0 1 N N N N N N 77.622 -23.981 103.146 3.610 2.946 0.351 H27 3CY 72
3CY HN4 HN4 H 0 1 N N N N N N 80.022 -25.766 103.034 4.412 3.906 -2.281 HN4 3CY 73
3CY H311 1H31 H 0 0 N N N N N N 79.454 -27.866 104.103 7.462 4.194 -1.961 H311 3CY 74
3CY H312 2H31 H 0 0 N N N N N N 78.119 -28.744 103.200 6.230 5.450 -2.231 H312 3CY 75
3CY H313 3H31 H 0 0 N N N N N N 79.646 -28.082 102.426 7.242 5.496 -0.768 H313 3CY 76
3CY H281 1H28 H 0 0 N N N N N N 79.318 -22.053 103.030 2.349 2.684 -2.414 H281 3CY 77
3CY H282 2H28 H 0 0 N N N N N N 80.598 -23.149 102.758 1.608 2.082 -0.912 H282 3CY 78
3CY HO8 HO8 H 0 1 N N N N N N 81.056 -23.398 106.179 0.223 5.481 -1.424 HO8 3CY 79
#
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
3CY C1 C2 DOUB Y N 1
3CY C1 C6 SING Y N 2
3CY C1 H1 SING N N 3
3CY C2 C3 SING Y N 4
3CY C2 H2 SING N N 5
3CY C3 C4 DOUB Y N 6
3CY C3 H3 SING N N 7
3CY C4 C5 SING Y N 8
3CY C4 H4 SING N N 9
3CY C5 C6 DOUB Y N 10
3CY C5 H5 SING N N 11
3CY C6 C7 SING N N 12
3CY C7 S1 SING N N 13
3CY C7 H71 SING N N 14
3CY C7 H72 SING N N 15
3CY S1 C8 SING N N 16
3CY C8 C9 SING N N 17
3CY C8 H81 SING N N 18
3CY C8 H82 SING N N 19
3CY C9 C10 SING N N 20
3CY C9 O1 DOUB N N 21
3CY C10 N1 SING N N 22
3CY C10 C11 SING N N 23
3CY C10 H10 SING N N 24
3CY N1 C13 SING N N 25
3CY N1 HN1 SING N N 26
3CY C11 C12 SING N N 27
3CY C11 H111 SING N N 28
3CY C11 H112 SING N N 29
3CY C12 O2 DOUB N N 30
3CY C12 O3 SING N N 31
3CY O3 HO3 SING N N 32
3CY C13 O4 DOUB N N 33
3CY C13 C14 SING N N 34
3CY C21 N2 SING N N 35
3CY C21 C16 DOUB Y N 36
3CY C21 C20 SING Y N 37
3CY N2 C14 SING N N 38
3CY N2 C25 SING N N 39
3CY C14 C15 SING N N 40
3CY C14 H14 SING N N 41
3CY C15 C16 SING N N 42
3CY C15 H151 SING N N 43
3CY C15 H152 SING N N 44
3CY C16 C17 SING Y N 45
3CY C17 C18 DOUB Y N 46
3CY C17 H17 SING N N 47
3CY C18 C19 SING Y N 48
3CY C18 H18 SING N N 49
3CY C19 C20 DOUB Y N 50
3CY C19 H19 SING N N 51
3CY C20 C22 SING N N 52
3CY C22 C23 SING N N 53
3CY C22 H221 SING N N 54
3CY C22 H222 SING N N 55
3CY C23 C24 SING N N 56
3CY C23 H231 SING N N 57
3CY C23 H232 SING N N 58
3CY C24 C25 SING N N 59
3CY C24 N3 SING N N 60
3CY C24 H24 SING N N 61
3CY C25 O5 DOUB N N 62
3CY N3 C26 SING N N 63
3CY N3 HN3 SING N N 64
3CY C26 C27 SING N N 65
3CY C26 O6 DOUB N N 66
3CY C27 N4 SING N N 67
3CY C27 C28 SING N N 68
3CY C27 H27 SING N N 69
3CY N4 C30 SING N N 70
3CY N4 HN4 SING N N 71
3CY C30 C31 SING N N 72
3CY C30 O9 DOUB N N 73
3CY C31 H311 SING N N 74
3CY C31 H312 SING N N 75
3CY C31 H313 SING N N 76
3CY C28 C29 SING N N 77
3CY C28 H281 SING N N 78
3CY C28 H282 SING N N 79
3CY C29 O8 SING N N 80
3CY C29 O7 DOUB N N 81
3CY O8 HO8 SING N N 82
#
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
3CY SMILES ACDLabs 10.04 "O=C(O)CC(C(=O)CSCc1ccccc1)NC(=O)C4N3c2c(cccc2CCC(C3=O)NC(=O)C(NC(=O)C)CC(=O)O)C4"
3CY SMILES_CANONICAL CACTVS 3.341 "CC(=O)N[C@@H](CC(O)=O)C(=O)N[C@H]1CCc2cccc3C[C@H](N(C1=O)c23)C(=O)N[C@@H](CC(O)=O)C(=O)CSCc4ccccc4"
3CY SMILES CACTVS 3.341 "CC(=O)N[CH](CC(O)=O)C(=O)N[CH]1CCc2cccc3C[CH](N(C1=O)c23)C(=O)N[CH](CC(O)=O)C(=O)CSCc4ccccc4"
3CY SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "CC(=O)N[C@@H](CC(=O)O)C(=O)N[C@H]1CCc2cccc3c2N(C1=O)[C@@H](C3)C(=O)N[C@@H](CC(=O)O)C(=O)CSCc4ccccc4"
3CY SMILES "OpenEye OEToolkits" 1.5.0 "CC(=O)NC(CC(=O)O)C(=O)NC1CCc2cccc3c2N(C1=O)C(C3)C(=O)NC(CC(=O)O)C(=O)CSCc4ccccc4"
3CY InChI InChI 1.03 "InChI=1S/C31H34N4O9S/c1-17(36)32-23(14-27(40)41)29(42)33-21-11-10-19-8-5-9-20-12-24(35(28(19)20)31(21)44)30(43)34-22(13-26(38)39)25(37)16-45-15-18-6-3-2-4-7-18/h2-9,21-24H,10-16H2,1H3,(H,32,36)(H,33,42)(H,34,43)(H,38,39)(H,40,41)/t21-,22-,23-,24-/m0/s1"
3CY InChIKey InChI 1.03 PEECWFLPGAWBQR-ZJZGAYNASA-N
#
_pdbx_chem_comp_identifier.comp_id 3CY
_pdbx_chem_comp_identifier.type "SYSTEMATIC NAME"
_pdbx_chem_comp_identifier.program ACDLabs
_pdbx_chem_comp_identifier.program_version 10.04
_pdbx_chem_comp_identifier.identifier "(3S)-3-[({(2S,5S)-5-[(N-acetyl-L-alpha-aspartyl)amino]-4-oxo-1,2,4,5,6,7-hexahydroazepino[3,2,1-hi]indol-2-yl}carbonyl)amino]-5-(benzylsulfanyl)-4-oxopentanoic 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
3CY "Create component" 2003-11-24 RCSB
3CY "Modify descriptor" 2011-06-04 RCSB
3CY "Modify PCM" 2024-09-27 PDBE
#
_pdbx_chem_comp_pcm.pcm_id 1
_pdbx_chem_comp_pcm.comp_id 3CY
_pdbx_chem_comp_pcm.modified_residue_id CYS
_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 C9
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom SG
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession ?
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession ?
#