data_YBT # _chem_comp.id YBT _chem_comp.name "BIS-(2-HYDROXYETHYL)AMINO-TRIS(HYDROXYMETHYL)METHANE YTTRIUM" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C8 H19 N O5 Y" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 3 _chem_comp.pdbx_initial_date 2002-08-09 _chem_comp.pdbx_modified_date 2026-09-01 _chem_comp.pdbx_ambiguous_flag Y _chem_comp.pdbx_release_status REL _chem_comp.pdbx_replaced_by ? _chem_comp.pdbx_replaces ? _chem_comp.formula_weight 298.146 _chem_comp.one_letter_code ? _chem_comp.three_letter_code YBT _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag N _chem_comp.pdbx_ideal_coordinates_details MetalCoord _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code ? _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site RCSB _chem_comp.pdbx_comp_type "metal-containing ligand" _chem_comp.pdbx_pcm Y # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.alt_atom_id _chem_comp_atom.type_symbol _chem_comp_atom.charge _chem_comp_atom.pdbx_align _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_leaving_atom_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_backbone_atom_flag _chem_comp_atom.pdbx_n_terminal_atom_flag _chem_comp_atom.pdbx_c_terminal_atom_flag _chem_comp_atom.model_Cartn_x _chem_comp_atom.model_Cartn_y _chem_comp_atom.model_Cartn_z _chem_comp_atom.pdbx_model_Cartn_x_ideal _chem_comp_atom.pdbx_model_Cartn_y_ideal _chem_comp_atom.pdbx_model_Cartn_z_ideal _chem_comp_atom.pdbx_component_atom_id _chem_comp_atom.pdbx_component_comp_id _chem_comp_atom.pdbx_ordinal YBT Y1 Y1 Y 3 1 N N N N N N 40.039 39.599 7.214 39.936 39.893 6.684 Y1 YBT 1 YBT O1 O1 O 0 1 N N N N N N 40.765 39.708 4.938 41.103 40.898 5.078 O1 YBT 2 YBT O2 O2 O 0 1 N N N N N N 38.429 38.547 5.829 39.118 38.593 5.030 O2 YBT 3 YBT O3 O3 O 0 1 N N N N N N 38.182 42.426 2.816 38.038 43.139 3.282 O3 YBT 4 YBT O4 O4 O 0 1 N N N N N N 38.134 40.481 8.313 37.998 39.687 7.956 O4 YBT 5 YBT O5 O5 O 0 1 N N N N N N 40.983 41.768 7.324 40.499 41.682 7.896 O5 YBT 6 YBT N1 N1 N 0 1 N N N N N N 38.644 41.337 5.718 38.389 41.383 5.743 N1 YBT 7 YBT C1 C1 C 0 1 N N N N N N 38.510 40.526 4.365 38.758 40.978 4.311 C1 YBT 8 YBT C2 C2 C 0 1 N N N N N N 39.879 40.135 3.837 40.264 41.181 3.976 C2 YBT 9 YBT C3 C3 C 0 1 N N N N N N 37.765 39.185 4.708 38.534 39.459 4.041 C3 YBT 10 YBT C4 C4 C 0 1 N N N N N N 37.648 41.170 3.252 37.975 41.718 3.190 C4 YBT 11 YBT C5 C5 C 0 1 N N N N N N 37.329 41.733 6.390 36.990 41.107 6.216 C5 YBT 12 YBT C6 C6 C 0 1 N N N N N N 36.946 40.842 7.535 36.848 39.928 7.164 C6 YBT 13 YBT C7 C7 C 0 1 N N N N N N 39.519 42.592 5.600 38.909 42.688 6.274 C7 YBT 14 YBT C8 C8 C 0 1 N N N N N N 40.212 42.925 6.908 39.465 42.639 7.702 C8 YBT 15 YBT HO1 HO1 H 0 1 N N N N N N 41.505 40.304 4.926 41.854 40.595 4.832 HO1 YBT 16 YBT HO2 HO2 H 0 1 N N N N N N 38.863 37.784 5.467 38.504 38.194 5.449 HO2 YBT 17 YBT HO3 HO3 H 0 1 N N N N N N 37.627 42.788 2.135 37.592 43.475 2.646 HO3 YBT 18 YBT HO4 HO4 H 0 1 N N N N N N 37.859 39.832 8.950 38.006 40.211 8.618 HO4 YBT 19 YBT HO5 HO5 H 0 1 N N N N N N 41.226 41.914 8.231 41.219 41.979 7.563 HO5 YBT 20 YBT H21 H21 H 0 1 N N N N N N 40.329 41.000 3.327 40.531 40.614 3.215 H21 YBT 21 YBT H22 H22 H 0 1 N N N N N N 39.766 39.306 3.123 40.419 42.116 3.706 H22 YBT 22 YBT H31 H31 H 0 1 N N N N N N 37.790 38.516 3.835 37.566 39.279 4.012 H31 YBT 23 YBT H32 H32 H 0 1 N N N N N N 36.720 39.402 4.974 38.894 39.214 3.157 H32 YBT 24 YBT H41 H41 H 0 1 N N N N N N 36.631 41.332 3.640 38.324 41.447 2.308 H41 YBT 25 YBT H42 H42 H 0 1 N N N N N N 37.608 40.484 2.393 37.027 41.449 3.224 H42 YBT 26 YBT H51 H51 H 0 1 N N N N N N 37.428 42.761 6.768 36.409 40.943 5.446 H51 YBT 27 YBT H52 H52 H 0 1 N N N N N N 36.528 41.694 5.637 36.633 41.897 6.673 H52 YBT 28 YBT H61 H61 H 0 1 N N N N N N 36.476 39.928 7.143 36.085 40.089 7.758 H61 YBT 29 YBT H62 H62 H 0 1 N N N N N N 36.233 41.371 8.184 36.649 39.123 6.642 H62 YBT 30 YBT H71 H71 H 0 1 N N N N N N 40.282 42.422 4.827 38.191 43.357 6.249 H71 YBT 31 YBT H72 H72 H 0 1 N N N N N N 38.884 43.442 5.308 39.616 43.025 5.695 H72 YBT 32 YBT H81 H81 H 0 1 N N N N N N 39.462 43.167 7.675 39.815 43.526 7.932 H81 YBT 33 YBT H82 H82 H 0 1 N N N N N N 40.881 43.786 6.765 38.734 42.444 8.324 H82 YBT 34 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_metal_coordination_flag _chem_comp_bond.pdbx_metal_pi_flag YBT Y1 O1 SING N N 1 Y N YBT Y1 O2 SING N N 2 Y N YBT Y1 O4 SING N N 3 Y N YBT Y1 O5 SING N N 4 Y N YBT Y1 N1 SING N N 5 Y N YBT O1 C2 SING N N 6 N N YBT O1 HO1 SING N N 7 N N YBT O2 C3 SING N N 8 N N YBT O2 HO2 SING N N 9 N N YBT O3 C4 SING N N 10 N N YBT O3 HO3 SING N N 11 N N YBT O4 C6 SING N N 12 N N YBT O4 HO4 SING N N 13 N N YBT O5 C8 SING N N 14 N N YBT O5 HO5 SING N N 15 N N YBT N1 C1 SING N N 16 N N YBT N1 C5 SING N N 17 N N YBT N1 C7 SING N N 18 N N YBT C1 C2 SING N N 19 N N YBT C1 C3 SING N N 20 N N YBT C1 C4 SING N N 21 N N YBT C2 H21 SING N N 22 N N YBT C2 H22 SING N N 23 N N YBT C3 H31 SING N N 24 N N YBT C3 H32 SING N N 25 N N YBT C4 H41 SING N N 26 N N YBT C4 H42 SING N N 27 N N YBT C5 C6 SING N N 28 N N YBT C5 H51 SING N N 29 N N YBT C5 H52 SING N N 30 N N YBT C6 H61 SING N N 31 N N YBT C6 H62 SING N N 32 N N YBT C7 C8 SING N N 33 N N YBT C7 H71 SING N N 34 N N YBT C7 H72 SING N N 35 N N YBT C8 H81 SING N N 36 N N YBT C8 H82 SING N N 37 N N # loop_ _pdbx_chem_comp_descriptor.comp_id _pdbx_chem_comp_descriptor.type _pdbx_chem_comp_descriptor.program _pdbx_chem_comp_descriptor.program_version _pdbx_chem_comp_descriptor.descriptor YBT InChI InChI 1.06 "InChI=1S/C8H19NO5.Y/c10-3-1-9(2-4-11)8(5-12,6-13)7-14;/h10-14H,1-7H2;" YBT InChIKey InChI 1.06 KSJVCBJVYSTBHB-UHFFFAOYSA-N YBT SMILES_CANONICAL CACTVS 3.385 "[Y].OCCN(CCO)C(CO)(CO)CO" YBT SMILES CACTVS 3.385 "[Y].OCCN(CCO)C(CO)(CO)CO" YBT SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C1C[O@@H][Y]234[N]1(CC[O@@H]2)C(C[OH]3)(C[OH]4)CO" YBT SMILES "OpenEye OEToolkits" 2.0.7 "C1C[OH][Y]234[N]1(CC[OH]2)C(C[OH]3)(C[OH]4)CO" # _pdbx_chem_comp_atom_coordination.geometry_id 1 _pdbx_chem_comp_atom_coordination.comp_id YBT _pdbx_chem_comp_atom_coordination.atom_id Y1 _pdbx_chem_comp_atom_coordination.number 6 _pdbx_chem_comp_atom_coordination.geometry_calculated "trigonal prism" _pdbx_chem_comp_atom_coordination.geometry_generic "trigonal prismatic" _pdbx_chem_comp_atom_coordination.geometry_abbr TPR _pdbx_chem_comp_atom_coordination.provenance FindGeo _pdbx_chem_comp_atom_coordination.representative_entry_id 1R6Q # loop_ _pdbx_chem_comp_pcm.pcm_id _pdbx_chem_comp_pcm.comp_id _pdbx_chem_comp_pcm.modified_residue_id _pdbx_chem_comp_pcm.type _pdbx_chem_comp_pcm.category _pdbx_chem_comp_pcm.polypeptide_position _pdbx_chem_comp_pcm.comp_id_linking_atom _pdbx_chem_comp_pcm.modified_residue_id_linking_atom _pdbx_chem_comp_pcm.uniprot_specific_ptm_accession _pdbx_chem_comp_pcm.uniprot_generic_ptm_accession _pdbx_chem_comp_pcm.position 1 YBT ASN None "Metal coordination" "Any position" Y1 OD1 ? ? "Amino-acid side chain" 2 YBT GLU None "Metal coordination" "Any position" Y1 OE1 ? ? "Amino-acid side chain" 3 YBT GLU None "Metal coordination" "Any position" Y1 OE2 ? ? "Amino-acid side chain" 4 YBT HIS None "Metal coordination" "Any position" Y1 ND1 ? ? "Amino-acid side chain" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site YBT "Create component" 2002-08-09 RCSB YBT "Modify descriptor" 2023-09-23 RCSB YBT "Other modification" 2026-07-17 RCSB YBT "Other modification" 2026-07-31 RCSB YBT "Other modification" 2026-09-01 RCSB #