data_PED # _chem_comp.id PED _chem_comp.name PENTANE-3,4-DIOL-5-PHOSPHATE _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C5 H13 O6 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ;OPEN FORM OF 1'-2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE ; _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2001-01-11 _chem_comp.pdbx_modified_date 2024-09-27 _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 200.127 _chem_comp.one_letter_code ? _chem_comp.three_letter_code PED _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag Y _chem_comp.pdbx_ideal_coordinates_details Corina _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 1K3X _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 PED P P P 0 1 N N N N N N 45.270 -15.691 -105.416 -2.567 0.061 -0.043 P PED 1 PED O1P O1P O 0 1 N N N N N N 44.443 -15.097 -106.521 -2.764 -0.106 -1.500 O1P PED 2 PED O2P O2P O 0 1 N N N N N N 45.505 -14.929 -104.155 -2.795 1.604 0.357 O2P PED 3 PED O3P O3P O 0 1 N N N N N N ? ? ? -3.623 -0.860 0.750 O3P PED 4 PED "O5'" O5* O 0 1 N N N N N N 46.701 -16.052 -106.088 -1.069 -0.380 0.351 "O5'" PED 5 PED "C2'" C2* C 0 1 N N N N N N 50.063 -17.545 -107.257 3.844 -0.413 0.375 "C2'" PED 6 PED "C5'" C5* C 0 1 N N N N N N 47.809 -16.475 -105.249 0.093 0.178 -0.265 "C5'" PED 7 PED "C4'" C4* C 0 1 N N R N N N 48.998 -15.631 -105.815 1.346 -0.460 0.339 "C4'" PED 8 PED "O4'" O4* O 0 1 N N N N N N 50.074 -15.796 -104.875 1.377 -1.851 0.013 "O4'" PED 9 PED "C3'" C3* C 0 1 N N S N N N 49.427 -16.156 -107.213 2.591 0.225 -0.229 "C3'" PED 10 PED "C1'" C1* C 0 1 N N N N N N 51.531 -17.569 -106.817 5.088 0.185 -0.284 "C1'" PED 11 PED "O3'" O3* O 0 1 N N N N N N 50.450 -15.256 -107.731 2.560 1.616 0.097 "O3'" PED 12 PED HOP2 2HOP H 0 0 N N N N N N 45.555 -15.533 -103.424 -2.681 1.787 1.299 HOP2 PED 13 PED HOP3 3HOP H 0 0 N N N N N N ? ? ? -4.548 -0.650 0.562 HOP3 PED 14 PED "H2'1" 1H2* H 0 0 N N N N N N 49.494 -18.201 -106.582 3.871 -0.217 1.447 "H2'1" PED 15 PED "H2'2" 2H2* H 0 0 N N N N N N 50.035 -17.879 -108.305 3.823 -1.489 0.203 "H2'2" PED 16 PED "H5'1" 1H5* H 0 0 N N N N N N 47.624 -16.262 -104.186 0.066 -0.018 -1.337 "H5'1" PED 17 PED "H5'2" 2H5* H 0 0 N N N N N N 47.990 -17.560 -105.278 0.114 1.254 -0.093 "H5'2" PED 18 PED "H4'1" 1H4* H 0 0 N N N N N N 48.717 -14.575 -105.938 1.328 -0.341 1.422 "H4'1" PED 19 PED "HO'4" 4HO* H 0 0 N N N N N N 50.900 -15.832 -105.342 1.394 -2.032 -0.936 "HO'4" PED 20 PED "H3'" H3* H 0 1 N N N N N N 48.490 -16.208 -107.787 2.609 0.105 -1.312 "H3'" PED 21 PED "H1'1" 1H1* H 0 0 N N N N N N 52.180 -17.575 -107.705 5.062 -0.012 -1.356 "H1'1" PED 22 PED "H1'2" 2H1* H 0 0 N N N N N N 51.747 -16.677 -106.211 5.109 1.261 -0.112 "H1'2" PED 23 PED "H1'3" 3H1* H 0 0 N N N N N N 51.720 -18.473 -106.219 5.981 -0.270 0.146 "H1'3" PED 24 PED H3T H3T H 0 1 N N N N N N 50.268 -15.060 -108.643 2.543 1.797 1.047 H3T PED 25 # 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 PED P O1P DOUB N N 1 PED P O2P SING N N 2 PED P O3P SING N N 3 PED P "O5'" SING N N 4 PED O2P HOP2 SING N N 5 PED O3P HOP3 SING N N 6 PED "O5'" "C5'" SING N N 7 PED "C2'" "C3'" SING N N 8 PED "C2'" "C1'" SING N N 9 PED "C2'" "H2'1" SING N N 10 PED "C2'" "H2'2" SING N N 11 PED "C5'" "C4'" SING N N 12 PED "C5'" "H5'1" SING N N 13 PED "C5'" "H5'2" SING N N 14 PED "C4'" "O4'" SING N N 15 PED "C4'" "C3'" SING N N 16 PED "C4'" "H4'1" SING N N 17 PED "O4'" "HO'4" SING N N 18 PED "C3'" "O3'" SING N N 19 PED "C3'" "H3'" SING N N 20 PED "C1'" "H1'1" SING N N 21 PED "C1'" "H1'2" SING N N 22 PED "C1'" "H1'3" SING N N 23 PED "O3'" H3T SING N N 24 # 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 PED SMILES ACDLabs 10.04 "O=P(O)(O)OCC(O)C(O)CC" PED InChI InChI 1.03 "InChI=1S/C5H13O6P/c1-2-4(6)5(7)3-11-12(8,9)10/h4-7H,2-3H2,1H3,(H2,8,9,10)/t4-,5+/m0/s1" PED InChIKey InChI 1.03 FQKLTSRHTQGSQZ-CRCLSJGQSA-N PED SMILES_CANONICAL CACTVS 3.385 "CC[C@H](O)[C@H](O)CO[P](O)(O)=O" PED SMILES CACTVS 3.385 "CC[CH](O)[CH](O)CO[P](O)(O)=O" PED SMILES_CANONICAL "OpenEye OEToolkits" 1.7.5 "CC[C@@H]([C@@H](COP(=O)(O)O)O)O" PED SMILES "OpenEye OEToolkits" 1.7.5 "CCC(C(COP(=O)(O)O)O)O" # 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 PED "SYSTEMATIC NAME" ACDLabs 10.04 1,2-dideoxy-5-O-phosphono-D-erythro-pentitol PED "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S)-2,3-dihydroxypentyl] dihydrogen phosphate" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site PED "Create component" 2001-01-11 RCSB PED "Modify descriptor" 2011-06-04 RCSB PED "Modify descriptor" 2012-01-05 RCSB PED "Modify coordinates" 2012-01-05 RCSB PED "Modify synonyms" 2020-06-05 PDBE PED "Modify PCM" 2024-09-27 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id PED _pdbx_chem_comp_synonyms.name ;OPEN FORM OF 1'-2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE ; _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? # 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 PED ALA None "Covalent chemical modification" "Amino-acid backbone" N-terminal "C1'" N ? ? 2 PED CYS None "Covalent chemical modification" "Amino-acid backbone" N-terminal "C1'" N ? ? 3 PED MET None "Covalent chemical modification" "Amino-acid backbone" N-terminal "C1'" N ? ? 4 PED THR None "Covalent chemical modification" "Amino-acid backbone" N-terminal "C1'" N ? ? 5 PED PRO None "Covalent chemical modification" "Amino-acid backbone" N-terminal "C1'" N ? ? 6 PED CYS None "Covalent chemical modification" "Amino-acid side chain" "Any position" "C1'" SG ? ? 7 PED LYS None "Covalent chemical modification" "Amino-acid side chain" "Any position" "C1'" NZ ? ? #