data_3CKR # _model_server_result.job_id As84wG91CByEom7rOZU-2Q _model_server_result.datetime_utc '2025-01-03 03:17:03' _model_server_result.server_version 0.9.12 _model_server_result.query_name ligand _model_server_result.source_id pdb-bcif _model_server_result.entry_id 3ckr # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":501}' # _entry.id 3CKR # _exptl.entry_id 3CKR _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 605.769 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (4S)-1,4-dibenzyl-N-[(1S,2R)-1-benzyl-3-{[3-(dimethylamino)benzyl]amino}-2-hydroxypropyl]-2-oxoimidazolidine-4-carboxamide _entity.pdbx_number_of_molecules 3 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 100.87 _cell.angle_gamma 90 _cell.entry_id 3CKR _cell.length_a 224.457 _cell.length_b 108.126 _cell.length_c 61.135 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3CKR _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_defined_assembly 2 PISA monomeric 1 author_and_software_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,D,G 1 1 B,E,H 2 1 C,F,I 3 1 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 D N N ? 2 E N N ? 2 F N N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order disulf ? disulf1 A SG CYS 174 A CYS 155 1_555 A SG CYS 378 A CYS 359 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? disulf ? disulf2 A SG CYS 236 A CYS 217 1_555 A SG CYS 401 A CYS 382 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf3 A SG CYS 288 A CYS 269 1_555 A SG CYS 338 A CYS 319 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf4 B SG CYS 174 B CYS 155 1_555 B SG CYS 378 B CYS 359 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf5 B SG CYS 236 B CYS 217 1_555 B SG CYS 401 B CYS 382 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf6 B SG CYS 288 B CYS 269 1_555 B SG CYS 338 B CYS 319 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf7 C SG CYS 174 C CYS 155 1_555 C SG CYS 378 C CYS 359 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf8 C SG CYS 236 C CYS 217 1_555 C SG CYS 401 C CYS 382 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf9 C SG CYS 288 C CYS 269 1_555 C SG CYS 338 C CYS 319 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? # _chem_comp.formula 'C37 H43 N5 O3' _chem_comp.formula_weight 605.769 _chem_comp.id 009 _chem_comp.mon_nstd_flag . _chem_comp.name (4S)-1,4-dibenzyl-N-[(1S,2R)-1-benzyl-3-{[3-(dimethylamino)benzyl]amino}-2-hydroxypropyl]-2-oxoimidazolidine-4-carboxamide _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag C O 009 doub 1 n n C N 009 sing 2 n n C C30 009 sing 3 n n N CA 009 sing 4 n n CA CB 009 sing 5 n n CA C1 009 sing 6 n n CB CG 009 sing 7 n n CG CD1 009 doub 8 n y CG CD2 009 sing 9 n y CD1 CE1 009 sing 10 n y CD2 CE2 009 doub 11 n y CE1 CZ 009 doub 12 n y CE2 CZ 009 sing 13 n y C1 OG 009 sing 14 n n C1 C2 009 sing 15 n n C2 N2 009 sing 16 n n N2 C20 009 sing 17 n n C20 C21 009 sing 18 n n C21 C22 009 doub 19 n y C21 C26 009 sing 20 n y C22 C23 009 sing 21 n y C23 C24 009 doub 22 n y C24 C25 009 sing 23 n y C25 C26 009 doub 24 n y C25 N27 009 sing 25 n n N27 C28 009 sing 26 n n N27 C29 009 sing 27 n n C30 N31 009 sing 28 n n C30 C35 009 sing 29 n n C30 C51 009 sing 30 n n N31 C32 009 sing 31 n n C32 O33 009 doub 32 n n C32 N34 009 sing 33 n n N34 C35 009 sing 34 n n N34 C36 009 sing 35 n n C36 C41 009 sing 36 n n C41 C42 009 doub 37 n y C41 C43 009 sing 38 n y C42 C45 009 sing 39 n y C43 C44 009 doub 40 n y C44 C46 009 sing 41 n y C45 C46 009 doub 42 n y C51 C56 009 sing 43 n n C52 C53 009 doub 44 n y C52 C57 009 sing 45 n y C53 C54 009 sing 46 n y C54 C55 009 doub 47 n y C55 C56 009 sing 48 n y C56 C57 009 doub 49 n y N HN 009 sing 50 n n CA HA 009 sing 51 n n CB HB 009 sing 52 n n CB HBA 009 sing 53 n n CD1 HD1 009 sing 54 n n CD2 HD2 009 sing 55 n n CE1 HE1 009 sing 56 n n CE2 HE2 009 sing 57 n n CZ HZ 009 sing 58 n n C1 H1 009 sing 59 n n OG HOG 009 sing 60 n n C2 H2 009 sing 61 n n C2 H2A 009 sing 62 n n N2 HN2 009 sing 63 n n C20 H20 009 sing 64 n n C20 H20A 009 sing 65 n n C22 H22 009 sing 66 n n C23 H23 009 sing 67 n n C24 H24 009 sing 68 n n C26 H26 009 sing 69 n n C28 H28 009 sing 70 n n C28 H28A 009 sing 71 n n C28 H28B 009 sing 72 n n C29 H29 009 sing 73 n n C29 H29A 009 sing 74 n n C29 H29B 009 sing 75 n n N31 HN31 009 sing 76 n n C35 H35 009 sing 77 n n C35 H35A 009 sing 78 n n C36 H36 009 sing 79 n n C36 H36A 009 sing 80 n n C42 H42 009 sing 81 n n C43 H43 009 sing 82 n n C44 H44 009 sing 83 n n C45 H45 009 sing 84 n n C46 H46 009 sing 85 n n C51 H51 009 sing 86 n n C51 H51A 009 sing 87 n n C52 H52 009 sing 88 n n C53 H53 009 sing 89 n n C54 H54 009 sing 90 n n C55 H55 009 sing 91 n n C57 H57 009 sing 92 n n # _atom_sites.entry_id 3CKR _atom_sites.fract_transf_matrix[1][1] 0.004455 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000855 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009248 _atom_sites.fract_transf_matrix[2][3] 0 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.016656 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_ins_code D 2 009 A 1 501 501 009 009 . E 2 009 B 1 502 502 009 009 . F 2 009 C 1 503 503 009 009 . G 3 HOH A 1 502 1 HOH HOH . G 3 HOH A 2 503 2 HOH HOH . G 3 HOH A 3 504 3 HOH HOH . G 3 HOH A 4 505 5 HOH HOH . G 3 HOH A 5 506 7 HOH HOH . G 3 HOH A 6 507 9 HOH HOH . G 3 HOH A 7 508 11 HOH HOH . G 3 HOH A 8 509 12 HOH HOH . G 3 HOH A 9 510 18 HOH HOH . G 3 HOH A 10 511 20 HOH HOH . G 3 HOH A 11 512 22 HOH HOH . G 3 HOH A 12 513 23 HOH HOH . G 3 HOH A 13 514 27 HOH HOH . G 3 HOH A 14 515 28 HOH HOH . G 3 HOH A 15 516 30 HOH HOH . G 3 HOH A 16 517 31 HOH HOH . G 3 HOH A 17 518 32 HOH HOH . G 3 HOH A 18 519 33 HOH HOH . G 3 HOH A 19 520 38 HOH HOH . G 3 HOH A 20 521 39 HOH HOH . G 3 HOH A 21 522 41 HOH HOH . G 3 HOH A 22 523 44 HOH HOH . G 3 HOH A 23 524 45 HOH HOH . G 3 HOH A 24 525 52 HOH HOH . G 3 HOH A 25 526 56 HOH HOH . G 3 HOH A 26 527 59 HOH HOH . G 3 HOH A 27 528 64 HOH HOH . G 3 HOH A 28 529 66 HOH HOH . G 3 HOH A 29 530 68 HOH HOH . G 3 HOH A 30 531 71 HOH HOH . G 3 HOH A 31 532 72 HOH HOH . G 3 HOH A 32 533 76 HOH HOH . G 3 HOH A 33 534 78 HOH HOH . G 3 HOH A 34 535 79 HOH HOH . G 3 HOH A 35 536 80 HOH HOH . G 3 HOH A 36 537 82 HOH HOH . G 3 HOH A 37 538 90 HOH HOH . G 3 HOH A 38 539 91 HOH HOH . H 3 HOH B 1 503 4 HOH HOH . H 3 HOH B 2 504 8 HOH HOH . H 3 HOH B 3 505 10 HOH HOH . H 3 HOH B 4 506 13 HOH HOH . H 3 HOH B 5 507 14 HOH HOH . H 3 HOH B 6 508 16 HOH HOH . H 3 HOH B 7 509 17 HOH HOH . H 3 HOH B 8 510 19 HOH HOH . H 3 HOH B 9 511 21 HOH HOH . H 3 HOH B 10 512 25 HOH HOH . H 3 HOH B 11 513 29 HOH HOH . H 3 HOH B 12 514 35 HOH HOH . H 3 HOH B 13 515 36 HOH HOH . H 3 HOH B 14 516 37 HOH HOH . H 3 HOH B 15 517 40 HOH HOH . H 3 HOH B 16 518 42 HOH HOH . H 3 HOH B 17 519 46 HOH HOH . H 3 HOH B 18 520 47 HOH HOH . H 3 HOH B 19 521 48 HOH HOH . H 3 HOH B 20 522 49 HOH HOH . H 3 HOH B 21 523 53 HOH HOH . H 3 HOH B 22 524 58 HOH HOH . H 3 HOH B 23 525 60 HOH HOH . H 3 HOH B 24 526 62 HOH HOH . H 3 HOH B 25 527 63 HOH HOH . H 3 HOH B 26 528 67 HOH HOH . H 3 HOH B 27 529 70 HOH HOH . H 3 HOH B 28 530 75 HOH HOH . H 3 HOH B 29 531 81 HOH HOH . H 3 HOH B 30 532 83 HOH HOH . H 3 HOH B 31 533 86 HOH HOH . H 3 HOH B 32 534 87 HOH HOH . H 3 HOH B 33 535 88 HOH HOH . H 3 HOH B 34 536 89 HOH HOH . H 3 HOH B 35 537 92 HOH HOH . I 3 HOH C 1 504 6 HOH HOH . I 3 HOH C 2 505 15 HOH HOH . I 3 HOH C 3 506 24 HOH HOH . I 3 HOH C 4 507 26 HOH HOH . I 3 HOH C 5 508 34 HOH HOH . I 3 HOH C 6 509 43 HOH HOH . I 3 HOH C 7 510 50 HOH HOH . I 3 HOH C 8 511 54 HOH HOH . I 3 HOH C 9 512 55 HOH HOH . I 3 HOH C 10 513 57 HOH HOH . I 3 HOH C 11 514 61 HOH HOH . I 3 HOH C 12 515 65 HOH HOH . I 3 HOH C 13 516 69 HOH HOH . I 3 HOH C 14 517 73 HOH HOH . I 3 HOH C 15 518 74 HOH HOH . I 3 HOH C 16 519 77 HOH HOH . I 3 HOH C 17 520 84 HOH HOH . I 3 HOH C 18 521 85 HOH HOH . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 C C 009 . . . D 2 30.075 7.267 10.416 1 45.94 ? C 009 501 A 1 HETATM 2 O O 009 . . . D 2 31.213 7.724 10.253 1 46.88 ? O 009 501 A 1 HETATM 3 N N 009 . . . D 2 29.755 5.938 10.241 1 45.16 ? N 009 501 A 1 HETATM 4 C CA 009 . . . D 2 30.742 4.882 9.846 1 44.1 ? CA 009 501 A 1 HETATM 5 C CB 009 . . . D 2 30.745 3.817 10.981 1 42.16 ? CB 009 501 A 1 HETATM 6 C CG 009 . . . D 2 31.101 4.478 12.284 1 41.18 ? CG 009 501 A 1 HETATM 7 C CD1 009 . . . D 2 30.239 4.398 13.392 1 40.37 ? CD1 009 501 A 1 HETATM 8 C CD2 009 . . . D 2 32.312 5.214 12.405 1 41.42 ? CD2 009 501 A 1 HETATM 9 C CE1 009 . . . D 2 30.572 5.037 14.599 1 38.63 ? CE1 009 501 A 1 HETATM 10 C CE2 009 . . . D 2 32.646 5.857 13.614 1 40.97 ? CE2 009 501 A 1 HETATM 11 C CZ 009 . . . D 2 31.769 5.766 14.715 1 40.4 ? CZ 009 501 A 1 HETATM 12 C C1 009 . . . D 2 30.374 4.286 8.478 1 45.6 ? C1 009 501 A 1 HETATM 13 O OG 009 . . . D 2 31.337 3.286 8.18 1 44.11 ? OG 009 501 A 1 HETATM 14 C C2 009 . . . D 2 30.434 5.344 7.385 1 48.05 ? C2 009 501 A 1 HETATM 15 N N2 009 . . . D 2 30.725 4.713 6.084 1 53.32 ? N2 009 501 A 1 HETATM 16 C C20 009 . . . D 2 30.886 5.651 4.962 1 53.45 ? C20 009 501 A 1 HETATM 17 C C21 009 . . . D 2 32.318 6.102 4.96 1 53.91 ? C21 009 501 A 1 HETATM 18 C C22 009 . . . D 2 32.661 7.469 5.077 1 54.42 ? C22 009 501 A 1 HETATM 19 C C23 009 . . . D 2 34.024 7.861 5.093 1 55.96 ? C23 009 501 A 1 HETATM 20 C C24 009 . . . D 2 35.053 6.879 4.994 1 56.35 ? C24 009 501 A 1 HETATM 21 C C25 009 . . . D 2 34.722 5.491 4.877 1 55.74 ? C25 009 501 A 1 HETATM 22 C C26 009 . . . D 2 33.35 5.125 4.862 1 55.2 ? C26 009 501 A 1 HETATM 23 N N27 009 . . . D 2 35.715 4.518 4.782 1 56.12 ? N27 009 501 A 1 HETATM 24 C C28 009 . . . D 2 36.576 4.239 5.926 1 55.37 ? C28 009 501 A 1 HETATM 25 C C29 009 . . . D 2 35.904 3.761 3.543 1 56.49 ? C29 009 501 A 1 HETATM 26 C C30 009 . . . D 2 28.857 8.175 10.89 1 45.81 ? C30 009 501 A 1 HETATM 27 N N31 009 . . . D 2 27.647 7.796 10.146 1 45.85 ? N31 009 501 A 1 HETATM 28 C C32 009 . . . D 2 26.603 7.862 11.001 1 46.06 ? C32 009 501 A 1 HETATM 29 O O33 009 . . . D 2 25.434 7.619 10.7 1 43.46 ? O33 009 501 A 1 HETATM 30 N N34 009 . . . D 2 26.982 8.275 12.32 1 47.53 ? N34 009 501 A 1 HETATM 31 C C35 009 . . . D 2 28.413 7.902 12.339 1 45.51 ? C35 009 501 A 1 HETATM 32 C C36 009 . . . D 2 26.092 7.82 13.45 1 51.87 ? C36 009 501 A 1 HETATM 33 C C41 009 . . . D 2 26.438 6.543 14.181 1 53.56 ? C41 009 501 A 1 HETATM 34 C C42 009 . . . D 2 26.109 5.279 13.63 1 54.63 ? C42 009 501 A 1 HETATM 35 C C43 009 . . . D 2 27.102 6.599 15.438 1 54.05 ? C43 009 501 A 1 HETATM 36 C C44 009 . . . D 2 27.435 5.412 16.128 1 55.01 ? C44 009 501 A 1 HETATM 37 C C45 009 . . . D 2 26.439 4.093 14.314 1 56.18 ? C45 009 501 A 1 HETATM 38 C C46 009 . . . D 2 27.107 4.159 15.566 1 55.58 ? C46 009 501 A 1 HETATM 39 C C51 009 . . . D 2 29.224 9.702 10.607 1 45.27 ? C51 009 501 A 1 HETATM 40 C C52 009 . . . D 2 27.633 12.385 12.947 1 45.18 ? C52 009 501 A 1 HETATM 41 C C53 009 . . . D 2 26.501 12.782 12.186 1 43.79 ? C53 009 501 A 1 HETATM 42 C C54 009 . . . D 2 26.258 12.195 10.918 1 43.3 ? C54 009 501 A 1 HETATM 43 C C55 009 . . . D 2 27.135 11.205 10.398 1 43.44 ? C55 009 501 A 1 HETATM 44 C C56 009 . . . D 2 28.275 10.787 11.146 1 45.5 ? C56 009 501 A 1 HETATM 45 C C57 009 . . . D 2 28.514 11.395 12.431 1 45.9 ? C57 009 501 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 33 _model_server_stats.query_time_ms 294 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 45 #