data_3VS1 # _model_server_result.job_id mGsRJg6rbrLxGB6hrLeWhQ _model_server_result.datetime_utc '2024-10-17 19:28:01' _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 3vs1 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":602}' # _entry.id 3VS1 # _exptl.entry_id 3VS1 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 412.487 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 1-[4-(4-amino-7-cyclopentyl-7H-pyrrolo[2,3-d]pyrimidin-5-yl)phenyl]-3-phenylurea _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 96.21 _cell.angle_gamma 90 _cell.entry_id 3VS1 _cell.length_a 49.03 _cell.length_b 73.27 _cell.length_c 179.85 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3VS1 _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 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 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,E,I 1 1 B,F,G,H,J 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 ? 4 E N N ? 4 H 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 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? 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 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale4 B C PTR 450 B PTR 527 1_555 B N GLU 451 B GLU 528 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? metalc ? metalc1 A OE2 GLU 413 A GLU 490 1_555 F CA CA . B CA 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.179 ? metalc ? metalc2 A O GLU 447 A GLU 524 1_555 C CA CA . A CA 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.105 ? metalc ? metalc3 A O PTR 450 A PTR 527 1_555 C CA CA . A CA 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.022 ? metalc ? metalc4 I O HOH . A HOH 750 1_555 F CA CA . B CA 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.093 ? metalc ? metalc5 B O GLU 447 B GLU 524 1_555 F CA CA . B CA 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.924 ? metalc ? metalc6 B O PTR 450 B PTR 527 1_555 F CA CA . B CA 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.937 ? # _chem_comp.formula 'C24 H24 N6 O' _chem_comp.formula_weight 412.487 _chem_comp.id VSA _chem_comp.mon_nstd_flag . _chem_comp.name 1-[4-(4-amino-7-cyclopentyl-7H-pyrrolo[2,3-d]pyrimidin-5-yl)phenyl]-3-phenylurea _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 CAP CBD VSA sing 405 n n CAP CAN VSA sing 406 n n C2 N3 VSA doub 407 n y C2 N1 VSA sing 408 n y N3 C4 VSA sing 409 n y CBD NBE VSA sing 410 n n CBD CAQ VSA sing 411 n n N1 C6 VSA doub 412 n y C4 NBE VSA sing 413 n y C4 C5 VSA doub 414 n y CAN CAO VSA sing 415 n n NBE CAM VSA sing 416 n y C6 C5 VSA sing 417 n y C6 NAA VSA sing 418 n n C5 CBA VSA sing 419 n y CAM CBA VSA doub 420 n y CAQ CAO VSA sing 421 n n CBA CAY VSA sing 422 n n CAK CAY VSA doub 423 n y CAK CAI VSA sing 424 n y CAY CAJ VSA sing 425 n y CAI CAX VSA doub 426 n y CAJ CAH VSA doub 427 n y CAX CAH VSA sing 428 n y CAX NAU VSA sing 429 n n OAB CAV VSA doub 430 n n CAV NAU VSA sing 431 n n CAV NAT VSA sing 432 n n NAT CAW VSA sing 433 n n CAW CAF VSA doub 434 n y CAW CAG VSA sing 435 n y CAF CAD VSA sing 436 n y CAG CAE VSA doub 437 n y CAD CAC VSA doub 438 n y CAE CAC VSA sing 439 n y CAP H1 VSA sing 440 n n CAP H2 VSA sing 441 n n CAN H3 VSA sing 442 n n CAN H4 VSA sing 443 n n CAO H5 VSA sing 444 n n CAO H6 VSA sing 445 n n CAQ H7 VSA sing 446 n n CAQ H8 VSA sing 447 n n CBD H9 VSA sing 448 n n CAM H10 VSA sing 449 n n C2 H11 VSA sing 450 n n NAA H12 VSA sing 451 n n NAA H13 VSA sing 452 n n CAK H14 VSA sing 453 n n CAI H15 VSA sing 454 n n CAJ H16 VSA sing 455 n n CAH H17 VSA sing 456 n n NAU H18 VSA sing 457 n n NAT H19 VSA sing 458 n n CAF H20 VSA sing 459 n n CAD H21 VSA sing 460 n n CAC H22 VSA sing 461 n n CAE H23 VSA sing 462 n n CAG H24 VSA sing 463 n n # _atom_sites.entry_id 3VS1 _atom_sites.fract_transf_matrix[1][1] 0.020396 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002219 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013648 _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] 0.005593 _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 CA A 1 601 600 CA CA . D 3 CL A 1 603 601 CL CL . E 4 VSA A 1 602 1 VSA LIG . F 2 CA B 1 601 600 CA CA . G 3 CL B 1 603 601 CL CL . H 4 VSA B 1 602 1 VSA LIG . I 5 HOH A 1 701 1 HOH HOH . I 5 HOH A 2 702 2 HOH HOH . I 5 HOH A 3 703 3 HOH HOH . I 5 HOH A 4 704 4 HOH HOH . I 5 HOH A 5 705 5 HOH HOH . I 5 HOH A 6 706 6 HOH HOH . I 5 HOH A 7 707 8 HOH HOH . I 5 HOH A 8 708 9 HOH HOH . I 5 HOH A 9 709 10 HOH HOH . I 5 HOH A 10 710 11 HOH HOH . I 5 HOH A 11 711 12 HOH HOH . I 5 HOH A 12 712 13 HOH HOH . I 5 HOH A 13 713 16 HOH HOH . I 5 HOH A 14 714 19 HOH HOH . I 5 HOH A 15 715 20 HOH HOH . I 5 HOH A 16 716 22 HOH HOH . I 5 HOH A 17 717 23 HOH HOH . I 5 HOH A 18 718 25 HOH HOH . I 5 HOH A 19 719 26 HOH HOH . I 5 HOH A 20 720 27 HOH HOH . I 5 HOH A 21 721 28 HOH HOH . I 5 HOH A 22 722 32 HOH HOH . I 5 HOH A 23 723 33 HOH HOH . I 5 HOH A 24 724 37 HOH HOH . I 5 HOH A 25 725 38 HOH HOH . I 5 HOH A 26 726 39 HOH HOH . I 5 HOH A 27 727 41 HOH HOH . I 5 HOH A 28 728 43 HOH HOH . I 5 HOH A 29 729 44 HOH HOH . I 5 HOH A 30 730 45 HOH HOH . I 5 HOH A 31 731 46 HOH HOH . I 5 HOH A 32 732 52 HOH HOH . I 5 HOH A 33 733 56 HOH HOH . I 5 HOH A 34 734 57 HOH HOH . I 5 HOH A 35 735 58 HOH HOH . I 5 HOH A 36 736 60 HOH HOH . I 5 HOH A 37 737 61 HOH HOH . I 5 HOH A 38 738 62 HOH HOH . I 5 HOH A 39 739 63 HOH HOH . I 5 HOH A 40 740 66 HOH HOH . I 5 HOH A 41 741 67 HOH HOH . I 5 HOH A 42 742 69 HOH HOH . I 5 HOH A 43 743 71 HOH HOH . I 5 HOH A 44 744 72 HOH HOH . I 5 HOH A 45 745 73 HOH HOH . I 5 HOH A 46 746 74 HOH HOH . I 5 HOH A 47 747 76 HOH HOH . I 5 HOH A 48 748 77 HOH HOH . I 5 HOH A 49 749 78 HOH HOH . I 5 HOH A 50 750 79 HOH HOH . I 5 HOH A 51 751 80 HOH HOH . I 5 HOH A 52 752 81 HOH HOH . J 5 HOH B 1 701 7 HOH HOH . J 5 HOH B 2 702 14 HOH HOH . J 5 HOH B 3 703 15 HOH HOH . J 5 HOH B 4 704 17 HOH HOH . J 5 HOH B 5 705 18 HOH HOH . J 5 HOH B 6 706 21 HOH HOH . J 5 HOH B 7 707 24 HOH HOH . J 5 HOH B 8 708 29 HOH HOH . J 5 HOH B 9 709 30 HOH HOH . J 5 HOH B 10 710 31 HOH HOH . J 5 HOH B 11 711 34 HOH HOH . J 5 HOH B 12 712 35 HOH HOH . J 5 HOH B 13 713 36 HOH HOH . J 5 HOH B 14 714 40 HOH HOH . J 5 HOH B 15 715 42 HOH HOH . J 5 HOH B 16 716 47 HOH HOH . J 5 HOH B 17 717 48 HOH HOH . J 5 HOH B 18 718 49 HOH HOH . J 5 HOH B 19 719 50 HOH HOH . J 5 HOH B 20 720 51 HOH HOH . J 5 HOH B 21 721 53 HOH HOH . J 5 HOH B 22 722 54 HOH HOH . J 5 HOH B 23 723 55 HOH HOH . J 5 HOH B 24 724 59 HOH HOH . J 5 HOH B 25 725 64 HOH HOH . J 5 HOH B 26 726 65 HOH HOH . J 5 HOH B 27 727 68 HOH HOH . J 5 HOH B 28 728 70 HOH HOH . J 5 HOH B 29 729 75 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 CAP VSA . . . E 4 3.441 -8.376 11.052 1 45.08 ? CAP VSA 602 A 1 HETATM 2 C CAN VSA . . . E 4 3.588 -9.688 11.815 1 55.3 ? CAN VSA 602 A 1 HETATM 3 C CAO VSA . . . E 4 4.823 -9.57 12.699 1 55.47 ? CAO VSA 602 A 1 HETATM 4 C CAQ VSA . . . E 4 5.235 -8.104 12.686 1 53.74 ? CAQ VSA 602 A 1 HETATM 5 C CBD VSA . . . E 4 4.548 -7.432 11.5 1 45.99 ? CBD VSA 602 A 1 HETATM 6 N NBE VSA . . . E 4 3.924 -6.173 11.959 1 41.75 ? NBE VSA 602 A 1 HETATM 7 C CAM VSA . . . E 4 2.775 -6.118 12.63 1 41.14 ? CAM VSA 602 A 1 HETATM 8 C C4 VSA . . . E 4 4.381 -4.929 11.771 1 42.46 ? C4 VSA 602 A 1 HETATM 9 N N3 VSA . . . E 4 5.493 -4.465 11.157 1 40.69 ? N3 VSA 602 A 1 HETATM 10 C C2 VSA . . . E 4 5.738 -3.149 11.114 1 42.89 ? C2 VSA 602 A 1 HETATM 11 N N1 VSA . . . E 4 4.901 -2.264 11.673 1 42.86 ? N1 VSA 602 A 1 HETATM 12 C C6 VSA . . . E 4 3.779 -2.676 12.302 1 42.66 ? C6 VSA 602 A 1 HETATM 13 N NAA VSA . . . E 4 2.948 -1.764 12.86 1 39.9 ? NAA VSA 602 A 1 HETATM 14 C C5 VSA . . . E 4 3.494 -4.033 12.361 1 42.53 ? C5 VSA 602 A 1 HETATM 15 C CBA VSA . . . E 4 2.473 -4.799 12.914 1 42.88 ? CBA VSA 602 A 1 HETATM 16 C CAY VSA . . . E 4 1.232 -4.434 13.651 1 48.15 ? CAY VSA 602 A 1 HETATM 17 C CAK VSA . . . E 4 0.314 -3.487 13.201 1 45.51 ? CAK VSA 602 A 1 HETATM 18 C CAI VSA . . . E 4 -0.844 -3.234 13.937 1 50.85 ? CAI VSA 602 A 1 HETATM 19 C CAJ VSA . . . E 4 0.968 -5.153 14.803 1 54.87 ? CAJ VSA 602 A 1 HETATM 20 C CAH VSA . . . E 4 -0.178 -4.899 15.533 1 60.59 ? CAH VSA 602 A 1 HETATM 21 C CAX VSA . . . E 4 -1.083 -3.936 15.115 1 61.11 ? CAX VSA 602 A 1 HETATM 22 N NAU VSA . . . E 4 -2.218 -3.786 15.926 1 70.97 ? NAU VSA 602 A 1 HETATM 23 C CAV VSA . . . E 4 -3.183 -2.868 15.912 1 68.33 ? CAV VSA 602 A 1 HETATM 24 O OAB VSA . . . E 4 -3.216 -1.929 15.139 1 69 ? OAB VSA 602 A 1 HETATM 25 N NAT VSA . . . E 4 -4.117 -3.083 16.839 1 74.51 ? NAT VSA 602 A 1 HETATM 26 C CAW VSA . . . E 4 -5.253 -2.305 17.094 1 75.6 ? CAW VSA 602 A 1 HETATM 27 C CAF VSA . . . E 4 -5.196 -0.923 17.195 1 76.94 ? CAF VSA 602 A 1 HETATM 28 C CAD VSA . . . E 4 -6.35 -0.199 17.471 1 74.99 ? CAD VSA 602 A 1 HETATM 29 C CAC VSA . . . E 4 -7.559 -0.856 17.658 1 76.99 ? CAC VSA 602 A 1 HETATM 30 C CAE VSA . . . E 4 -7.614 -2.24 17.569 1 86.47 ? CAE VSA 602 A 1 HETATM 31 C CAG VSA . . . E 4 -6.46 -2.961 17.296 1 84.8 ? CAG VSA 602 A 1 # _model_server_stats.io_time_ms 42 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 12 _model_server_stats.query_time_ms 343 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 31 #