data_7LYY # _model_server_result.job_id ky6luL8UC3kJLCiZ865vjA _model_server_result.datetime_utc '2025-07-15 13:19:21' _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 7lyy # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":701}' # _entry.id 7LYY # _exptl.entry_id 7LYY _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 428.609 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (1s,3R,5S,7s)-N-[(1r,4r)-4-aminocyclohexyl]-3,5-diphenyladamantane-1-carboxamide _entity.pdbx_number_of_molecules 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 120 _cell.entry_id 7LYY _cell.length_a 114.4 _cell.length_b 114.4 _cell.length_c 307.89 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7LYY _symmetry.cell_setting ? _symmetry.Int_Tables_number 155 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'H 3 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K,L,M _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 2_565 -y,x-y+1,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 -57.2 99.073306 0 3 'crystal symmetry operation' 3_455 -x+y-1,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 -114.4 0 0 # _struct_asym.details ? _struct_asym.entity_id 6 _struct_asym.id J _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _pdbx_entity_branch.entity_id 3 _pdbx_entity_branch.type oligosaccharide # loop_ _pdbx_entity_branch_link.link_id _pdbx_entity_branch_link.details _pdbx_entity_branch_link.entity_id _pdbx_entity_branch_link.entity_branch_list_num_1 _pdbx_entity_branch_link.entity_branch_list_num_2 _pdbx_entity_branch_link.comp_id_1 _pdbx_entity_branch_link.comp_id_2 _pdbx_entity_branch_link.atom_id_1 _pdbx_entity_branch_link.leaving_atom_id_1 _pdbx_entity_branch_link.atom_stereo_config_1 _pdbx_entity_branch_link.atom_id_2 _pdbx_entity_branch_link.leaving_atom_id_2 _pdbx_entity_branch_link.atom_stereo_config_2 _pdbx_entity_branch_link.value_order 1 ? 3 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 3 3 2 BMA NAG C1 O1 . O4 HO4 . sing 3 ? 3 4 3 MAN BMA C1 O1 . O6 HO6 . sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 3 n C NAG 1 C 1 NAG C 1 NAG 3 n C NAG 2 C 2 NAG C 2 NAG 3 n C BMA 3 C 3 BMA C 3 BMA 3 n C MAN 4 C 4 MAN C 4 MAN # 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 26 A CYS 53 1_555 B SG CYS 108 B CYS 609 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf2 A SG CYS 81 A CYS 108 1_555 A SG CYS 108 A CYS 135 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf3 A SG CYS 94 A CYS 121 1_555 A SG CYS 120 A CYS 147 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? disulf ? disulf4 B SG CYS 10 B CYS 511 1_555 B SG CYS 55 B CYS 556 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf5 B SG CYS 100 B CYS 601 1_555 B SG CYS 107 B CYS 608 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? covale ? covale1 A ND2 ASN 201 A ASN 228 1_555 G C1 NAG . A NAG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? covale ? covale2 A ND2 ASN 211 A ASN 238 1_555 E C1 NAG . A NAG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale3 A ND2 ASN 230 A ASN 257 1_555 D C1 NAG . A NAG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale4 A ND2 ASN 241 A ASN 268 1_555 F C1 NAG . A NAG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale5 B ND2 ASN 62 B ASN 563 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale6 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale7 C O4 NAG . C NAG 2 1_555 C C1 BMA . C BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale8 C O6 BMA . C BMA 3 1_555 C C1 MAN . C MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? # _chem_comp.formula 'C29 H36 N2 O' _chem_comp.formula_weight 428.609 _chem_comp.id YPM _chem_comp.mon_nstd_flag . _chem_comp.name (1s,3R,5S,7s)-N-[(1r,4r)-4-aminocyclohexyl]-3,5-diphenyladamantane-1-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 C19 C18 YPM doub 463 n y C19 C20 YPM sing 464 n y C18 C17 YPM sing 465 n y C20 C15 YPM doub 466 n y C17 C16 YPM doub 467 n y C15 C16 YPM sing 468 n y C15 C13 YPM sing 469 n n C12 C13 YPM sing 470 n n C12 C11 YPM sing 471 n n O01 C02 YPM doub 472 n n C13 C14 YPM sing 473 n n C13 C21 YPM sing 474 n n C14 C24 YPM sing 475 n n C09 C10 YPM sing 476 n n C09 C07 YPM sing 477 n n C10 C04 YPM sing 478 n n C02 C11 YPM sing 479 n n C02 N03 YPM sing 480 n n N08 C07 YPM sing 481 n n C11 C25 YPM sing 482 n n C11 C32 YPM sing 483 n n C25 C24 YPM sing 484 n n C24 C23 YPM sing 485 n n C21 C22 YPM sing 486 n n C04 N03 YPM sing 487 n n C04 C05 YPM sing 488 n n C07 C06 YPM sing 489 n n C32 C22 YPM sing 490 n n C06 C05 YPM sing 491 n n C22 C23 YPM sing 492 n n C22 C26 YPM sing 493 n n C27 C26 YPM doub 494 n y C27 C28 YPM sing 495 n y C26 C31 YPM sing 496 n y C28 C29 YPM doub 497 n y C31 C30 YPM doub 498 n y C29 C30 YPM sing 499 n y C10 H1 YPM sing 500 n n C10 H2 YPM sing 501 n n C04 H3 YPM sing 502 n n C05 H4 YPM sing 503 n n C05 H5 YPM sing 504 n n C06 H6 YPM sing 505 n n C06 H7 YPM sing 506 n n C07 H8 YPM sing 507 n n C09 H9 YPM sing 508 n n C09 H10 YPM sing 509 n n C12 H11 YPM sing 510 n n C12 H12 YPM sing 511 n n C14 H13 YPM sing 512 n n C14 H14 YPM sing 513 n n C16 H15 YPM sing 514 n n C17 H16 YPM sing 515 n n C18 H17 YPM sing 516 n n C19 H18 YPM sing 517 n n C20 H19 YPM sing 518 n n C21 H20 YPM sing 519 n n C21 H21 YPM sing 520 n n C23 H22 YPM sing 521 n n C23 H23 YPM sing 522 n n C24 H24 YPM sing 523 n n C25 H25 YPM sing 524 n n C25 H26 YPM sing 525 n n C27 H27 YPM sing 526 n n C28 H28 YPM sing 527 n n C29 H29 YPM sing 528 n n C30 H30 YPM sing 529 n n C31 H31 YPM sing 530 n n C32 H32 YPM sing 531 n n C32 H33 YPM sing 532 n n N03 H34 YPM sing 533 n n N08 H35 YPM sing 534 n n N08 H36 YPM sing 535 n n # _atom_sites.entry_id 7LYY _atom_sites.fract_transf_matrix[1][1] 0.008741 _atom_sites.fract_transf_matrix[1][2] 0.005047 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010094 _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] 0.003248 _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 4 NAG A 1 601 601 NAG NAG . E 4 NAG A 1 602 602 NAG NAG . F 4 NAG A 1 603 603 NAG NAG . G 4 NAG A 1 604 604 NAG NAG . H 5 EDO A 1 605 611 EDO EDO . I 5 EDO A 1 606 612 EDO EDO . J 6 YPM B 1 701 610 YPM 164 . K 5 EDO B 1 702 705 EDO EDO . L 7 HOH A 1 701 8 HOH HOH . L 7 HOH A 2 702 35 HOH HOH . L 7 HOH A 3 703 5 HOH HOH . L 7 HOH A 4 704 1 HOH HOH . L 7 HOH A 5 705 55 HOH HOH . L 7 HOH A 6 706 33 HOH HOH . L 7 HOH A 7 707 9 HOH HOH . L 7 HOH A 8 708 7 HOH HOH . L 7 HOH A 9 709 70 HOH HOH . L 7 HOH A 10 710 123 HOH HOH . L 7 HOH A 11 711 4 HOH HOH . L 7 HOH A 12 712 6 HOH HOH . L 7 HOH A 13 713 44 HOH HOH . L 7 HOH A 14 714 121 HOH HOH . L 7 HOH A 15 715 12 HOH HOH . L 7 HOH A 16 716 10 HOH HOH . L 7 HOH A 17 717 11 HOH HOH . L 7 HOH A 18 718 71 HOH HOH . L 7 HOH A 19 719 84 HOH HOH . L 7 HOH A 20 720 38 HOH HOH . L 7 HOH A 21 721 15 HOH HOH . L 7 HOH A 22 722 68 HOH HOH . L 7 HOH A 23 723 13 HOH HOH . L 7 HOH A 24 724 106 HOH HOH . L 7 HOH A 25 725 66 HOH HOH . L 7 HOH A 26 726 2 HOH HOH . L 7 HOH A 27 727 43 HOH HOH . L 7 HOH A 28 728 20 HOH HOH . L 7 HOH A 29 729 45 HOH HOH . L 7 HOH A 30 730 108 HOH HOH . L 7 HOH A 31 731 47 HOH HOH . L 7 HOH A 32 732 57 HOH HOH . L 7 HOH A 33 733 62 HOH HOH . L 7 HOH A 34 734 37 HOH HOH . L 7 HOH A 35 735 103 HOH HOH . L 7 HOH A 36 736 73 HOH HOH . L 7 HOH A 37 737 50 HOH HOH . L 7 HOH A 38 738 97 HOH HOH . L 7 HOH A 39 739 21 HOH HOH . L 7 HOH A 40 740 18 HOH HOH . L 7 HOH A 41 741 56 HOH HOH . L 7 HOH A 42 742 74 HOH HOH . L 7 HOH A 43 743 22 HOH HOH . L 7 HOH A 44 744 95 HOH HOH . L 7 HOH A 45 745 48 HOH HOH . L 7 HOH A 46 746 63 HOH HOH . L 7 HOH A 47 747 23 HOH HOH . L 7 HOH A 48 748 41 HOH HOH . L 7 HOH A 49 749 69 HOH HOH . L 7 HOH A 50 750 24 HOH HOH . M 7 HOH B 1 801 82 HOH HOH . M 7 HOH B 2 802 86 HOH HOH . M 7 HOH B 3 803 89 HOH HOH . M 7 HOH B 4 804 85 HOH HOH . M 7 HOH B 5 805 27 HOH HOH . M 7 HOH B 6 806 28 HOH HOH . M 7 HOH B 7 807 36 HOH HOH . M 7 HOH B 8 808 118 HOH HOH . M 7 HOH B 9 809 34 HOH HOH . M 7 HOH B 10 810 49 HOH HOH . M 7 HOH B 11 811 39 HOH HOH . M 7 HOH B 12 812 26 HOH HOH . M 7 HOH B 13 813 79 HOH HOH . M 7 HOH B 14 814 92 HOH HOH . M 7 HOH B 15 815 40 HOH HOH . M 7 HOH B 16 816 29 HOH HOH . M 7 HOH B 17 817 25 HOH HOH . M 7 HOH B 18 818 126 HOH HOH . M 7 HOH B 19 819 124 HOH HOH . M 7 HOH B 20 820 90 HOH HOH . M 7 HOH B 21 821 80 HOH HOH . M 7 HOH B 22 822 32 HOH HOH . M 7 HOH B 23 823 87 HOH HOH . M 7 HOH B 24 824 116 HOH HOH . M 7 HOH B 25 825 83 HOH HOH . M 7 HOH B 26 826 125 HOH HOH . M 7 HOH B 27 827 96 HOH HOH . M 7 HOH B 28 828 120 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 C10 YPM . . . J 6 -41.995 17.695 -7.879 1 87.93 ? C10 YPM 701 B 1 HETATM 2 C C11 YPM . . . J 6 -45.107 14.258 -7.356 1 77.62 ? C11 YPM 701 B 1 HETATM 3 C C02 YPM . . . J 6 -44.717 15.712 -7.592 1 83.71 ? C02 YPM 701 B 1 HETATM 4 C C04 YPM . . . J 6 -43.273 17.614 -7.032 1 90.66 ? C04 YPM 701 B 1 HETATM 5 C C05 YPM . . . J 6 -43.053 18.366 -5.708 1 95.55 ? C05 YPM 701 B 1 HETATM 6 C C06 YPM . . . J 6 -42.767 19.851 -5.976 1 96.12 ? C06 YPM 701 B 1 HETATM 7 C C07 YPM . . . J 6 -41.591 20.07 -6.953 1 106.46 ? C07 YPM 701 B 1 HETATM 8 C C09 YPM . . . J 6 -41.674 19.167 -8.209 1 99.68 ? C09 YPM 701 B 1 HETATM 9 C C12 YPM . . . J 6 -45.997 13.806 -8.533 1 72.02 ? C12 YPM 701 B 1 HETATM 10 C C13 YPM . . . J 6 -46.406 12.324 -8.383 1 72.55 ? C13 YPM 701 B 1 HETATM 11 C C14 YPM . . . J 6 -45.115 11.48 -8.31 1 73.89 ? C14 YPM 701 B 1 HETATM 12 C C15 YPM . . . J 6 -47.286 11.882 -9.56 1 72.13 ? C15 YPM 701 B 1 HETATM 13 C C16 YPM . . . J 6 -48.556 11.345 -9.318 1 74.49 ? C16 YPM 701 B 1 HETATM 14 C C17 YPM . . . J 6 -49.371 10.925 -10.359 1 69.06 ? C17 YPM 701 B 1 HETATM 15 C C18 YPM . . . J 6 -48.94 11.042 -11.677 1 67.02 ? C18 YPM 701 B 1 HETATM 16 C C19 YPM . . . J 6 -47.683 11.57 -11.938 1 64.54 ? C19 YPM 701 B 1 HETATM 17 C C20 YPM . . . J 6 -46.869 11.981 -10.888 1 69.11 ? C20 YPM 701 B 1 HETATM 18 C C21 YPM . . . J 6 -47.173 12.169 -7.051 1 76.14 ? C21 YPM 701 B 1 HETATM 19 C C22 YPM . . . J 6 -46.29 12.595 -5.848 1 82.22 ? C22 YPM 701 B 1 HETATM 20 C C23 YPM . . . J 6 -44.994 11.752 -5.82 1 80.17 ? C23 YPM 701 B 1 HETATM 21 C C24 YPM . . . J 6 -44.223 11.933 -7.133 1 78.47 ? C24 YPM 701 B 1 HETATM 22 C C25 YPM . . . J 6 -43.825 13.408 -7.305 1 77.32 ? C25 YPM 701 B 1 HETATM 23 C C26 YPM . . . J 6 -47.055 12.282 -4.553 1 83.13 ? C26 YPM 701 B 1 HETATM 24 C C27 YPM . . . J 6 -48.373 11.827 -4.619 1 82.56 ? C27 YPM 701 B 1 HETATM 25 C C28 YPM . . . J 6 -49.091 11.527 -3.472 1 86.94 ? C28 YPM 701 B 1 HETATM 26 C C29 YPM . . . J 6 -48.505 11.665 -2.221 1 87.93 ? C29 YPM 701 B 1 HETATM 27 C C30 YPM . . . J 6 -47.195 12.103 -2.135 1 93.11 ? C30 YPM 701 B 1 HETATM 28 C C31 YPM . . . J 6 -46.479 12.406 -3.29 1 89.81 ? C31 YPM 701 B 1 HETATM 29 C C32 YPM . . . J 6 -45.887 14.081 -6.037 1 77.94 ? C32 YPM 701 B 1 HETATM 30 N N03 YPM . . . J 6 -43.703 16.212 -6.846 1 89.94 ? N03 YPM 701 B 1 HETATM 31 N N08 YPM . . . J 6 -41.584 21.486 -7.386 1 105.89 ? N08 YPM 701 B 1 HETATM 32 O O01 YPM . . . J 6 -45.283 16.392 -8.438 1 80.81 ? O01 YPM 701 B 1 # _model_server_stats.io_time_ms 23 _model_server_stats.parse_time_ms 36 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 424 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 32 #