data_HPD # _chem_comp.id HPD _chem_comp.name 1-HYDROXY-PENTANE-3,4-DIOL-5-PHOSPHATE _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C5 H13 O7 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ;OPEN FORM OF 2'-DEOXY-RIBOFURANOSE-5'-PHOSPHATE ; _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2001-06-20 _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 216.126 _chem_comp.one_letter_code ? _chem_comp.three_letter_code HPD _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 1JCL _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 HPD P P P 0 1 N N N N N N 29.504 -3.470 19.268 0.062 -0.056 -2.927 P HPD 1 HPD "O5'" O5* O 0 1 N N N N N N 28.565 -2.165 19.123 -0.617 0.499 -1.578 "O5'" HPD 2 HPD O1P O1P O 0 1 N N N N N N 30.800 -3.234 18.567 -0.053 -1.531 -2.966 O1P HPD 3 HPD O2P O2P O 0 1 N N N N N N 28.694 -4.576 18.586 -0.687 0.574 -4.205 O2P HPD 4 HPD O3P O3P O 0 1 N N N N N N 29.727 -3.686 20.755 1.616 0.361 -2.957 O3P HPD 5 HPD "C5'" C5* C 0 1 N N N N N N 29.114 -0.880 19.469 0.087 -0.092 -0.486 "C5'" HPD 6 HPD "O4'" O4* O 0 1 N N N N N N 27.351 -0.339 20.975 -1.889 0.024 0.898 "O4'" HPD 7 HPD "O3'" O3* O 0 1 N N N N N N 28.922 1.940 18.609 1.621 0.135 1.938 "O3'" HPD 8 HPD "C1'" C1* C 0 1 N N N N N N 27.228 3.956 20.078 0.399 -0.382 4.492 "C1'" HPD 9 HPD "O1'" O1* O 0 1 N N N N N N 28.261 4.280 20.947 -0.160 0.075 5.725 "O1'" HPD 10 HPD "C3'" C3* C 0 1 N N S N N N 28.285 1.594 19.820 0.243 -0.237 2.003 "C3'" HPD 11 HPD "C4'" C4* C 0 1 N N R N N N 27.945 0.079 19.765 -0.511 0.397 0.833 "C4'" HPD 12 HPD "C2'" C2* C 0 1 N N N N N N 27.005 2.450 19.973 -0.356 0.252 3.323 "C2'" HPD 13 HPD HOP2 2HOP H 0 0 N N N N N N 29.246 -5.344 18.671 -0.250 0.216 -4.990 HOP2 HPD 14 HPD HOP3 3HOP H 0 0 N N N N N N 30.279 -4.454 20.840 1.647 1.327 -2.930 HOP3 HPD 15 HPD "H5'1" 1H5* H 0 0 N N N N N N 29.846 -0.937 20.307 1.138 0.191 -0.535 "H5'1" HPD 16 HPD "H5'2" 2H5* H 0 0 N N N N N N 29.807 -0.485 18.690 0.001 -1.177 -0.543 "H5'2" HPD 17 HPD "HO'4" 4HO* H 0 0 N N N N N N 26.630 0.252 21.157 -1.921 -0.940 0.844 "HO'4" HPD 18 HPD "HO'3" 3HO* H 0 0 N N N N N N 29.129 2.866 18.642 1.653 1.100 1.993 "HO'3" HPD 19 HPD "H1'1" 1H1* H 0 0 N N N N N N 26.286 4.482 20.359 1.450 -0.098 4.443 "H1'1" HPD 20 HPD "H1'2" 2H1* H 0 0 N N N N N N 27.392 4.408 19.072 0.313 -1.467 4.435 "H1'2" HPD 21 HPD "HO'1" 1HO* H 0 0 N N N N N N 28.399 5.217 21.012 0.342 -0.347 6.434 "HO'1" HPD 22 HPD "H3'" H3* H 0 1 N N N N N N 28.942 1.789 20.698 0.157 -1.322 1.945 "H3'" HPD 23 HPD "H4'" H4* H 0 1 N N N N N N 27.252 0.008 18.893 -0.425 1.482 0.891 "H4'" HPD 24 HPD "H2'1" 1H2* H 0 0 N N N N N N 26.408 2.091 20.844 -1.407 -0.031 3.372 "H2'1" HPD 25 HPD "H2'2" 2H2* H 0 0 N N N N N N 26.295 2.226 19.142 -0.269 1.337 3.380 "H2'2" HPD 26 # 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 HPD P "O5'" SING N N 1 HPD P O1P DOUB N N 2 HPD P O2P SING N N 3 HPD P O3P SING N N 4 HPD "O5'" "C5'" SING N N 5 HPD O2P HOP2 SING N N 6 HPD O3P HOP3 SING N N 7 HPD "C5'" "C4'" SING N N 8 HPD "C5'" "H5'1" SING N N 9 HPD "C5'" "H5'2" SING N N 10 HPD "O4'" "C4'" SING N N 11 HPD "O4'" "HO'4" SING N N 12 HPD "O3'" "C3'" SING N N 13 HPD "O3'" "HO'3" SING N N 14 HPD "C1'" "O1'" SING N N 15 HPD "C1'" "C2'" SING N N 16 HPD "C1'" "H1'1" SING N N 17 HPD "C1'" "H1'2" SING N N 18 HPD "O1'" "HO'1" SING N N 19 HPD "C3'" "C4'" SING N N 20 HPD "C3'" "C2'" SING N N 21 HPD "C3'" "H3'" SING N N 22 HPD "C4'" "H4'" SING N N 23 HPD "C2'" "H2'1" SING N N 24 HPD "C2'" "H2'2" SING N N 25 # 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 HPD SMILES ACDLabs 10.04 "O=P(O)(O)OCC(O)C(O)CCO" HPD SMILES_CANONICAL CACTVS 3.341 "OCC[C@H](O)[C@H](O)CO[P](O)(O)=O" HPD SMILES CACTVS 3.341 "OCC[CH](O)[CH](O)CO[P](O)(O)=O" HPD SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C(CO)[C@@H]([C@@H](COP(=O)(O)O)O)O" HPD SMILES "OpenEye OEToolkits" 1.5.0 "C(CO)C(C(COP(=O)(O)O)O)O" HPD InChI InChI 1.03 "InChI=1S/C5H13O7P/c6-2-1-4(7)5(8)3-12-13(9,10)11/h4-8H,1-3H2,(H2,9,10,11)/t4-,5+/m0/s1" HPD InChIKey InChI 1.03 YCHBTVQJICBXEI-CRCLSJGQSA-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 HPD "SYSTEMATIC NAME" ACDLabs 10.04 2-deoxy-5-O-phosphono-D-erythro-pentitol HPD "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S)-2,3,5-trihydroxypentyl] 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 HPD "Create component" 2001-06-20 RCSB HPD "Modify descriptor" 2011-06-04 RCSB HPD "Modify synonyms" 2020-06-05 PDBE HPD "Modify PCM" 2024-09-27 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id HPD _pdbx_chem_comp_synonyms.name ;OPEN FORM OF 2'-DEOXY-RIBOFURANOSE-5'-PHOSPHATE ; _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? # _pdbx_chem_comp_pcm.pcm_id 1 _pdbx_chem_comp_pcm.comp_id HPD _pdbx_chem_comp_pcm.modified_residue_id LYS _pdbx_chem_comp_pcm.type None _pdbx_chem_comp_pcm.category "Covalent chemical modification" _pdbx_chem_comp_pcm.position "Amino-acid side chain" _pdbx_chem_comp_pcm.polypeptide_position "Any position" _pdbx_chem_comp_pcm.comp_id_linking_atom "C1'" _pdbx_chem_comp_pcm.modified_residue_id_linking_atom NZ _pdbx_chem_comp_pcm.uniprot_specific_ptm_accession ? _pdbx_chem_comp_pcm.uniprot_generic_ptm_accession ? #