data_YLL # _chem_comp.id YLL _chem_comp.name "(1R,2S,3S,4S,5R,6R)-6-(HYDROXYMETHYL)CYCLOHEXANE-1,2,3,4,5-PENTOL" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C7 H14 O6" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2006-11-29 _chem_comp.pdbx_modified_date 2024-09-27 _chem_comp.pdbx_ambiguous_flag ? _chem_comp.pdbx_release_status REL _chem_comp.pdbx_replaced_by ? _chem_comp.pdbx_replaces ? _chem_comp.formula_weight 194.182 _chem_comp.one_letter_code ? _chem_comp.three_letter_code YLL _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag N _chem_comp.pdbx_ideal_coordinates_details "OpenEye/OEToolkits V1.4.2" _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_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 YLL O5 O5 O 0 1 N N N N N N -1.352 9.226 10.530 2.007 0.293 -0.078 O5 YLL 1 YLL C7 C7 C 0 1 N N R N N N -2.025 10.467 10.259 0.720 0.754 0.341 C7 YLL 2 YLL C5 C5 C 0 1 N N N N N N -2.489 10.510 8.779 0.418 2.115 -0.318 C5 YLL 3 YLL C6 C6 C 0 1 N N N N N N -3.426 9.382 8.366 0.368 1.980 -1.844 C6 YLL 4 YLL O6 O6 O 0 1 N N N N N N -2.805 8.111 8.562 0.078 3.251 -2.391 O6 YLL 5 YLL C4 C4 C 0 1 N N R N N N -1.246 10.624 7.860 -0.884 2.731 0.232 C4 YLL 6 YLL O4 O4 O 0 1 N N N N N N -1.607 10.758 6.486 -2.001 1.942 -0.170 O4 YLL 7 YLL C3 C3 C 0 1 N N S N N N -0.486 11.897 8.299 -0.854 2.832 1.761 C3 YLL 8 YLL O3 O3 O 0 1 N N N N N N 0.682 12.154 7.518 0.168 3.746 2.155 O3 YLL 9 YLL C2 C2 C 0 1 N N N N N N 0.014 11.853 9.737 -0.584 1.466 2.402 C2 YLL 10 YLL O2 O2 O 0 1 N N N N N N 0.611 13.109 10.023 -0.473 1.615 3.818 O2 YLL 11 YLL C1 C1 C 0 1 N N S N N N -1.111 11.629 10.699 0.702 0.827 1.874 C1 YLL 12 YLL OXT OXT O 0 1 N N N N N N -2.115 12.652 10.592 0.811 -0.499 2.399 OXT YLL 13 YLL H5 H5 H 0 1 N N N N N N -1.068 9.200 11.436 1.939 -0.670 -0.156 H5 YLL 14 YLL H7 H7 H 0 1 N N N N N N -2.964 10.568 10.851 0.000 -0.001 0.002 H7 YLL 15 YLL HA HA H 0 1 N N N N N N -3.125 11.418 8.662 1.253 2.793 -0.098 HA YLL 16 YLL H6C1 1H6C H 0 0 N N N N N N -3.787 9.508 7.319 -0.413 1.276 -2.121 H6C1 YLL 17 YLL H6C2 2H6C H 0 0 N N N N N N -4.408 9.447 8.891 1.331 1.635 -2.211 H6C2 YLL 18 YLL H4 H4 H 0 1 N N N N N N -0.629 9.700 7.954 -1.012 3.731 -0.199 H4 YLL 19 YLL H6 H6 H 0 1 N N N N N N -3.389 7.408 8.304 0.026 3.144 -3.357 H6 YLL 20 YLL HB HB H 0 1 N N N N N N -0.845 10.828 5.923 -1.915 1.809 -1.126 HB YLL 21 YLL H3 H3 H 0 1 N N N N N N -1.258 12.690 8.165 -1.804 3.225 2.141 H3 YLL 22 YLL HC HC H 0 1 N N N N N N 1.149 12.936 7.788 0.796 3.789 1.418 HC YLL 23 YLL H2 H2 H 0 1 N N N N N N 0.739 11.013 9.847 -1.430 0.791 2.227 H2 YLL 24 YLL HD HD H 0 1 N N N N N N 1.325 13.251 9.412 -0.333 2.559 3.983 HD YLL 25 YLL HXT HXT H 0 1 N N N N N N -2.337 12.971 11.459 0.039 -0.984 2.072 HXT YLL 26 YLL H1 H1 H 0 1 N N N N N N -0.592 11.525 11.663 1.584 1.364 2.242 H1 YLL 27 # 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 YLL O5 C7 SING N N 1 YLL O5 H5 SING N N 2 YLL C7 C5 SING N N 3 YLL C7 C1 SING N N 4 YLL C7 H7 SING N N 5 YLL C5 C6 SING N N 6 YLL C5 C4 SING N N 7 YLL C5 HA SING N N 8 YLL C6 O6 SING N N 9 YLL C6 H6C1 SING N N 10 YLL C6 H6C2 SING N N 11 YLL O6 H6 SING N N 12 YLL C4 O4 SING N N 13 YLL C4 C3 SING N N 14 YLL C4 H4 SING N N 15 YLL O4 HB SING N N 16 YLL C3 O3 SING N N 17 YLL C3 C2 SING N N 18 YLL C3 H3 SING N N 19 YLL O3 HC SING N N 20 YLL C2 O2 SING N N 21 YLL C2 C1 SING N N 22 YLL C2 H2 SING N N 23 YLL O2 HD SING N N 24 YLL C1 H1 SING N N 25 YLL C1 OXT SING N N 26 YLL OXT HXT SING N N 27 # 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 YLL SMILES ACDLabs 10.04 "OC1C(C(O)C(O)C(O)C1O)CO" YLL SMILES_CANONICAL CACTVS 3.341 "OC[C@@H]1[C@@H](O)[C@H](O)[C@@H](O)[C@@H](O)[C@@H]1O" YLL SMILES CACTVS 3.341 "OC[CH]1[CH](O)[CH](O)[CH](O)[CH](O)[CH]1O" YLL SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C(C1[C@H]([C@@H](C([C@H]([C@@H]1O)O)O)O)O)O" YLL SMILES "OpenEye OEToolkits" 1.5.0 "C(C1C(C(C(C(C1O)O)O)O)O)O" YLL InChI InChI 1.03 "InChI=1S/C7H14O6/c8-1-2-3(9)5(11)7(13)6(12)4(2)10/h2-13H,1H2/t2-,3-,4-,5+,6+,7-/m1/s1" YLL InChIKey InChI 1.03 QFYQIWDMMSKNFF-NYLBLOMBSA-N # loop_ _pdbx_chem_comp_identifier.comp_id _pdbx_chem_comp_identifier.type _pdbx_chem_comp_identifier.program _pdbx_chem_comp_identifier.program_version _pdbx_chem_comp_identifier.identifier YLL "SYSTEMATIC NAME" ACDLabs 10.04 "(1R,2S,3S,4S,5R,6R)-6-(hydroxymethyl)cyclohexane-1,2,3,4,5-pentol" YLL "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "(1R,2S,4S,5R)-6-(hydroxymethyl)cyclohexane-1,2,3,4,5-pentol" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site YLL "Create component" 2006-11-29 RCSB YLL "Modify descriptor" 2011-06-04 RCSB YLL "Modify PCM" 2024-09-27 PDBE # 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.position _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 1 YLL GLU None "Covalent chemical modification" "Amino-acid side chain" "Any position" C1 OE1 ? ? 2 YLL GLU None "Covalent chemical modification" "Amino-acid side chain" "Any position" C1 OE2 ? ? 3 YLL GLU None "Covalent chemical modification" "Amino-acid side chain" "Any position" C3 OE2 ? ? #