data_PPC # _chem_comp.id PPC _chem_comp.name "1-O-[(R)-hydroxy(phosphonomethyl)phosphoryl]-5-O-phosphono-alpha-D-ribofuranose" _chem_comp.type D-saccharide _chem_comp.pdbx_type ATOMS _chem_comp.formula "C6 H15 O13 P3" _chem_comp.mon_nstd_parent_comp_id RIB _chem_comp.pdbx_synonyms ;5-PHOSPHORIBOSYL-1-(BETA-METHYLENE) PYROPHOSPHATE; 1-O-[(R)-hydroxy(phosphonomethyl)phosphoryl]-5-O-phosphono-alpha-D-ribose; 1-O-[(R)-hydroxy(phosphonomethyl)phosphoryl]-5-O-phosphono-D-ribose; 1-O-[(R)-hydroxy(phosphonomethyl)phosphoryl]-5-O-phosphono-ribose ; _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 1999-07-08 _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 388.097 _chem_comp.one_letter_code ? _chem_comp.three_letter_code PPC _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag N _chem_comp.pdbx_ideal_coordinates_details ? _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 1QPR _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site RCSB # # loop_ _pdbx_chem_comp_synonyms.ordinal _pdbx_chem_comp_synonyms.comp_id _pdbx_chem_comp_synonyms.name _pdbx_chem_comp_synonyms.provenance _pdbx_chem_comp_synonyms.type 1 PPC "5-PHOSPHORIBOSYL-1-(BETA-METHYLENE) PYROPHOSPHATE" PDB ? 2 PPC "1-O-[(R)-hydroxy(phosphonomethyl)phosphoryl]-5-O-phosphono-alpha-D-ribose" PDB ? 3 PPC "1-O-[(R)-hydroxy(phosphonomethyl)phosphoryl]-5-O-phosphono-D-ribose" PDB ? 4 PPC "1-O-[(R)-hydroxy(phosphonomethyl)phosphoryl]-5-O-phosphono-ribose" PDB ? # # 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 PPC C1 C1 C 0 1 N N R 42.272 69.310 12.247 1.482 -0.779 0.113 C1 PPC 1 PPC C2 C2 C 0 1 N N R 41.963 69.833 10.954 2.866 -0.601 -0.550 C2 PPC 2 PPC C3 C3 C 0 1 N N S 40.596 69.753 10.788 2.555 0.122 -1.879 C3 PPC 3 PPC C4 C4 C 0 1 N N R 40.140 68.612 11.392 1.020 0.296 -1.865 C4 PPC 4 PPC C5 C5 C 0 1 N N N 40.467 67.233 10.586 0.443 0.109 -3.270 C5 PPC 5 PPC O1 O1 O 0 1 N N N 42.504 70.341 13.399 1.227 0.290 1.026 O1 PPC 6 PPC O2 O2 O 0 1 N N N 42.777 71.244 10.568 3.718 0.200 0.269 O2 PPC 7 PPC O3 O3 O 0 1 N N N 39.829 70.840 11.569 3.203 1.395 -1.919 O3 PPC 8 PPC P P P 0 1 N N N 38.250 65.797 11.485 -1.518 -0.000 -4.720 P PPC 9 PPC O1P O1P O 0 1 N N N 37.588 66.854 12.137 -3.125 0.093 -4.733 O1P PPC 10 PPC O2P O2P O 0 1 N N N 37.330 64.977 10.856 -0.905 1.145 -5.669 O2P PPC 11 PPC O3P O3P O 0 1 N N N 38.918 65.113 12.477 -1.098 -1.330 -5.217 O3P PPC 12 PPC PA PA P 0 1 N N R 42.123 69.862 15.115 0.282 -0.303 2.186 PA PPC 13 PPC O1A O1A O 0 1 N N N 40.694 69.112 15.041 -1.090 -0.840 1.537 O1A PPC 14 PPC O2A O2A O 0 1 N N N 43.201 68.871 15.737 0.976 -1.420 2.865 O2A PPC 15 PPC PB PB P 0 1 N N N 40.676 72.276 15.840 -1.160 0.334 4.710 PB PPC 16 PPC O1B O1B O 0 1 N N N 40.572 72.805 14.104 -1.489 1.491 5.780 O1B PPC 17 PPC O2B O2B O 0 1 N N N 40.856 73.670 16.813 -0.466 -0.782 5.389 O2B PPC 18 PPC O3B O3B O 0 1 N N N 39.175 71.595 16.241 -2.533 -0.202 4.061 O3B PPC 19 PPC C3A C3A C 0 1 N N N 41.990 71.197 16.171 -0.089 1.006 3.397 C3A PPC 20 PPC O5 O5 O 0 1 N N N 39.192 66.356 10.220 -0.981 0.204 -3.216 O5 PPC 21 PPC O4 O4 O 0 1 N N N 41.070 68.598 12.591 0.541 -0.743 -0.981 O4 PPC 22 PPC H1 H1 H 0 1 N N N 43.231 68.746 12.171 1.428 -1.738 0.628 H1 PPC 23 PPC H2 H2 H 0 1 N N N 42.390 69.212 10.132 3.325 -1.571 -0.741 H2 PPC 24 PPC H3 H3 H 0 1 N N N 40.430 69.825 9.687 2.863 -0.488 -2.728 H3 PPC 25 PPC H4 H4 H 0 1 N N N 39.034 68.632 11.532 0.755 1.279 -1.474 H4 PPC 26 PPC H51 H51 H 0 1 N N N 41.060 67.453 9.668 0.834 0.884 -3.929 H51 PPC 27 PPC H52 H52 H 0 1 N N N 41.207 66.620 11.152 0.728 -0.870 -3.652 H52 PPC 28 PPC HO2 HO2 H 0 1 N Y N 42.571 71.591 9.708 3.877 -0.300 1.081 HO2 PPC 29 PPC HO3 HO3 H 0 1 N Y N 38.887 70.784 11.454 4.155 1.225 -1.895 HO3 PPC 30 PPC HO1P HO1P H 0 0 N N N 38.219 67.417 12.568 -3.405 -0.034 -5.650 HO1P PPC 31 PPC HO2P HO2P H 0 0 N N N 37.776 64.263 10.415 -1.202 1.993 -5.311 HO2P PPC 32 PPC HO1A HO1A H 0 0 N N N 40.495 68.862 15.935 -1.510 -0.083 1.106 HO1A PPC 33 PPC HO1B HO1B H 0 0 N N N 40.472 72.030 13.563 -2.056 1.095 6.455 HO1B PPC 34 PPC HO3B HO3B H 0 0 N N N 39.229 71.318 17.148 -2.952 0.554 3.630 HO3B PPC 35 PPC H3A1 H3A1 H 0 0 N N N 41.939 70.845 17.227 0.839 1.370 3.836 H3A1 PPC 36 PPC H3A2 H3A2 H 0 0 N N N 42.951 71.761 16.197 -0.601 1.829 2.897 H3A2 PPC 37 # # 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 PPC C1 C2 SING N N 1 PPC C1 O1 SING N N 2 PPC C1 O4 SING N N 3 PPC C1 H1 SING N N 4 PPC C2 C3 SING N N 5 PPC C2 O2 SING N N 6 PPC C2 H2 SING N N 7 PPC C3 C4 SING N N 8 PPC C3 O3 SING N N 9 PPC C3 H3 SING N N 10 PPC C4 C5 SING N N 11 PPC C4 O4 SING N N 12 PPC C4 H4 SING N N 13 PPC C5 O5 SING N N 14 PPC C5 H51 SING N N 15 PPC C5 H52 SING N N 16 PPC O1 PA SING N N 17 PPC O2 HO2 SING N N 18 PPC O3 HO3 SING N N 19 PPC P O1P SING N N 20 PPC P O2P SING N N 21 PPC P O3P DOUB N N 22 PPC P O5 SING N N 23 PPC O1P HO1P SING N N 24 PPC O2P HO2P SING N N 25 PPC PA O1A SING N N 26 PPC PA O2A DOUB N N 27 PPC PA C3A SING N N 28 PPC O1A HO1A SING N N 29 PPC PB O1B SING N N 30 PPC PB O2B DOUB N N 31 PPC PB O3B SING N N 32 PPC PB C3A SING N N 33 PPC O1B HO1B SING N N 34 PPC O3B HO3B SING N N 35 PPC C3A H3A1 SING N N 36 PPC C3A H3A2 SING N N 37 # # 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 PPC SMILES ACDLabs 10.04 "O=P(OC1OC(C(O)C1O)COP(=O)(O)O)(O)CP(=O)(O)O" PPC SMILES_CANONICAL CACTVS 3.341 "O[C@H]1[C@@H](O)[C@H](O[C@@H]1CO[P](O)(O)=O)O[P@@](O)(=O)C[P](O)(O)=O" PPC SMILES CACTVS 3.341 "O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(O)=O)O[P](O)(=O)C[P](O)(O)=O" PPC SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C([C@@H]1[C@H]([C@H]([C@H](O1)O[P@@](=O)(CP(=O)(O)O)O)O)O)OP(=O)(O)O" PPC SMILES "OpenEye OEToolkits" 1.5.0 "C(C1C(C(C(O1)OP(=O)(CP(=O)(O)O)O)O)O)OP(=O)(O)O" PPC InChI InChI 1.03 "InChI=1S/C6H15O13P3/c7-4-3(1-17-22(14,15)16)18-6(5(4)8)19-21(12,13)2-20(9,10)11/h3-8H,1-2H2,(H,12,13)(H2,9,10,11)(H2,14,15,16)/t3-,4-,5-,6-/m1/s1" PPC InChIKey InChI 1.03 JFMKBQDEISBIPL-KVTDHHQDSA-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 PPC "SYSTEMATIC NAME" ACDLabs 10.04 "1-O-[(R)-hydroxy(phosphonomethyl)phosphoryl]-5-O-phosphono-alpha-D-ribofuranose" PPC "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[[(2R,3R,4S,5R)-3,4-dihydroxy-5-(phosphonooxymethyl)oxolan-2-yl]oxy-hydroxy-phosphoryl]methylphosphonic acid" # _pdbx_chem_comp_related.comp_id PPC _pdbx_chem_comp_related.related_comp_id RIB _pdbx_chem_comp_related.relationship_type "Carbohydrate core" _pdbx_chem_comp_related.details ? # # loop_ _pdbx_chem_comp_atom_related.ordinal _pdbx_chem_comp_atom_related.comp_id _pdbx_chem_comp_atom_related.atom_id _pdbx_chem_comp_atom_related.related_comp_id _pdbx_chem_comp_atom_related.related_atom_id _pdbx_chem_comp_atom_related.related_type 1 PPC C1 RIB C1 "Carbohydrate core" 2 PPC C2 RIB C2 "Carbohydrate core" 3 PPC C3 RIB C3 "Carbohydrate core" 4 PPC C4 RIB C4 "Carbohydrate core" 5 PPC C5 RIB C5 "Carbohydrate core" 6 PPC O1 RIB O1 "Carbohydrate core" 7 PPC O2 RIB O2 "Carbohydrate core" 8 PPC O3 RIB O3 "Carbohydrate core" 9 PPC O4 RIB O4 "Carbohydrate core" 10 PPC O5 RIB O5 "Carbohydrate core" 11 PPC H1 RIB H1 "Carbohydrate core" 12 PPC H2 RIB H2 "Carbohydrate core" 13 PPC H3 RIB H3 "Carbohydrate core" 14 PPC H4 RIB H4 "Carbohydrate core" 15 PPC H51 RIB H51 "Carbohydrate core" 16 PPC H52 RIB H52 "Carbohydrate core" 17 PPC HO2 RIB HO2 "Carbohydrate core" 18 PPC HO3 RIB HO3 "Carbohydrate core" # # 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 PPC "CARBOHYDRATE ISOMER" D PDB ? PPC "CARBOHYDRATE RING" furanose PDB ? PPC "CARBOHYDRATE ANOMER" alpha PDB ? PPC "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 PPC "Create component" 1999-07-08 RCSB PPC "Modify descriptor" 2011-06-04 RCSB PPC "Other modification" 2020-07-03 RCSB PPC "Modify parent residue" 2020-07-17 RCSB PPC "Modify name" 2020-07-17 RCSB PPC "Modify synonyms" 2020-07-17 RCSB PPC "Modify internal type" 2020-07-17 RCSB PPC "Modify linking type" 2020-07-17 RCSB PPC "Modify leaving atom flag" 2020-07-17 RCSB ##