data_D03
#
_chem_comp.id D03
_chem_comp.name "(S)-N-benzyl-3-((S)-2-cinnamamido-3-phenylpropanamido)-2-oxo-4-((S)-2-oxopyrrolidin-3-yl)butanamide"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C33 H36 N4 O5"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2017-02-06
_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 568.663
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code D03
_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 5N19
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site EBI
_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
D03 O01 O1 O 0 1 N N N N N N -16.225 1.671 -22.272 -4.246 -1.296 0.672 O01 D03 1
D03 C02 C1 C 0 1 N N N N N N -17.393 1.929 -22.278 -3.809 -0.224 0.297 C02 D03 2
D03 C03 C2 C 0 1 N N N N N N -17.954 3.204 -22.836 -4.709 0.920 0.140 C03 D03 3
D03 C05 C3 C 0 1 N N N N N N -17.226 4.004 -23.637 -6.023 0.786 0.409 C05 D03 4
D03 C07 C4 C 0 1 Y N N N N N -17.767 5.232 -24.280 -6.929 1.936 0.251 C07 D03 5
D03 C16 C5 C 0 1 Y N N N N N -16.850 6.083 -24.912 -8.292 1.800 0.530 C16 D03 6
D03 C14 C6 C 0 1 Y N N N N N -17.301 7.259 -25.544 -9.134 2.882 0.379 C14 D03 7
D03 C12 C7 C 0 1 Y N N N N N -18.663 7.581 -25.550 -8.632 4.100 -0.046 C12 D03 8
D03 C10 C8 C 0 1 Y N N N N N -19.591 6.732 -24.932 -7.284 4.241 -0.325 C10 D03 9
D03 C08 C9 C 0 1 Y N N N N N -19.150 5.556 -24.308 -6.428 3.171 -0.173 C08 D03 10
D03 N18 N1 N 0 1 N N N N N N -18.198 0.914 -22.035 -2.494 -0.088 0.033 N18 D03 11
D03 C20 C10 C 0 1 N N S N N N -17.689 -0.439 -21.804 -1.592 -1.230 0.197 C20 D03 12
D03 C22 C11 C 0 1 N N N N N N -18.810 -1.347 -21.247 -1.610 -2.080 -1.076 C22 D03 13
D03 C25 C12 C 0 1 Y N N N N N -19.076 -0.733 -19.869 -2.981 -2.678 -1.261 C25 D03 14
D03 C34 C13 C 0 1 Y N N N N N -18.265 -1.086 -18.802 -3.280 -3.908 -0.706 C34 D03 15
D03 C32 C14 C 0 1 Y N N N N N -18.474 -0.479 -17.546 -4.537 -4.456 -0.876 C32 D03 16
D03 C30 C15 C 0 1 Y N N N N N -19.556 0.431 -17.408 -5.496 -3.774 -1.602 C30 D03 17
D03 C28 C16 C 0 1 Y N N N N N -20.401 0.801 -18.490 -5.197 -2.543 -2.157 C28 D03 18
D03 C26 C17 C 0 1 Y N N N N N -20.146 0.215 -19.735 -3.941 -1.993 -1.982 C26 D03 19
D03 C36 C18 C 0 1 N N N N N N -17.040 -1.039 -22.998 -0.192 -0.733 0.449 C36 D03 20
D03 O37 O2 O 0 1 N N N N N N -17.548 -0.927 -24.105 0.031 0.458 0.488 O37 D03 21
D03 N38 N2 N 0 1 N N N N N N -15.827 -1.650 -22.812 0.813 -1.613 0.631 N38 D03 22
D03 C40 C19 C 0 1 N N S N N N -15.107 -2.175 -23.943 2.191 -1.133 0.766 C40 D03 23
D03 C42 C20 C 0 1 N N N N N N -13.768 -1.429 -24.136 2.487 -0.844 2.239 C42 D03 24
D03 C45 C21 C 0 1 N N S N N N -13.903 0.025 -24.486 3.791 -0.051 2.351 C45 D03 25
D03 C47 C22 C 0 1 N N N N N N -12.606 0.784 -24.676 3.636 1.315 1.718 C47 D03 26
D03 O48 O3 O 0 1 N N N N N N -11.797 0.899 -23.794 3.654 1.534 0.526 O48 D03 27
D03 N49 N3 N 0 1 N N N N N N -12.784 1.683 -25.662 3.475 2.250 2.671 N49 D03 28
D03 C51 C23 C 0 1 N N N N N N -14.106 1.583 -26.301 3.490 1.653 4.011 C51 D03 29
D03 C54 C24 C 0 1 N N N N N N -14.762 0.347 -25.728 4.117 0.249 3.832 C54 D03 30
D03 C57 C25 C 0 1 N N S N N N -14.821 -3.686 -23.776 3.156 -2.203 0.252 C57 D03 31
D03 O58 O4 O 0 1 N N N N N N -14.140 -4.195 -24.893 3.132 -3.329 1.132 O58 D03 32
D03 C66 C26 C 0 1 N N N N N N -16.075 -4.498 -23.706 4.552 -1.637 0.199 C66 D03 33
D03 O67 O5 O 0 1 N N N N N N -16.455 -4.913 -22.653 5.422 -2.102 0.905 O67 D03 34
D03 N68 N4 N 0 1 N N N N N N -16.802 -4.726 -24.769 4.833 -0.613 -0.631 N68 D03 35
D03 C70 C27 C 0 1 N N N N N N -18.063 -5.526 -24.514 6.189 -0.063 -0.683 C70 D03 36
D03 C73 C28 C 0 1 Y N N N N N -19.364 -4.908 -23.948 6.237 1.064 -1.683 C73 D03 37
D03 C74 C29 C 0 1 Y N N N N N -19.827 -3.627 -24.323 6.536 0.800 -3.006 C74 D03 38
D03 C76 C30 C 0 1 Y N N N N N -20.229 -5.676 -23.125 5.975 2.359 -1.278 C76 D03 39
D03 C78 C31 C 0 1 Y N N N N N -21.492 -5.217 -22.663 6.019 3.392 -2.195 C78 D03 40
D03 C80 C32 C 0 1 Y N N N N N -21.914 -3.936 -23.017 6.324 3.130 -3.517 C80 D03 41
D03 C82 C33 C 0 1 Y N N N N N -21.073 -3.136 -23.837 6.580 1.834 -3.924 C82 D03 42
D03 H1 H1 H 0 1 N N N N N N -18.967 3.487 -22.589 -4.321 1.872 -0.192 H1 D03 43
D03 H2 H2 H 0 1 N N N N N N -16.195 3.741 -23.823 -6.412 -0.166 0.741 H2 D03 44
D03 H3 H3 H 0 1 N N N N N N -15.798 5.838 -24.915 -8.685 0.850 0.861 H3 D03 45
D03 H4 H4 H 0 1 N N N N N N -16.592 7.915 -26.026 -10.187 2.779 0.594 H4 D03 46
D03 H5 H5 H 0 1 N N N N N N -19.000 8.487 -26.032 -9.296 4.943 -0.163 H5 D03 47
D03 H6 H6 H 0 1 N N N N N N -20.642 6.982 -24.936 -6.900 5.195 -0.657 H6 D03 48
D03 H7 H7 H 0 1 N N N N N N -19.866 4.893 -23.846 -5.376 3.283 -0.390 H7 D03 49
D03 H8 H8 H 0 1 N N N N N N -19.185 1.073 -22.008 -2.145 0.767 -0.265 H8 D03 50
D03 H9 H9 H 0 1 N N N N N N -16.923 -0.372 -21.018 -1.921 -1.835 1.042 H9 D03 51
D03 H10 H10 H 0 1 N N N N N N -19.708 -1.305 -21.881 -1.367 -1.454 -1.934 H10 D03 52
D03 H11 H11 H 0 1 N N N N N N -18.471 -2.390 -21.159 -0.874 -2.879 -0.989 H11 D03 53
D03 H12 H12 H 0 1 N N N N N N -17.481 -1.818 -18.931 -2.530 -4.441 -0.139 H12 D03 54
D03 H13 H13 H 0 1 N N N N N N -17.827 -0.701 -16.710 -4.770 -5.417 -0.443 H13 D03 55
D03 H14 H14 H 0 1 N N N N N N -19.746 0.862 -16.436 -6.478 -4.202 -1.735 H14 D03 56
D03 H15 H15 H 0 1 N N N N N N -21.208 1.506 -18.356 -5.946 -2.011 -2.723 H15 D03 57
D03 H16 H16 H 0 1 N N N N N N -20.751 0.475 -20.591 -3.709 -1.030 -2.412 H16 D03 58
D03 H17 H17 H 0 1 N N N N N N -15.443 -1.731 -21.892 0.624 -2.563 0.672 H17 D03 59
D03 H18 H18 H 0 1 N N N N N N -15.708 -2.040 -24.855 2.316 -0.220 0.184 H18 D03 60
D03 H19 H19 H 0 1 N N N N N N -13.213 -1.926 -24.945 1.671 -0.262 2.667 H19 D03 61
D03 H20 H20 H 0 1 N N N N N N -13.196 -1.504 -23.199 2.586 -1.784 2.781 H20 D03 62
D03 H21 H21 H 0 1 N N N N N N -14.414 0.501 -23.636 4.610 -0.597 1.883 H21 D03 63
D03 H22 H22 H 0 1 N N N N N N -12.090 2.350 -25.932 3.363 3.197 2.494 H22 D03 64
D03 H23 H23 H 0 1 N N N N N N -13.996 1.485 -27.391 4.100 2.255 4.685 H23 D03 65
D03 H24 H24 H 0 1 N N N N N N -14.708 2.475 -26.072 2.474 1.566 4.397 H24 D03 66
D03 H25 H25 H 0 1 N N N N N N -15.804 0.552 -25.443 3.643 -0.478 4.492 H25 D03 67
D03 H26 H26 H 0 1 N N N N N N -14.736 -0.483 -26.450 5.194 0.278 3.998 H26 D03 68
D03 H27 H27 H 0 1 N N N N N N -14.234 -3.837 -22.858 2.853 -2.516 -0.747 H27 D03 69
D03 H28 H28 H 0 1 N N N N N N -13.975 -5.122 -24.769 3.391 -3.123 2.041 H28 D03 70
D03 H29 H29 H 0 1 N N N N N N -16.546 -4.398 -25.678 4.136 -0.241 -1.195 H29 D03 71
D03 H30 H30 H 0 1 N N N N N N -18.338 -5.972 -25.481 6.466 0.314 0.302 H30 D03 72
D03 H31 H31 H 0 1 N N N N N N -17.777 -6.322 -23.811 6.887 -0.844 -0.982 H31 D03 73
D03 H32 H32 H 0 1 N N N N N N -19.231 -3.015 -24.984 6.737 -0.212 -3.323 H32 D03 74
D03 H33 H33 H 0 1 N N N N N N -19.909 -6.665 -22.833 5.736 2.564 -0.245 H33 D03 75
D03 H34 H34 H 0 1 N N N N N N -22.115 -5.850 -22.048 5.814 4.405 -1.879 H34 D03 76
D03 H35 H35 H 0 1 N N N N N N -22.865 -3.558 -22.673 6.358 3.937 -4.234 H35 D03 77
D03 H36 H36 H 0 1 N N N N N N -21.385 -2.135 -24.097 6.815 1.628 -4.958 H36 D03 78
#
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
D03 C51 C54 SING N N 1
D03 C51 N49 SING N N 2
D03 C54 C45 SING N N 3
D03 N49 C47 SING N N 4
D03 C12 C14 DOUB Y N 5
D03 C12 C10 SING Y N 6
D03 C14 C16 SING Y N 7
D03 C10 C08 DOUB Y N 8
D03 C16 C07 DOUB Y N 9
D03 O58 C57 SING N N 10
D03 N68 C70 SING N N 11
D03 N68 C66 SING N N 12
D03 C47 C45 SING N N 13
D03 C47 O48 DOUB N N 14
D03 C70 C73 SING N N 15
D03 C45 C42 SING N N 16
D03 C74 C73 DOUB Y N 17
D03 C74 C82 SING Y N 18
D03 C08 C07 SING Y N 19
D03 C07 C05 SING N N 20
D03 C42 C40 SING N N 21
D03 O37 C36 DOUB N N 22
D03 C73 C76 SING Y N 23
D03 C40 C57 SING N N 24
D03 C40 N38 SING N N 25
D03 C82 C80 DOUB Y N 26
D03 C57 C66 SING N N 27
D03 C66 O67 DOUB N N 28
D03 C05 C03 DOUB N E 29
D03 C76 C78 DOUB Y N 30
D03 C80 C78 SING Y N 31
D03 C36 N38 SING N N 32
D03 C36 C20 SING N N 33
D03 C03 C02 SING N N 34
D03 C02 O01 DOUB N N 35
D03 C02 N18 SING N N 36
D03 N18 C20 SING N N 37
D03 C20 C22 SING N N 38
D03 C22 C25 SING N N 39
D03 C25 C26 DOUB Y N 40
D03 C25 C34 SING Y N 41
D03 C26 C28 SING Y N 42
D03 C34 C32 DOUB Y N 43
D03 C28 C30 DOUB Y N 44
D03 C32 C30 SING Y N 45
D03 C03 H1 SING N N 46
D03 C05 H2 SING N N 47
D03 C16 H3 SING N N 48
D03 C14 H4 SING N N 49
D03 C12 H5 SING N N 50
D03 C10 H6 SING N N 51
D03 C08 H7 SING N N 52
D03 N18 H8 SING N N 53
D03 C20 H9 SING N N 54
D03 C22 H10 SING N N 55
D03 C22 H11 SING N N 56
D03 C34 H12 SING N N 57
D03 C32 H13 SING N N 58
D03 C30 H14 SING N N 59
D03 C28 H15 SING N N 60
D03 C26 H16 SING N N 61
D03 N38 H17 SING N N 62
D03 C40 H18 SING N N 63
D03 C42 H19 SING N N 64
D03 C42 H20 SING N N 65
D03 C45 H21 SING N N 66
D03 N49 H22 SING N N 67
D03 C51 H23 SING N N 68
D03 C51 H24 SING N N 69
D03 C54 H25 SING N N 70
D03 C54 H26 SING N N 71
D03 C57 H27 SING N N 72
D03 O58 H28 SING N N 73
D03 N68 H29 SING N N 74
D03 C70 H30 SING N N 75
D03 C70 H31 SING N N 76
D03 C74 H32 SING N N 77
D03 C76 H33 SING N N 78
D03 C78 H34 SING N N 79
D03 C80 H35 SING N N 80
D03 C82 H36 SING N N 81
#
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
D03 InChI InChI 1.03 "InChI=1S/C33H36N4O5/c38-29(17-16-23-10-4-1-5-11-23)36-28(20-24-12-6-2-7-13-24)32(41)37-27(21-26-18-19-34-31(26)40)30(39)33(42)35-22-25-14-8-3-9-15-25/h1-17,26-28,30,39H,18-22H2,(H,34,40)(H,35,42)(H,36,38)(H,37,41)/b17-16+/t26-,27-,28-,30-/m0/s1"
D03 InChIKey InChI 1.03 ZTFAWEJBUOCZIL-NHTHZNHESA-N
D03 SMILES_CANONICAL CACTVS 3.385 "O[C@@H]([C@H](C[C@@H]1CCNC1=O)NC(=O)[C@H](Cc2ccccc2)NC(=O)/C=C/c3ccccc3)C(=O)NCc4ccccc4"
D03 SMILES CACTVS 3.385 "O[CH]([CH](C[CH]1CCNC1=O)NC(=O)[CH](Cc2ccccc2)NC(=O)C=Cc3ccccc3)C(=O)NCc4ccccc4"
D03 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "c1ccc(cc1)C[C@@H](C(=O)N[C@@H](C[C@@H]2CCNC2=O)[C@@H](C(=O)NCc3ccccc3)O)NC(=O)/C=C/c4ccccc4"
D03 SMILES "OpenEye OEToolkits" 2.0.6 "c1ccc(cc1)CC(C(=O)NC(CC2CCNC2=O)C(C(=O)NCc3ccccc3)O)NC(=O)C=Cc4ccccc4"
#
_pdbx_chem_comp_identifier.comp_id D03
_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},3~{S})-2-oxidanyl-4-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]-~{N}-(phenylmethyl)-3-[[(2~{S})-3-phenyl-2-[[(~{E})-3-phenylprop-2-enoyl]amino]propanoyl]amino]butanamide"
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
D03 "Create component" 2017-02-06 EBI
D03 "Initial release" 2018-02-28 RCSB
D03 "Modify PCM" 2024-09-27 PDBE
#
_pdbx_chem_comp_pcm.pcm_id 1
_pdbx_chem_comp_pcm.comp_id D03
_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 C57
_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 ?
#