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 ? ?
#
_pdbe_chem_comp_synonyms.comp_id PED
_pdbe_chem_comp_synonyms.name "OPEN FORM OF 1'-2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE"
_pdbe_chem_comp_synonyms.provenance wwPDB
_pdbe_chem_comp_synonyms.type ?
#
loop_
_software.name
_software.version
_software.description
rdkit 2025.03.3 'Core functionality.'
pdbeccdutils 1.0.0 'Wrapper to provide 2D templates and molecular fragments.'
#
loop_
_pdbe_chem_comp_atom_depiction.comp_id
_pdbe_chem_comp_atom_depiction.atom_id
_pdbe_chem_comp_atom_depiction.element
_pdbe_chem_comp_atom_depiction.model_Cartn_x
_pdbe_chem_comp_atom_depiction.model_Cartn_y
_pdbe_chem_comp_atom_depiction.pdbx_ordinal
PED P P 5.104 -0.233 1
PED O1P O 3.805 -0.983 2
PED O2P O 4.354 1.067 3
PED O3P O 5.854 -1.532 4
PED "O5'" O 6.404 0.517 5
PED "C2'" C 10.301 -1.732 6
PED "C5'" C 7.702 -0.233 7
PED "C4'" C 9.002 0.517 8
PED "O4'" O 9.002 2.018 9
PED "C3'" C 10.301 -0.233 10
PED "C1'" C 11.600 -2.482 11
PED "O3'" O 11.600 0.517 12
#
loop_
_pdbe_chem_comp_bond_depiction.comp_id
_pdbe_chem_comp_bond_depiction.atom_id_1
_pdbe_chem_comp_bond_depiction.atom_id_2
_pdbe_chem_comp_bond_depiction.value_order
_pdbe_chem_comp_bond_depiction.bond_dir
_pdbe_chem_comp_bond_depiction.pdbx_ordinal
PED P O1P DOUBLE NONE 1
PED P O2P SINGLE NONE 2
PED P O3P SINGLE NONE 3
PED P "O5'" SINGLE NONE 4
PED "O5'" "C5'" SINGLE NONE 5
PED "C2'" "C3'" SINGLE NONE 6
PED "C2'" "C1'" SINGLE NONE 7
PED "C5'" "C4'" SINGLE NONE 8
PED "C4'" "O4'" SINGLE BEGINWEDGE 9
PED "C4'" "C3'" SINGLE NONE 10
PED "C3'" "O3'" SINGLE BEGINWEDGE 11
#
_pdbe_chem_comp_substructure.comp_id PED
_pdbe_chem_comp_substructure.substructure_name phosphate
_pdbe_chem_comp_substructure.id F1
_pdbe_chem_comp_substructure.substructure_type fragment
_pdbe_chem_comp_substructure.substructure_smiles O=P(O)(O)O
_pdbe_chem_comp_substructure.substructure_inchis InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4)
_pdbe_chem_comp_substructure.substructure_inchikeys NBIIXXVUZAFLBC-UHFFFAOYSA-N
#
loop_
_pdbe_chem_comp_substructure_mapping.comp_id
_pdbe_chem_comp_substructure_mapping.atom_id
_pdbe_chem_comp_substructure_mapping.substructure_id
_pdbe_chem_comp_substructure_mapping.substructure_ordinal
PED O2P F1 1
PED P F1 1
PED O1P F1 1
PED O3P F1 1
PED "O5'" F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id PED
_pdbe_chem_comp_rdkit_properties.exactmw 200.045
_pdbe_chem_comp_rdkit_properties.amw 200.127
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 6
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 4
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 10
_pdbe_chem_comp_rdkit_properties.NumHBD 4
_pdbe_chem_comp_rdkit_properties.NumHBA 6
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 12
_pdbe_chem_comp_rdkit_properties.NumAtoms 25
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 7
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 1
_pdbe_chem_comp_rdkit_properties.NumRings 0
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 0
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 0
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumSpiroAtoms 0
_pdbe_chem_comp_rdkit_properties.NumBridgeheadAtoms 0
_pdbe_chem_comp_rdkit_properties.NumAtomStereoCenters 2
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 88.650
_pdbe_chem_comp_rdkit_properties.tpsa 107.220
_pdbe_chem_comp_rdkit_properties.CrippenClogP -0.773
_pdbe_chem_comp_rdkit_properties.CrippenMR 40.301
_pdbe_chem_comp_rdkit_properties.chi0v 6.291
_pdbe_chem_comp_rdkit_properties.chi1v 3.803
_pdbe_chem_comp_rdkit_properties.chi2v 0.885
_pdbe_chem_comp_rdkit_properties.chi3v 0.885
_pdbe_chem_comp_rdkit_properties.chi4v 0.395
_pdbe_chem_comp_rdkit_properties.chi0n 18.397
_pdbe_chem_comp_rdkit_properties.chi1n 8.476
_pdbe_chem_comp_rdkit_properties.chi2n 0.570
_pdbe_chem_comp_rdkit_properties.chi3n 0.570
_pdbe_chem_comp_rdkit_properties.chi4n 0.200
_pdbe_chem_comp_rdkit_properties.hallKierAlpha 0.030
_pdbe_chem_comp_rdkit_properties.kappa1 2.535
_pdbe_chem_comp_rdkit_properties.kappa2 4.912
_pdbe_chem_comp_rdkit_properties.kappa3 5.651
_pdbe_chem_comp_rdkit_properties.Phi 1.037
#
loop_
_pdbe_chem_comp_external_mappings.comp_id
_pdbe_chem_comp_external_mappings.source
_pdbe_chem_comp_external_mappings.resource
_pdbe_chem_comp_external_mappings.resource_id
PED UniChem ZINC ZINC000015614168
PED UniChem PubChem 657102
#
loop_
_pdbe_chem_comp_rdkit_conformer.comp_id
_pdbe_chem_comp_rdkit_conformer.atom_id
_pdbe_chem_comp_rdkit_conformer.Cartn_x_rdkit
_pdbe_chem_comp_rdkit_conformer.Cartn_y_rdkit
_pdbe_chem_comp_rdkit_conformer.Cartn_z_rdkit
_pdbe_chem_comp_rdkit_conformer.rdkit_method
_pdbe_chem_comp_rdkit_conformer.rdkit_ordinal
PED P 3.430 0.381 0.005 ETKDGv3 1
PED O1P 3.478 1.664 0.804 ETKDGv3 2
PED O2P 4.908 -0.425 0.171 ETKDGv3 3
PED O3P 3.175 0.740 -1.630 ETKDGv3 4
PED "O5'" 2.183 -0.624 0.592 ETKDGv3 5
PED "C2'" -2.006 -0.156 -0.748 ETKDGv3 6
PED "C5'" 0.948 0.005 0.344 ETKDGv3 7
PED "C4'" -0.186 -0.870 0.913 ETKDGv3 8
PED "O4'" 0.049 -1.156 2.270 ETKDGv3 9
PED "C3'" -1.596 -0.250 0.736 ETKDGv3 10
PED "C1'" -3.489 0.173 -0.910 ETKDGv3 11
PED "O3'" -1.635 1.025 1.328 ETKDGv3 12
PED HOP2 4.807 -1.248 -0.371 ETKDGv3 13
PED HOP3 3.973 1.258 -1.903 ETKDGv3 14
PED "H2'1" -1.412 0.631 -1.260 ETKDGv3 15
PED "H2'2" -1.808 -1.126 -1.254 ETKDGv3 16
PED "H5'1" 0.795 0.119 -0.751 ETKDGv3 17
PED "H5'2" 0.910 1.006 0.831 ETKDGv3 18
PED "H4'1" -0.166 -1.840 0.369 ETKDGv3 19
PED "HO'4" 0.083 -0.293 2.760 ETKDGv3 20
PED "H3'" -2.310 -0.936 1.253 ETKDGv3 21
PED "H1'1" -3.716 1.172 -0.481 ETKDGv3 22
PED "H1'2" -3.748 0.190 -1.990 ETKDGv3 23
PED "H1'3" -4.114 -0.595 -0.409 ETKDGv3 24
PED H3T -2.552 1.154 1.688 ETKDGv3 25
#