data_2WP # _chem_comp.id 2WP _chem_comp.name S-ribosylhomocysteine _chem_comp.type "D-saccharide, alpha linking" _chem_comp.pdbx_type ATOMS _chem_comp.formula "C9 H17 N O6 S" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "(2S)-2-amino-4-({[(2S,3S,4R,5S)-3,4,5-trihydroxytetrahydrofuran-2-yl]methyl}sulfanyl)butanoic acid" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2014-03-13 _chem_comp.pdbx_modified_date 2020-07-17 _chem_comp.pdbx_ambiguous_flag N _chem_comp.pdbx_release_status REL _chem_comp.pdbx_replaced_by ? _chem_comp.pdbx_replaces ? _chem_comp.formula_weight 267.299 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 2WP _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag N _chem_comp.pdbx_ideal_coordinates_details Corina _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 4OJT _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site RCSB # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id 2WP _pdbx_chem_comp_synonyms.name "(2S)-2-amino-4-({[(2S,3S,4R,5S)-3,4,5-trihydroxytetrahydrofuran-2-yl]methyl}sulfanyl)butanoic acid" _pdbx_chem_comp_synonyms.provenance PDB _pdbx_chem_comp_synonyms.type ? # # 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.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 2WP C1 C1 C 0 1 N N S 38.744 -4.139 31.086 -4.030 1.308 -0.462 C1 2WP 1 2WP O1 O1 O 0 1 N Y N 40.188 -4.156 30.997 -4.376 1.974 0.754 O1 2WP 2 2WP C2 C2 C 0 1 N N R 38.293 -3.673 32.510 -4.677 -0.090 -0.495 C2 2WP 3 2WP O2 O2 O 0 1 N N N 39.034 -2.598 32.979 -5.456 -0.309 0.683 O2 2WP 4 2WP C3 C3 C 0 1 N N S 38.585 -4.961 33.298 -3.475 -1.065 -0.538 C3 2WP 5 2WP O3 O3 O 0 1 N N N 39.949 -5.235 33.393 -3.703 -2.194 0.307 O3 2WP 6 2WP C4 C4 C 0 1 N N S 38.024 -6.035 32.321 -2.324 -0.185 0.015 C4 2WP 7 2WP O4 O4 O 0 1 N N N 38.206 -5.461 31.011 -2.606 1.121 -0.533 O4 2WP 8 2WP C5 CE C 0 1 N N N 36.528 -6.279 32.591 -0.970 -0.696 -0.480 C5 2WP 9 2WP N N N 0 1 N N N 35.377 -11.613 31.527 4.470 -1.789 0.026 N 2WP 10 2WP CA CA C 0 1 N N S 36.492 -11.570 32.482 4.357 -0.395 -0.422 CA 2WP 11 2WP CB CB C 0 1 N N N 36.295 -10.347 33.425 3.091 0.229 0.169 CB 2WP 12 2WP CG CG C 0 1 N N N 36.453 -9.054 32.640 1.860 -0.479 -0.400 CG 2WP 13 2WP SD SD S 0 1 N N N 36.262 -7.641 33.801 0.359 0.261 0.300 SD 2WP 14 2WP C C C 0 1 N N N 36.529 -12.880 33.349 5.563 0.381 0.042 C 2WP 15 2WP O O O 0 1 N N N 35.412 -13.384 33.577 6.234 -0.036 0.956 O 2WP 16 2WP OXT OXT O 0 1 N N N 37.638 -13.310 33.726 5.891 1.534 -0.561 OXT 2WP 17 2WP H1 H1 H 0 1 N N N 38.304 -3.479 30.324 -4.370 1.894 -1.316 H1 2WP 18 2WP HO1 H2 H 0 1 N Y N 40.519 -3.267 31.049 -3.999 2.861 0.837 HO1 2WP 19 2WP H2 H3 H 0 1 N N N 37.212 -3.468 32.509 -5.294 -0.204 -1.386 H2 2WP 20 2WP HO2 H4 H 0 1 N Y N 38.725 -2.352 33.843 -6.190 0.312 0.790 HO2 2WP 21 2WP H3 H5 H 0 1 N N N 38.055 -4.978 34.262 -3.266 -1.381 -1.560 H3 2WP 22 2WP HO3 H6 H 0 1 N Y N 40.358 -4.610 33.980 -4.470 -2.726 0.053 HO3 2WP 23 2WP H4 H7 H 0 1 N N N 38.587 -6.973 32.433 -2.349 -0.160 1.104 H4 2WP 24 2WP H51 H8 H 0 1 N N N 36.084 -5.356 32.991 -0.861 -1.748 -0.219 H51 2WP 25 2WP H52 H9 H 0 1 N N N 36.034 -6.543 31.644 -0.912 -0.582 -1.563 H52 2WP 26 2WP H10 H10 H 0 1 N N N 35.369 -10.773 30.985 4.522 -1.843 1.033 H10 2WP 27 2WP H11 H11 H 0 1 N N N 35.488 -12.400 30.920 3.705 -2.346 -0.326 H11 2WP 28 2WP H13 H13 H 0 1 N N N 37.449 -11.466 31.950 4.303 -0.366 -1.510 H13 2WP 29 2WP H14 H14 H 0 1 N N N 35.288 -10.385 33.865 3.104 0.121 1.253 H14 2WP 30 2WP H15 H15 H 0 1 N N N 37.047 -10.380 34.227 3.053 1.288 -0.090 H15 2WP 31 2WP H16 H16 H 0 1 N N N 37.450 -9.021 32.176 1.847 -0.371 -1.484 H16 2WP 32 2WP H17 H17 H 0 1 N N N 35.682 -8.998 31.857 1.898 -1.537 -0.141 H17 2WP 33 2WP H18 H18 H 0 1 N N N 37.515 -14.105 34.231 6.673 1.996 -0.228 H18 2WP 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 2WP O1 C1 SING N N 1 2WP O4 C1 SING N N 2 2WP O4 C4 SING N N 3 2WP C1 C2 SING N N 4 2WP N CA SING N N 5 2WP C4 C5 SING N N 6 2WP C4 C3 SING N N 7 2WP CA C SING N N 8 2WP CA CB SING N N 9 2WP C2 O2 SING N N 10 2WP C2 C3 SING N N 11 2WP C5 SD SING N N 12 2WP CG CB SING N N 13 2WP CG SD SING N N 14 2WP C3 O3 SING N N 15 2WP C O DOUB N N 16 2WP C OXT SING N N 17 2WP C1 H1 SING N N 18 2WP O1 HO1 SING N N 19 2WP C2 H2 SING N N 20 2WP O2 HO2 SING N N 21 2WP C3 H3 SING N N 22 2WP O3 HO3 SING N N 23 2WP C4 H4 SING N N 24 2WP C5 H51 SING N N 25 2WP C5 H52 SING N N 26 2WP N H10 SING N N 27 2WP N H11 SING N N 28 2WP CA H13 SING N N 29 2WP CB H14 SING N N 30 2WP CB H15 SING N N 31 2WP CG H16 SING N N 32 2WP CG H17 SING N N 33 2WP OXT H18 SING N N 34 # # 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 2WP SMILES ACDLabs 12.01 "O=C(O)C(N)CCSCC1OC(O)C(O)C1O" 2WP InChI InChI 1.03 "InChI=1S/C9H17NO6S/c10-4(8(13)14)1-2-17-3-5-6(11)7(12)9(15)16-5/h4-7,9,11-12,15H,1-3,10H2,(H,13,14)/t4-,5+,6+,7+,9-/m0/s1" 2WP InChIKey InChI 1.03 IQFWYNFDWRYSRA-LYNCRYNASA-N 2WP SMILES_CANONICAL CACTVS 3.385 "N[C@@H](CCSC[C@H]1O[C@H](O)[C@H](O)[C@@H]1O)C(O)=O" 2WP SMILES CACTVS 3.385 "N[CH](CCSC[CH]1O[CH](O)[CH](O)[CH]1O)C(O)=O" 2WP SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "C(CSC[C@@H]1[C@H]([C@H]([C@H](O1)O)O)O)[C@@H](C(=O)O)N" 2WP SMILES "OpenEye OEToolkits" 1.7.6 "C(CSCC1C(C(C(O1)O)O)O)C(C(=O)O)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 2WP "SYSTEMATIC NAME" ACDLabs 12.01 ;(2S)-2-amino-4-({[(2S,3S,4R,5S)-3,4,5-trihydroxytetrahydrofuran-2-yl]methyl}sulfanyl)butanoic acid (non-preferred name) ; 2WP "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "(2S)-2-azanyl-4-[[(2S,3S,4R,5S)-3,4,5-tris(oxidanyl)oxolan-2-yl]methylsulfanyl]butanoic acid" # # loop_ _pdbx_chem_comp_feature.comp_id _pdbx_chem_comp_feature.type _pdbx_chem_comp_feature.value _pdbx_chem_comp_feature.source _pdbx_chem_comp_feature.support 2WP "CARBOHYDRATE ISOMER" D PDB ? 2WP "CARBOHYDRATE RING" furanose PDB ? 2WP "CARBOHYDRATE ANOMER" alpha PDB ? 2WP "CARBOHYDRATE PRIMARY CARBONYL GROUP" aldose PDB ? # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site 2WP "Create component" 2014-03-13 RCSB 2WP "Initial release" 2014-03-26 RCSB 2WP "Other modification" 2020-07-03 RCSB 2WP "Modify name" 2020-07-17 RCSB 2WP "Modify synonyms" 2020-07-17 RCSB 2WP "Modify internal type" 2020-07-17 RCSB 2WP "Modify linking type" 2020-07-17 RCSB 2WP "Modify atom id" 2020-07-17 RCSB 2WP "Modify component atom id" 2020-07-17 RCSB 2WP "Modify leaving atom flag" 2020-07-17 RCSB ##