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 ? ? 
# 
