data_7M2D # _model_server_result.job_id QbSQ8NAVMAu5YklBhIKvxQ _model_server_result.datetime_utc '2024-11-08 01:39:17' _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 7m2d # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":605}' # _entry.id 7M2D # _exptl.entry_id 7M2D _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 410.592 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (1R,3S,5R,7R)-N-[(1r,4R)-4-aminocyclohexyl]-3-(ethoxymethyl)-5-phenyladamantane-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 7M2D _cell.length_a 115.11 _cell.length_b 115.11 _cell.length_c 309.02 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7M2D _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 _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 -57.555 99.688184 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 -115.11 0 0 # _struct_asym.details ? _struct_asym.entity_id 5 _struct_asym.id H _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 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf2 A SG CYS 81 A CYS 108 1_555 A SG CYS 108 A CYS 135 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? disulf ? disulf3 A SG CYS 94 A CYS 121 1_555 A SG CYS 120 A CYS 147 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf4 B SG CYS 10 B CYS 511 1_555 B SG CYS 55 B CYS 556 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? disulf ? disulf5 B SG CYS 100 B CYS 601 1_555 B SG CYS 107 B CYS 608 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? covale ? covale1 A ND2 ASN 201 A ASN 228 1_555 G C1 NAG . A NAG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.453 ? covale ? covale2 A ND2 ASN 211 A ASN 238 1_555 E C1 NAG . A NAG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? 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 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale5 B ND2 ASN 62 B ASN 563 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale6 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale7 C O4 NAG . C NAG 2 1_555 C C1 BMA . C BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale8 C O6 BMA . C BMA 3 1_555 C C1 MAN . C MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.464 ? # _chem_comp.formula 'C26 H38 N2 O2' _chem_comp.formula_weight 410.592 _chem_comp.id YPS _chem_comp.mon_nstd_flag . _chem_comp.name (1R,3S,5R,7R)-N-[(1r,4R)-4-aminocyclohexyl]-3-(ethoxymethyl)-5-phenyladamantane-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 YPS doub 454 n y C19 C20 YPS sing 455 n y C18 C17 YPS sing 456 n y C20 C15 YPS doub 457 n y C17 C16 YPS doub 458 n y C15 C16 YPS sing 459 n y C15 C13 YPS sing 460 n n C12 C13 YPS sing 461 n n C12 C11 YPS sing 462 n n O01 C02 YPS doub 463 n n C13 C14 YPS sing 464 n n C13 C21 YPS sing 465 n n C09 C10 YPS sing 466 n n C09 C07 YPS sing 467 n n C14 C24 YPS sing 468 n n C10 C04 YPS sing 469 n n C02 C11 YPS sing 470 n n C02 N03 YPS sing 471 n n C04 N03 YPS sing 472 n n C04 C05 YPS sing 473 n n C11 C25 YPS sing 474 n n C11 C30 YPS sing 475 n n N08 C07 YPS sing 476 n n C25 C24 YPS sing 477 n n C21 C22 YPS sing 478 n n C07 C06 YPS sing 479 n n C24 C23 YPS sing 480 n n C06 C05 YPS sing 481 n n C30 C22 YPS sing 482 n n C22 C23 YPS sing 483 n n C22 C26 YPS sing 484 n n C26 O27 YPS sing 485 n n O27 C28 YPS sing 486 n n C28 C29 YPS sing 487 n n C25 H1 YPS sing 488 n n C25 H2 YPS sing 489 n n C24 H3 YPS sing 490 n n C23 H4 YPS sing 491 n n C23 H5 YPS sing 492 n n C18 H6 YPS sing 493 n n C19 H7 YPS sing 494 n n C17 H8 YPS sing 495 n n C16 H9 YPS sing 496 n n C12 H10 YPS sing 497 n n C12 H11 YPS sing 498 n n C10 H12 YPS sing 499 n n C10 H13 YPS sing 500 n n C04 H14 YPS sing 501 n n C05 H15 YPS sing 502 n n C05 H16 YPS sing 503 n n C06 H17 YPS sing 504 n n C06 H18 YPS sing 505 n n C07 H19 YPS sing 506 n n C09 H20 YPS sing 507 n n C09 H21 YPS sing 508 n n C14 H22 YPS sing 509 n n C14 H23 YPS sing 510 n n C20 H24 YPS sing 511 n n C21 H25 YPS sing 512 n n C21 H26 YPS sing 513 n n C26 H27 YPS sing 514 n n C26 H28 YPS sing 515 n n C28 H29 YPS sing 516 n n C28 H30 YPS sing 517 n n C29 H31 YPS sing 518 n n C29 H32 YPS sing 519 n n C29 H33 YPS sing 520 n n C30 H34 YPS sing 521 n n C30 H35 YPS sing 522 n n N03 H36 YPS sing 523 n n N08 H37 YPS sing 524 n n N08 H38 YPS sing 525 n n # _atom_sites.entry_id 7M2D _atom_sites.fract_transf_matrix[1][1] 0.008687 _atom_sites.fract_transf_matrix[1][2] 0.005016 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010031 _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] 0.003236 _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 YPS A 1 605 605 YPS 953 . I 6 HOH A 1 701 109 HOH HOH . I 6 HOH A 2 702 125 HOH HOH . I 6 HOH A 3 703 37 HOH HOH . I 6 HOH A 4 704 73 HOH HOH . I 6 HOH A 5 705 108 HOH HOH . I 6 HOH A 6 706 84 HOH HOH . I 6 HOH A 7 707 82 HOH HOH . I 6 HOH A 8 708 69 HOH HOH . I 6 HOH A 9 709 1 HOH HOH . I 6 HOH A 10 710 38 HOH HOH . I 6 HOH A 11 711 88 HOH HOH . I 6 HOH A 12 712 5 HOH HOH . I 6 HOH A 13 713 79 HOH HOH . I 6 HOH A 14 714 66 HOH HOH . I 6 HOH A 15 715 71 HOH HOH . I 6 HOH A 16 716 80 HOH HOH . I 6 HOH A 17 717 67 HOH HOH . I 6 HOH A 18 718 9 HOH HOH . I 6 HOH A 19 719 4 HOH HOH . I 6 HOH A 20 720 89 HOH HOH . I 6 HOH A 21 721 35 HOH HOH . I 6 HOH A 22 722 119 HOH HOH . I 6 HOH A 23 723 52 HOH HOH . I 6 HOH A 24 724 15 HOH HOH . I 6 HOH A 25 725 60 HOH HOH . I 6 HOH A 26 726 7 HOH HOH . I 6 HOH A 27 727 120 HOH HOH . I 6 HOH A 28 728 42 HOH HOH . I 6 HOH A 29 729 3 HOH HOH . I 6 HOH A 30 730 6 HOH HOH . I 6 HOH A 31 731 14 HOH HOH . I 6 HOH A 32 732 33 HOH HOH . I 6 HOH A 33 733 75 HOH HOH . I 6 HOH A 34 734 12 HOH HOH . I 6 HOH A 35 735 53 HOH HOH . I 6 HOH A 36 736 8 HOH HOH . I 6 HOH A 37 737 101 HOH HOH . I 6 HOH A 38 738 13 HOH HOH . I 6 HOH A 39 739 114 HOH HOH . I 6 HOH A 40 740 10 HOH HOH . I 6 HOH A 41 741 83 HOH HOH . I 6 HOH A 42 742 43 HOH HOH . I 6 HOH A 43 743 56 HOH HOH . I 6 HOH A 44 744 68 HOH HOH . I 6 HOH A 45 745 31 HOH HOH . I 6 HOH A 46 746 112 HOH HOH . I 6 HOH A 47 747 95 HOH HOH . I 6 HOH A 48 748 32 HOH HOH . I 6 HOH A 49 749 48 HOH HOH . I 6 HOH A 50 750 127 HOH HOH . I 6 HOH A 51 751 122 HOH HOH . I 6 HOH A 52 752 76 HOH HOH . I 6 HOH A 53 753 77 HOH HOH . I 6 HOH A 54 754 11 HOH HOH . I 6 HOH A 55 755 117 HOH HOH . I 6 HOH A 56 756 143 HOH HOH . I 6 HOH A 57 757 113 HOH HOH . I 6 HOH A 58 758 118 HOH HOH . I 6 HOH A 59 759 126 HOH HOH . J 6 HOH B 1 701 16 HOH HOH . J 6 HOH B 2 702 28 HOH HOH . J 6 HOH B 3 703 17 HOH HOH . J 6 HOH B 4 704 29 HOH HOH . J 6 HOH B 5 705 140 HOH HOH . J 6 HOH B 6 706 18 HOH HOH . J 6 HOH B 7 707 19 HOH HOH . J 6 HOH B 8 708 65 HOH HOH . J 6 HOH B 9 709 105 HOH HOH . J 6 HOH B 10 710 21 HOH HOH . J 6 HOH B 11 711 99 HOH HOH . J 6 HOH B 12 712 39 HOH HOH . J 6 HOH B 13 713 100 HOH HOH . J 6 HOH B 14 714 93 HOH HOH . J 6 HOH B 15 715 94 HOH HOH . J 6 HOH B 16 716 121 HOH HOH . J 6 HOH B 17 717 44 HOH HOH . J 6 HOH B 18 718 22 HOH HOH . J 6 HOH B 19 719 30 HOH HOH . J 6 HOH B 20 720 98 HOH HOH . J 6 HOH B 21 721 133 HOH HOH . J 6 HOH B 22 722 40 HOH HOH . J 6 HOH B 23 723 132 HOH HOH . J 6 HOH B 24 724 137 HOH HOH . J 6 HOH B 25 725 106 HOH HOH . J 6 HOH B 26 726 142 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 C25 YPS . . . H 5 -44.128 13.79 -7.308 1 66.15 ? C25 YPS 605 A 1 HETATM 2 C C24 YPS . . . H 5 -44.596 12.36 -6.981 1 65.9 ? C24 YPS 605 A 1 HETATM 3 C C23 YPS . . . H 5 -45.435 12.369 -5.693 1 62.84 ? C23 YPS 605 A 1 HETATM 4 C C18 YPS . . . H 5 -49.118 11.247 -11.689 1 61.05 ? C18 YPS 605 A 1 HETATM 5 C C19 YPS . . . H 5 -47.902 11.852 -11.934 1 56.72 ? C19 YPS 605 A 1 HETATM 6 C C17 YPS . . . H 5 -49.548 11.106 -10.377 1 61.79 ? C17 YPS 605 A 1 HETATM 7 C C16 YPS . . . H 5 -48.773 11.573 -9.332 1 58.55 ? C16 YPS 605 A 1 HETATM 8 C C15 YPS . . . H 5 -47.542 12.192 -9.56 1 59.73 ? C15 YPS 605 A 1 HETATM 9 C C11 YPS . . . H 5 -45.357 14.683 -7.511 1 65.88 ? C11 YPS 605 A 1 HETATM 10 C C12 YPS . . . H 5 -46.212 14.132 -8.673 1 58.35 ? C12 YPS 605 A 1 HETATM 11 C C10 YPS . . . H 5 -42.196 18.199 -8.032 1 78.97 ? C10 YPS 605 A 1 HETATM 12 C C02 YPS . . . H 5 -45.055 16.141 -7.844 1 69.27 ? C02 YPS 605 A 1 HETATM 13 C C04 YPS . . . H 5 -43.647 18.123 -7.535 1 76.66 ? C04 YPS 605 A 1 HETATM 14 C C05 YPS . . . H 5 -43.842 18.998 -6.285 1 74.78 ? C05 YPS 605 A 1 HETATM 15 C C06 YPS . . . H 5 -43.406 20.444 -6.551 1 76.9 ? C06 YPS 605 A 1 HETATM 16 C C07 YPS . . . H 5 -41.938 20.51 -7.006 1 82.49 ? C07 YPS 605 A 1 HETATM 17 C C09 YPS . . . H 5 -41.741 19.652 -8.268 1 84.58 ? C09 YPS 605 A 1 HETATM 18 C C13 YPS . . . H 5 -46.693 12.693 -8.38 1 60.15 ? C13 YPS 605 A 1 HETATM 19 C C14 YPS . . . H 5 -45.443 11.815 -8.148 1 61.13 ? C14 YPS 605 A 1 HETATM 20 C C20 YPS . . . H 5 -47.127 12.316 -10.881 1 58.15 ? C20 YPS 605 A 1 HETATM 21 C C21 YPS . . . H 5 -47.514 12.706 -7.066 1 59.33 ? C21 YPS 605 A 1 HETATM 22 C C22 YPS . . . H 5 -46.673 13.255 -5.895 1 66.14 ? C22 YPS 605 A 1 HETATM 23 C C26 YPS . . . H 5 -47.505 13.282 -4.615 1 70.23 ? C26 YPS 605 A 1 HETATM 24 C C28 YPS . . . H 5 -48.831 11.822 -3.197 1 68.45 ? C28 YPS 605 A 1 HETATM 25 C C29 YPS . . . H 5 -49.194 10.345 -3.09 1 71.72 ? C29 YPS 605 A 1 HETATM 26 C C30 YPS . . . H 5 -46.211 14.682 -6.224 1 61.73 ? C30 YPS 605 A 1 HETATM 27 N N03 YPS . . . H 5 -43.99 16.719 -7.259 1 74.7 ? N03 YPS 605 A 1 HETATM 28 N N08 YPS . . . H 5 -41.594 21.907 -7.329 1 83.98 ? N08 YPS 605 A 1 HETATM 29 O O01 YPS . . . H 5 -45.775 16.751 -8.629 1 63.27 ? O01 YPS 605 A 1 HETATM 30 O O27 YPS . . . H 5 -48.003 11.959 -4.364 1 74.9 ? O27 YPS 605 A 1 # _model_server_stats.io_time_ms 52 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 311 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 30 #