data_PPB
#
_chem_comp.id PPB
_chem_comp.name "1-{[1-(2-AMINO-3-PHENYL-PROPIONYL)-PYRROLIDINE-2-CARBONYL]-AMINO}-2-(3-CYANO-PHENYL)-ETHANEBORONIC ACID"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C23 H27 B N4 O4"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms "(D)PHE-PRO-BOROPHE(M-CN)"
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 1999-07-08
_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 434.296
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code PPB
_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 N
_chem_comp.pdbx_model_coordinates_db_code 1AUJ
_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
PPB C3 C3 C 0 1 N N N N N N 28.688 14.344 20.059 -0.061 -1.453 -3.800 C3 PPB 1
PPB C4 C4 C 0 1 Y N N N N N 29.130 14.032 18.618 0.727 -0.889 -4.954 C4 PPB 2
PPB N1 N1 N 0 1 N N N N N N 27.216 12.443 20.326 -0.943 -0.945 -1.576 N1 PPB 3
PPB B1 B1 B 0 1 N N N N N N 28.018 13.488 22.326 -0.910 0.870 -3.263 B1 PPB 4
PPB C2 C2 C 0 1 N N R N N N 28.364 13.117 20.921 -0.177 -0.398 -2.698 C2 PPB 5
PPB O2 O2 O 0 1 N N N N N N 29.265 13.850 23.004 -2.231 0.759 -3.772 O2 PPB 6
PPB O1 O1 O 0 1 N N N N N N 27.679 12.259 23.042 -0.252 2.128 -3.265 O1 PPB 7
PPB N5 N5 N 0 1 N N N N N N 26.027 9.657 18.557 -1.051 -0.469 2.095 N5 PPB 8
PPB C7 C7 C 0 1 N N S N N N 25.861 10.794 19.452 -1.484 -1.085 0.832 C7 PPB 9
PPB C8 C8 C 0 1 N N N N N N 27.200 11.159 19.993 -0.696 -0.522 -0.321 C8 PPB 10
PPB O3 O3 O 0 1 N N N N N N 28.068 10.307 20.221 0.160 0.312 -0.120 O3 PPB 11
PPB C9 C9 C 0 1 N N N N N N 25.054 10.236 20.624 -2.982 -0.759 0.654 C9 PPB 12
PPB C10 C10 C 0 1 N N N N N N 25.043 8.711 20.527 -3.447 -0.448 2.101 C10 PPB 13
PPB C11 C11 C 0 1 N N N N N N 25.717 8.372 19.185 -2.195 0.248 2.687 C11 PPB 14
PPB C12 C12 C 0 1 N N N N N N 26.430 9.905 17.298 0.187 -0.543 2.621 C12 PPB 15
PPB O4 O4 O 0 1 N N N N N N 27.002 10.955 16.985 1.054 -1.164 2.044 O4 PPB 16
PPB C14 C14 C 0 1 N N R N N N 26.504 8.656 16.401 0.494 0.145 3.925 C14 PPB 17
PPB C16 C16 C 0 1 Y N N N N N 29.598 12.775 18.193 0.075 -0.233 -5.977 C16 PPB 18
PPB C23 C23 C 0 1 Y N N N N N 30.098 12.631 16.891 0.808 0.292 -7.044 C23 PPB 19
PPB C24 C24 C 0 1 Y N N N N N 29.155 15.116 17.709 2.102 -1.037 -4.988 C24 PPB 20
PPB C25 C25 C 0 1 Y N N N N N 29.674 14.977 16.401 2.834 -0.523 -6.044 C25 PPB 21
PPB C5 C5 C 0 1 Y N N N N N 30.148 13.724 16.014 2.195 0.140 -7.071 C5 PPB 22
PPB C6 C6 C 0 1 N N N N N N 30.541 11.293 16.344 0.138 0.980 -8.107 C6 PPB 23
PPB N2 N2 N 0 1 N N N N N N 30.900 10.240 15.895 -0.392 1.525 -8.950 N2 PPB 24
PPB C13 C13 C 0 1 N N N N N N 25.505 8.587 15.237 0.222 -0.814 5.085 C13 PPB 25
PPB N6 N6 N 0 1 N N N N N N 27.860 8.557 15.869 1.906 0.549 3.945 N6 PPB 26
PPB C17 C17 C 0 1 Y N N N N N 22.272 6.972 16.713 2.081 0.428 8.127 C17 PPB 27
PPB C18 C18 C 0 1 Y N N N N N 21.300 7.480 15.813 1.092 1.136 8.784 C18 PPB 28
PPB C19 C19 C 0 1 Y N N N N N 21.647 8.391 14.806 -0.177 1.213 8.244 C19 PPB 29
PPB C20 C20 C 0 1 Y N N N N N 23.006 8.786 14.703 -0.459 0.581 7.048 C20 PPB 30
PPB C21 C21 C 0 1 Y N N N N N 24.022 8.285 15.568 0.529 -0.126 6.390 C21 PPB 31
PPB C22 C22 C 0 1 Y N N N N N 23.626 7.379 16.593 1.798 -0.206 6.932 C22 PPB 32
PPB H31 1H3 H 0 1 N N N N N N 29.451 14.978 20.566 0.447 -2.333 -3.408 H31 PPB 33
PPB H32 2H3 H 0 1 N N N N N N 27.823 15.047 20.051 -1.057 -1.731 -4.143 H32 PPB 34
PPB HN1 HN1 H 0 1 N N N N N N 26.336 12.917 20.122 -1.628 -1.613 -1.737 HN1 PPB 35
PPB H2 H2 H 0 1 N N N N N N 29.266 12.462 20.953 0.819 -0.119 -2.356 H2 PPB 36
PPB HO2 HO2 H 0 1 N N N N N N 29.045 14.085 23.897 -2.493 1.642 -4.065 HO2 PPB 37
PPB HO1 HO1 H 0 1 N N N N N N 27.459 12.494 23.935 0.624 1.986 -2.882 HO1 PPB 38
PPB H7 H7 H 0 1 N N N N N N 25.389 11.670 18.950 -1.344 -2.165 0.885 H7 PPB 39
PPB H91 1H9 H 0 1 N N N N N N 25.426 10.598 21.610 -3.521 -1.617 0.251 H91 PPB 40
PPB H92 2H9 H 0 1 N N N N N N 24.027 10.667 20.679 -3.110 0.112 0.012 H92 PPB 41
PPB H101 1H10 H 0 0 N N N N N N 25.512 8.204 21.402 -3.674 -1.366 2.644 H101 PPB 42
PPB H102 2H10 H 0 0 N N N N N N 24.028 8.263 20.642 -4.305 0.224 2.100 H102 PPB 43
PPB H111 1H11 H 0 0 N N N N N N 25.109 7.695 18.539 -2.181 0.153 3.773 H111 PPB 44
PPB H112 2H11 H 0 0 N N N N N N 26.601 7.701 19.287 -2.175 1.298 2.397 H112 PPB 45
PPB H14 H14 H 0 1 N N N N N N 26.222 7.802 17.060 -0.137 1.027 4.028 H14 PPB 46
PPB H16 H16 H 0 1 N N N N N N 29.573 11.908 18.875 -0.998 -0.118 -5.950 H16 PPB 47
PPB H24 H24 H 0 1 N N N N N N 28.759 16.094 18.028 2.607 -1.555 -4.186 H24 PPB 48
PPB H25 H25 H 0 1 N N N N N N 29.708 15.826 15.698 3.907 -0.641 -6.064 H25 PPB 49
PPB H5 H5 H 0 1 N N N N N N 30.567 13.595 15.002 2.767 0.541 -7.895 H5 PPB 50
PPB H131 1H13 H 0 0 N N N N N N 25.562 9.532 14.649 -0.825 -1.114 5.070 H131 PPB 51
PPB H132 2H13 H 0 0 N N N N N N 25.869 7.847 14.485 0.853 -1.697 4.982 H132 PPB 52
PPB HN61 1HN6 H 0 0 N N N N N N 27.909 7.729 15.274 2.450 -0.294 3.848 HN61 PPB 53
PPB HN62 2HN6 H 0 0 N N N N N N 28.570 8.558 16.600 2.064 1.093 3.111 HN62 PPB 54
PPB H17 H17 H 0 1 N N N N N N 21.975 6.262 17.503 3.073 0.369 8.548 H17 PPB 55
PPB H18 H18 H 0 1 N N N N N N 20.248 7.158 15.898 1.312 1.630 9.719 H18 PPB 56
PPB H19 H19 H 0 1 N N N N N N 20.878 8.783 14.119 -0.950 1.766 8.758 H19 PPB 57
PPB H20 H20 H 0 1 N N N N N N 23.283 9.511 13.919 -1.452 0.641 6.626 H20 PPB 58
PPB H22 H22 H 0 1 N N N N N N 24.375 6.988 17.301 2.570 -0.760 6.419 H22 PPB 59
#
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
PPB C3 C4 SING N N 1
PPB C3 C2 SING N N 2
PPB C3 H31 SING N N 3
PPB C3 H32 SING N N 4
PPB C4 C16 DOUB Y N 5
PPB C4 C24 SING Y N 6
PPB N1 C2 SING N N 7
PPB N1 C8 SING N N 8
PPB N1 HN1 SING N N 9
PPB B1 C2 SING N N 10
PPB B1 O2 SING N N 11
PPB B1 O1 SING N N 12
PPB C2 H2 SING N N 13
PPB O2 HO2 SING N N 14
PPB O1 HO1 SING N N 15
PPB N5 C7 SING N N 16
PPB N5 C11 SING N N 17
PPB N5 C12 SING N N 18
PPB C7 C8 SING N N 19
PPB C7 C9 SING N N 20
PPB C7 H7 SING N N 21
PPB C8 O3 DOUB N N 22
PPB C9 C10 SING N N 23
PPB C9 H91 SING N N 24
PPB C9 H92 SING N N 25
PPB C10 C11 SING N N 26
PPB C10 H101 SING N N 27
PPB C10 H102 SING N N 28
PPB C11 H111 SING N N 29
PPB C11 H112 SING N N 30
PPB C12 O4 DOUB N N 31
PPB C12 C14 SING N N 32
PPB C14 C13 SING N N 33
PPB C14 N6 SING N N 34
PPB C14 H14 SING N N 35
PPB C16 C23 SING Y N 36
PPB C16 H16 SING N N 37
PPB C23 C5 DOUB Y N 38
PPB C23 C6 SING N N 39
PPB C24 C25 DOUB Y N 40
PPB C24 H24 SING N N 41
PPB C25 C5 SING Y N 42
PPB C25 H25 SING N N 43
PPB C5 H5 SING N N 44
PPB C6 N2 TRIP N N 45
PPB C13 C21 SING N N 46
PPB C13 H131 SING N N 47
PPB C13 H132 SING N N 48
PPB N6 HN61 SING N N 49
PPB N6 HN62 SING N N 50
PPB C17 C18 DOUB Y N 51
PPB C17 C22 SING Y N 52
PPB C17 H17 SING N N 53
PPB C18 C19 SING Y N 54
PPB C18 H18 SING N N 55
PPB C19 C20 DOUB Y N 56
PPB C19 H19 SING N N 57
PPB C20 C21 SING Y N 58
PPB C20 H20 SING N N 59
PPB C21 C22 DOUB Y N 60
PPB C22 H22 SING N N 61
#
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
PPB SMILES ACDLabs 10.04 "O=C(NC(B(O)O)Cc1cccc(C#N)c1)C3N(C(=O)C(N)Cc2ccccc2)CCC3"
PPB SMILES_CANONICAL CACTVS 3.341 "N[C@H](Cc1ccccc1)C(=O)N2CCC[C@H]2C(=O)N[C@@H](Cc3cccc(c3)C#N)B(O)O"
PPB SMILES CACTVS 3.341 "N[CH](Cc1ccccc1)C(=O)N2CCC[CH]2C(=O)N[CH](Cc3cccc(c3)C#N)B(O)O"
PPB SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "B([C@H](Cc1cccc(c1)C#N)NC(=O)[C@@H]2CCCN2C(=O)[C@@H](Cc3ccccc3)N)(O)O"
PPB SMILES "OpenEye OEToolkits" 1.5.0 "B(C(Cc1cccc(c1)C#N)NC(=O)C2CCCN2C(=O)C(Cc3ccccc3)N)(O)O"
PPB InChI InChI 1.03 "InChI=1S/C23H27BN4O4/c25-15-18-9-4-8-17(12-18)14-21(24(31)32)27-22(29)20-10-5-11-28(20)23(30)19(26)13-16-6-2-1-3-7-16/h1-4,6-9,12,19-21,31-32H,5,10-11,13-14,26H2,(H,27,29)/t19-,20+,21+/m1/s1"
PPB InChIKey InChI 1.03 UFOIPTZMXQILSG-HKBOAZHASA-N
#
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
PPB "SYSTEMATIC NAME" ACDLabs 10.04 "D-phenylalanyl-N-[(1R)-2-(3-cyanophenyl)-1-(dihydroxyboranyl)ethyl]-L-prolinamide"
PPB "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(1R)-1-[[(2S)-1-[(2R)-2-amino-3-phenyl-propanoyl]pyrrolidin-2-yl]carbonylamino]-2-(3-cyanophenyl)ethyl]boronic 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
PPB "Create component" 1999-07-08 RCSB
PPB "Modify descriptor" 2011-06-04 RCSB
PPB "Modify synonyms" 2021-03-01 PDBE
PPB "Modify PCM" 2024-09-27 PDBE
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id PPB
_pdbx_chem_comp_synonyms.name "(D)PHE-PRO-BOROPHE(M-CN)"
_pdbx_chem_comp_synonyms.provenance ?
_pdbx_chem_comp_synonyms.type ?
#
_pdbx_chem_comp_pcm.pcm_id 1
_pdbx_chem_comp_pcm.comp_id PPB
_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 B1
_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 ?
#