data_3VS5 # _model_server_result.job_id qC05uA08uFpFFV9jnhq8Cg _model_server_result.datetime_utc '2024-11-24 14:36:45' _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 3vs5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":601}' # _entry.id 3VS5 # _exptl.entry_id 3VS5 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 399.488 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 7-(1-methylpiperidin-4-yl)-5-(4-phenoxyphenyl)-7H-pyrrolo[2,3-d]pyrimidin-4-amine _entity.pdbx_number_of_molecules 2 _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 90 _cell.entry_id 3VS5 _cell.length_a 73.489 _cell.length_b 94.826 _cell.length_c 179.982 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3VS5 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # 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 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,G 1 1 B,E,F,H 2 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 C 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 covale ? covale1 A C GLN 449 A GLN 526 1_555 A N PTR 450 A PTR 527 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale2 A C PTR 450 A PTR 527 1_555 A N GLU 451 A GLU 528 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale3 B C GLN 449 B GLN 526 1_555 B N PTR 450 B PTR 527 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale4 B C PTR 450 B PTR 527 1_555 B N GLU 451 B GLU 528 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? metalc ? metalc1 A OE2 GLU 413 A GLU 490 1_555 E CA CA . B CA 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.875 ? metalc ? metalc2 A OE1 GLU 413 A GLU 490 1_555 E CA CA . B CA 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.154 ? metalc ? metalc3 A O GLU 447 A GLU 524 1_555 D CA CA . A CA 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.792 ? metalc ? metalc4 A O PTR 450 A PTR 527 1_555 D CA CA . A CA 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.955 ? metalc ? metalc5 A OE2 GLU 452 A GLU 529 1_555 D CA CA . A CA 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.945 ? metalc ? metalc6 D CA CA . A CA 602 1_555 B OE2 GLU 413 B GLU 490 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.889 ? metalc ? metalc7 B O GLU 447 B GLU 524 1_555 E CA CA . B CA 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.955 ? metalc ? metalc8 B O PTR 450 B PTR 527 1_555 E CA CA . B CA 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.864 ? # _chem_comp.formula 'C24 H25 N5 O' _chem_comp.formula_weight 399.488 _chem_comp.id VSG _chem_comp.mon_nstd_flag . _chem_comp.name 7-(1-methylpiperidin-4-yl)-5-(4-phenoxyphenyl)-7H-pyrrolo[2,3-d]pyrimidin-4-amine _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 CAR CAS VSG sing 405 n n CAR CAQ VSG sing 406 n n C2 N3 VSG doub 407 n y C2 N1 VSG sing 408 n y CAS NAT VSG sing 409 n n CAW NAT VSG sing 410 n n N3 C4 VSG sing 411 n y N1 C6 VSG doub 412 n y C4 NAG VSG sing 413 n y C4 C5 VSG doub 414 n y CAQ NAG VSG sing 415 n n CAQ CAV VSG sing 416 n n NAT CAU VSG sing 417 n n C6 C5 VSG sing 418 n y C6 NAK VSG sing 419 n n NAG CAH VSG sing 420 n y C5 CAI VSG sing 421 n y CAP CAO VSG doub 422 n y CAP CAJ VSG sing 423 n y CAH CAI VSG doub 424 n y CAI CAJ VSG sing 425 n n CAO CAN VSG sing 426 n y CAJ CAL VSG doub 427 n y CAU CAV VSG sing 428 n n CAN OAX VSG sing 429 n n CAN CAM VSG doub 430 n y OAX CAY VSG sing 431 n n CAL CAM VSG sing 432 n y CAY CAZ VSG doub 433 n y CAY CBD VSG sing 434 n y CAZ CBA VSG sing 435 n y CBD CBC VSG doub 436 n y CBA CBB VSG doub 437 n y CBC CBB VSG sing 438 n y CAR H1 VSG sing 439 n n CAR H2 VSG sing 440 n n CAS H3 VSG sing 441 n n CAS H4 VSG sing 442 n n CAW H6 VSG sing 443 n n CAW H7 VSG sing 444 n n CAW H8 VSG sing 445 n n CAU H9 VSG sing 446 n n CAU H10 VSG sing 447 n n CAV H11 VSG sing 448 n n CAV H12 VSG sing 449 n n CAQ H13 VSG sing 450 n n CAH H14 VSG sing 451 n n C2 H15 VSG sing 452 n n NAK H16 VSG sing 453 n n NAK H17 VSG sing 454 n n CAP H18 VSG sing 455 n n CAO H19 VSG sing 456 n n CAL H20 VSG sing 457 n n CAM H21 VSG sing 458 n n CAZ H22 VSG sing 459 n n CBA H23 VSG sing 460 n n CBB H24 VSG sing 461 n n CBC H25 VSG sing 462 n n CBD H26 VSG sing 463 n n # _atom_sites.entry_id 3VS5 _atom_sites.fract_transf_matrix[1][1] 0.013607 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010546 _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] 0.005556 _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 C 2 VSG A 1 601 1 VSG LIG . D 3 CA A 1 602 600 CA CA . E 3 CA B 1 602 600 CA CA . F 2 VSG B 1 601 1 VSG LIG . G 4 HOH A 1 701 1 HOH HOH . G 4 HOH A 2 702 2 HOH HOH . G 4 HOH A 3 703 4 HOH HOH . G 4 HOH A 4 704 8 HOH HOH . G 4 HOH A 5 705 9 HOH HOH . G 4 HOH A 6 706 10 HOH HOH . G 4 HOH A 7 707 12 HOH HOH . G 4 HOH A 8 708 15 HOH HOH . G 4 HOH A 9 709 19 HOH HOH . G 4 HOH A 10 710 21 HOH HOH . G 4 HOH A 11 711 25 HOH HOH . G 4 HOH A 12 712 28 HOH HOH . G 4 HOH A 13 713 29 HOH HOH . G 4 HOH A 14 714 30 HOH HOH . G 4 HOH A 15 715 31 HOH HOH . G 4 HOH A 16 716 33 HOH HOH . G 4 HOH A 17 717 35 HOH HOH . G 4 HOH A 18 718 38 HOH HOH . H 4 HOH B 1 701 3 HOH HOH . H 4 HOH B 2 702 5 HOH HOH . H 4 HOH B 3 703 6 HOH HOH . H 4 HOH B 4 704 7 HOH HOH . H 4 HOH B 5 705 11 HOH HOH . H 4 HOH B 6 706 13 HOH HOH . H 4 HOH B 7 707 14 HOH HOH . H 4 HOH B 8 708 16 HOH HOH . H 4 HOH B 9 709 17 HOH HOH . H 4 HOH B 10 710 18 HOH HOH . H 4 HOH B 11 711 20 HOH HOH . H 4 HOH B 12 712 22 HOH HOH . H 4 HOH B 13 713 23 HOH HOH . H 4 HOH B 14 714 24 HOH HOH . H 4 HOH B 15 715 26 HOH HOH . H 4 HOH B 16 716 27 HOH HOH . H 4 HOH B 17 717 32 HOH HOH . H 4 HOH B 18 718 34 HOH HOH . H 4 HOH B 19 719 36 HOH HOH . H 4 HOH B 20 720 37 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 CAR VSG . . . C 2 -8.83 -2.846 15.091 1 57.27 ? CAR VSG 601 A 1 HETATM 2 C CAS VSG . . . C 2 -10.209 -2.381 15.545 1 65.47 ? CAS VSG 601 A 1 HETATM 3 N NAT VSG . . . C 2 -10.812 -3.524 16.21 1 64.69 ? NAT VSG 601 A 1 HETATM 4 C CAW VSG . . . C 2 -12.041 -4.103 15.682 1 60.26 ? CAW VSG 601 A 1 HETATM 5 C CAU VSG . . . C 2 -10.21 -4.068 17.424 1 57.21 ? CAU VSG 601 A 1 HETATM 6 C CAV VSG . . . C 2 -8.768 -3.571 17.509 1 59.38 ? CAV VSG 601 A 1 HETATM 7 C CAQ VSG . . . C 2 -8.025 -3.567 16.17 1 65.96 ? CAQ VSG 601 A 1 HETATM 8 N NAG VSG . . . C 2 -6.71 -2.884 16.351 1 64.08 ? NAG VSG 601 A 1 HETATM 9 C CAH VSG . . . C 2 -6.539 -1.622 16.784 1 57.97 ? CAH VSG 601 A 1 HETATM 10 C C4 VSG . . . C 2 -5.505 -3.434 16.134 1 57.04 ? C4 VSG 601 A 1 HETATM 11 N N3 VSG . . . C 2 -5.164 -4.673 15.697 1 51.67 ? N3 VSG 601 A 1 HETATM 12 C C2 VSG . . . C 2 -3.875 -5.009 15.543 1 49.31 ? C2 VSG 601 A 1 HETATM 13 N N1 VSG . . . C 2 -2.893 -4.14 15.814 1 49.84 ? N1 VSG 601 A 1 HETATM 14 C C6 VSG . . . C 2 -3.167 -2.882 16.246 1 51.18 ? C6 VSG 601 A 1 HETATM 15 N NAK VSG . . . C 2 -2.118 -2.057 16.5 1 45.11 ? NAK VSG 601 A 1 HETATM 16 C C5 VSG . . . C 2 -4.507 -2.491 16.418 1 58.37 ? C5 VSG 601 A 1 HETATM 17 C CAI VSG . . . C 2 -5.177 -1.335 16.857 1 60.15 ? CAI VSG 601 A 1 HETATM 18 C CAJ VSG . . . C 2 -4.642 0.011 17.249 1 61.91 ? CAJ VSG 601 A 1 HETATM 19 C CAP VSG . . . C 2 -3.491 0.498 16.634 1 55.28 ? CAP VSG 601 A 1 HETATM 20 C CAO VSG . . . C 2 -2.981 1.756 16.942 1 55.97 ? CAO VSG 601 A 1 HETATM 21 C CAL VSG . . . C 2 -5.321 0.845 18.143 1 66.7 ? CAL VSG 601 A 1 HETATM 22 C CAM VSG . . . C 2 -4.81 2.113 18.451 1 71.02 ? CAM VSG 601 A 1 HETATM 23 C CAN VSG . . . C 2 -3.623 2.567 17.87 1 65.18 ? CAN VSG 601 A 1 HETATM 24 O OAX VSG . . . C 2 -3.103 3.822 18.113 1 57.02 ? OAX VSG 601 A 1 HETATM 25 C CAY VSG . . . C 2 -2.643 4.332 19.309 1 62.89 ? CAY VSG 601 A 1 HETATM 26 C CAZ VSG . . . C 2 -2.83 5.69 19.588 1 57.61 ? CAZ VSG 601 A 1 HETATM 27 C CBA VSG . . . C 2 -2.361 6.244 20.777 1 63.17 ? CBA VSG 601 A 1 HETATM 28 C CBB VSG . . . C 2 -1.685 5.447 21.7 1 59.38 ? CBB VSG 601 A 1 HETATM 29 C CBC VSG . . . C 2 -1.49 4.096 21.425 1 59.75 ? CBC VSG 601 A 1 HETATM 30 C CBD VSG . . . C 2 -1.961 3.544 20.228 1 64.85 ? CBD VSG 601 A 1 # _model_server_stats.io_time_ms 48 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 224 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 30 #