data_UPS
#
_chem_comp.id UPS
_chem_comp.name "2'-deoxy-5'-O-thiophosphonouridine"
_chem_comp.type "DNA linking"
_chem_comp.pdbx_type ATOMN
_chem_comp.formula "C9 H13 N2 O7 P S"
_chem_comp.mon_nstd_parent_comp_id DU
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2009-02-10
_chem_comp.pdbx_modified_date 2011-06-04
_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 324.247
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code UPS
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag N
_chem_comp.pdbx_ideal_coordinates_details Corina
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code 3G3C
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site PDBJ
#
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
UPS OP3 O3P O 0 1 N Y N N N N 3.477 3.404 -32.752 3.365 -2.220 0.794 OP3 UPS 1
UPS P P P 0 1 N N N N N N 3.979 1.981 -33.280 3.769 -1.017 -0.197 P UPS 2
UPS S1P S1P S 0 1 N N N N N N 4.054 2.071 -34.758 4.978 0.114 0.659 S1P UPS 3
UPS OP2 O2P O 0 1 N N N N N N 3.146 0.920 -32.675 4.448 -1.620 -1.526 OP2 UPS 4
UPS "O5'" "O5'" O 0 1 N N N N N N 5.450 1.878 -32.657 2.449 -0.186 -0.598 "O5'" UPS 5
UPS "C5'" "C5'" C 0 1 N N N N N N 6.564 2.213 -33.457 1.800 0.722 0.294 "C5'" UPS 6
UPS "C4'" "C4'" C 0 1 N N R N N N 7.829 2.058 -32.656 0.584 1.338 -0.400 "C4'" UPS 7
UPS "O4'" "O4'" O 0 1 N N N N N N 7.595 2.620 -31.349 -0.448 0.344 -0.583 "O4'" UPS 8
UPS "C1'" "C1'" C 0 1 N N R N N N 8.557 2.048 -30.496 -1.670 1.092 -0.764 "C1'" UPS 9
UPS N1 N1 N 0 1 N N N N N N 8.188 2.333 -29.040 -2.832 0.249 -0.474 N1 UPS 10
UPS C2 C2 C 0 1 N N N N N N 9.148 2.884 -28.185 -2.911 -0.395 0.704 C2 UPS 11
UPS O2 O2 O 0 1 N N N N N N 10.293 3.143 -28.526 -2.015 -0.270 1.517 O2 UPS 12
UPS N3 N3 N 0 1 N N N N N N 8.728 3.127 -26.889 -3.968 -1.176 0.997 N3 UPS 13
UPS C4 C4 C 0 1 N N N N N N 7.458 2.875 -26.372 -4.970 -1.325 0.107 C4 UPS 14
UPS O4 O4 O 0 1 N N N N N N 7.226 3.135 -25.191 -5.926 -2.030 0.371 O4 UPS 15
UPS C5 C5 C 0 1 N N N N N N 6.511 2.300 -27.311 -4.899 -0.653 -1.137 C5 UPS 16
UPS C6 C6 C 0 1 N N N N N N 6.901 2.065 -28.578 -3.830 0.128 -1.402 C6 UPS 17
UPS "C2'" "C2'" C 0 1 N N N N N N 8.630 0.587 -30.941 -1.578 2.250 0.255 "C2'" UPS 18
UPS "C3'" "C3'" C 0 1 N N S N N N 8.288 0.616 -32.438 -0.061 2.415 0.499 "C3'" UPS 19
UPS "O3'" "O3'" O 0 1 N N N N N N 9.402 0.318 -33.334 0.370 3.720 0.106 "O3'" UPS 20
UPS HOP3 HO3P H 0 0 N Y N N N N 3.377 3.375 -31.808 2.737 -2.849 0.413 HOP3 UPS 21
UPS HOP2 HO2P H 0 0 N N N N N N 2.967 0.249 -33.323 5.250 -2.134 -1.360 HOP2 UPS 22
UPS "H5'" "H5'" H 0 1 N N N N N N 6.601 1.545 -34.330 1.476 0.185 1.186 "H5'" UPS 23
UPS "H5'A" "H5'A" H 0 0 N N N N N N 6.471 3.256 -33.793 2.495 1.512 0.578 "H5'A" UPS 24
UPS "H4'" "H4'" H 0 1 N N N N N N 8.616 2.563 -33.235 0.873 1.768 -1.360 "H4'" UPS 25
UPS "H1'" "H1'" H 0 1 N N N N N N 9.572 2.468 -30.560 -1.729 1.482 -1.780 "H1'" UPS 26
UPS H5 H5 H 0 1 N N N N N N 5.505 2.064 -26.996 -5.692 -0.760 -1.862 H5 UPS 27
UPS H6 H6 H 0 1 N N N N N N 6.182 1.649 -29.269 -3.761 0.652 -2.345 H6 UPS 28
UPS "H2'" "H2'" H 0 1 N N N N N N 9.635 0.172 -30.773 -1.999 3.163 -0.166 "H2'" UPS 29
UPS "H2'A" "H2'A" H 0 0 N N N N N N 7.940 -0.054 -30.372 -2.090 1.986 1.180 "H2'A" UPS 30
UPS "H3'" "H3'" H 0 1 N N N N N N 7.547 -0.162 -32.674 0.179 2.232 1.547 "H3'" UPS 31
UPS "HO3'" "HO3'" H 0 0 N Y N N N N 9.083 0.253 -34.226 -0.005 4.435 0.638 "HO3'" UPS 32
UPS HN3 HN3 H 0 1 N N N N N N 9.400 3.521 -26.263 -4.009 -1.633 1.852 HN3 UPS 33
#
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
UPS P OP3 SING N N 1
UPS S1P P DOUB N N 2
UPS P OP2 SING N N 3
UPS P "O5'" SING N N 4
UPS OP3 HOP3 SING N N 5
UPS OP2 HOP2 SING N N 6
UPS "C5'" "O5'" SING N N 7
UPS "C5'" "C4'" SING N N 8
UPS "C5'" "H5'" SING N N 9
UPS "C5'" "H5'A" SING N N 10
UPS "C4'" "C3'" SING N N 11
UPS "C4'" "O4'" SING N N 12
UPS "C4'" "H4'" SING N N 13
UPS "O4'" "C1'" SING N N 14
UPS "C2'" "C1'" SING N N 15
UPS "C1'" N1 SING N N 16
UPS "C1'" "H1'" SING N N 17
UPS N1 C6 SING N N 18
UPS N1 C2 SING N N 19
UPS O2 C2 DOUB N N 20
UPS C2 N3 SING N N 21
UPS N3 C4 SING N N 22
UPS C5 C4 SING N N 23
UPS C4 O4 DOUB N N 24
UPS C6 C5 DOUB N N 25
UPS C5 H5 SING N N 26
UPS C6 H6 SING N N 27
UPS "C3'" "C2'" SING N N 28
UPS "C2'" "H2'" SING N N 29
UPS "C2'" "H2'A" SING N N 30
UPS "O3'" "C3'" SING N N 31
UPS "C3'" "H3'" SING N N 32
UPS "O3'" "HO3'" SING N N 33
UPS N3 HN3 SING N N 34
#
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
UPS SMILES ACDLabs 10.04 O=C1NC(=O)N(C=C1)C2OC(C(O)C2)COP(=S)(O)O
UPS SMILES_CANONICAL CACTVS 3.341 O[C@H]1C[C@@H](O[C@@H]1CO[P](O)(O)=S)N2C=CC(=O)NC2=O
UPS SMILES CACTVS 3.341 O[CH]1C[CH](O[CH]1CO[P](O)(O)=S)N2C=CC(=O)NC2=O
UPS SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 C1[C@@H]([C@H](O[C@H]1N2C=CC(=O)NC2=O)COP(=S)(O)O)O
UPS SMILES "OpenEye OEToolkits" 1.5.0 C1C(C(OC1N2C=CC(=O)NC2=O)COP(=S)(O)O)O
UPS InChI InChI 1.03 InChI=1S/C9H13N2O7PS/c12-5-3-8(11-2-1-7(13)10-9(11)14)18-6(5)4-17-19(15,16)20/h1-2,5-6,8,12H,3-4H2,(H,10,13,14)(H2,15,16,20)/t5-,6+,8+/m0/s1
UPS InChIKey InChI 1.03 LGZBLTPUGKWVDT-SHYZEUOFSA-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
UPS "SYSTEMATIC NAME" ACDLabs 10.04 "2'-deoxy-5'-O-thiophosphonouridine"
UPS "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 1-[(2R,4S,5R)-5-(dihydroxyphosphinothioyloxymethyl)-4-hydroxy-oxolan-2-yl]pyrimidine-2,4-dione
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
UPS 'Create component' 2009-02-10 PDBJ
UPS 'Modify descriptor' 2011-06-04 RCSB
#
loop_
_software.name
_software.version
_software.description
rdkit 2023.03.3 'Core functionality.'
pdbeccdutils 0.8.4 '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
UPS OP3 O 8.348 -5.564 1
UPS P P 9.562 -4.683 2
UPS S1P S 10.444 -5.896 3
UPS OP2 O 10.775 -3.801 4
UPS "O5'" O 8.680 -3.469 5
UPS "C5'" C 7.188 -3.626 6
UPS "C4'" C 6.307 -2.412 7
UPS "O4'" O 6.770 -0.986 8
UPS "C1'" C 5.557 -0.104 9
UPS N1 N 5.557 1.396 10
UPS C2 C 6.856 2.146 11
UPS O2 O 8.155 1.396 12
UPS N3 N 6.856 3.646 13
UPS C4 C 5.557 4.396 14
UPS O4 O 5.557 5.896 15
UPS C5 C 4.258 3.646 16
UPS C6 C 4.258 2.146 17
UPS "C2'" C 4.343 -0.986 18
UPS "C3'" C 4.807 -2.412 19
UPS "O3'" O 3.925 -3.626 20
#
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
UPS P OP3 SINGLE NONE 1
UPS S1P P DOUBLE NONE 2
UPS P OP2 SINGLE NONE 3
UPS P "O5'" SINGLE NONE 4
UPS "C5'" "O5'" SINGLE NONE 5
UPS "C4'" "C5'" SINGLE BEGINDASH 6
UPS "C4'" "C3'" SINGLE NONE 7
UPS "C4'" "O4'" SINGLE NONE 8
UPS "O4'" "C1'" SINGLE NONE 9
UPS "C2'" "C1'" SINGLE NONE 10
UPS "C1'" N1 SINGLE BEGINDASH 11
UPS N1 C6 SINGLE NONE 12
UPS N1 C2 SINGLE NONE 13
UPS O2 C2 DOUBLE NONE 14
UPS C2 N3 SINGLE NONE 15
UPS N3 C4 SINGLE NONE 16
UPS C5 C4 SINGLE NONE 17
UPS C4 O4 DOUBLE NONE 18
UPS C6 C5 DOUBLE NONE 19
UPS "C3'" "C2'" SINGLE NONE 20
UPS "C3'" "O3'" SINGLE BEGINWEDGE 21
#
loop_
_pdbe_chem_comp_substructure.comp_id
_pdbe_chem_comp_substructure.substructure_name
_pdbe_chem_comp_substructure.id
_pdbe_chem_comp_substructure.substructure_type
_pdbe_chem_comp_substructure.substructure_smiles
_pdbe_chem_comp_substructure.substructure_inchis
_pdbe_chem_comp_substructure.substructure_inchikeys
UPS MurckoScaffold S1 scaffold 'O=c1ccn([C@H]2CCCO2)c(=O)[nH]1' InChI=1S/C8H10N2O3/c11-6-3-4-10(8(12)9-6)7-2-1-5-13-7/h3-4,7H,1-2,5H2,(H,9,11,12)/t7-/m1/s1 CWWIKVUHBBTKHC-SSDOTTSWSA-N
UPS deoxyribose F1 fragment 'OCC1OC[CH2]C1O' InChI=1S/C5H10O3/c6-3-5-4(7)1-2-8-5/h4-7H,1-3H2 NSMOSDAEGJTOIQ-UHFFFAOYSA-N
UPS pyrimidine F2 fragment c1cncnc1 InChI=1S/C4H4N2/c1-2-5-4-6-3-1/h1-4H CZPWVGJYEJSRLH-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
UPS "C4'" S1 1
UPS "O4'" S1 1
UPS "C1'" S1 1
UPS N1 S1 1
UPS C2 S1 1
UPS O2 S1 1
UPS N3 S1 1
UPS C4 S1 1
UPS O4 S1 1
UPS C5 S1 1
UPS C6 S1 1
UPS "C2'" S1 1
UPS "C3'" S1 1
UPS "C1'" F1 1
UPS "C2'" F1 1
UPS "C3'" F1 1
UPS "O3'" F1 1
UPS "C4'" F1 1
UPS "O4'" F1 1
UPS "C5'" F1 1
UPS "O5'" F1 1
UPS C5 F2 1
UPS C4 F2 1
UPS N3 F2 1
UPS C2 F2 1
UPS N1 F2 1
UPS C6 F2 1
#
_pdbe_chem_comp_rdkit_properties.comp_id UPS
_pdbe_chem_comp_rdkit_properties.exactmw 324.018
_pdbe_chem_comp_rdkit_properties.amw 324.251
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 9
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 4
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 7
_pdbe_chem_comp_rdkit_properties.NumHBD 4
_pdbe_chem_comp_rdkit_properties.NumHBA 9
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 20
_pdbe_chem_comp_rdkit_properties.NumAtoms 33
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 11
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.556
_pdbe_chem_comp_rdkit_properties.NumRings 2
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 1
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 1
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 1
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 2
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumSpiroAtoms 0
_pdbe_chem_comp_rdkit_properties.NumBridgeheadAtoms 0
_pdbe_chem_comp_rdkit_properties.NumAtomStereoCenters 3
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 135.795
_pdbe_chem_comp_rdkit_properties.tpsa 134.010
_pdbe_chem_comp_rdkit_properties.CrippenClogP 0.210
_pdbe_chem_comp_rdkit_properties.CrippenMR 70.747
_pdbe_chem_comp_rdkit_properties.chi0v 10.819
_pdbe_chem_comp_rdkit_properties.chi1v 7.129
_pdbe_chem_comp_rdkit_properties.chi2v 2.280
_pdbe_chem_comp_rdkit_properties.chi3v 2.280
_pdbe_chem_comp_rdkit_properties.chi4v 1.349
_pdbe_chem_comp_rdkit_properties.chi0n 22.108
_pdbe_chem_comp_rdkit_properties.chi1n 10.745
_pdbe_chem_comp_rdkit_properties.chi2n 1.742
_pdbe_chem_comp_rdkit_properties.chi3n 1.742
_pdbe_chem_comp_rdkit_properties.chi4n 1.043
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.870
_pdbe_chem_comp_rdkit_properties.kappa1 5.729
_pdbe_chem_comp_rdkit_properties.kappa2 5.860
_pdbe_chem_comp_rdkit_properties.kappa3 3.826
_pdbe_chem_comp_rdkit_properties.Phi 1.679
#
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
UPS UniChem PDBe UPS
UPS UniChem eMolecules 1933359
UPS UniChem SureChEMBL SCHEMBL20266298
UPS UniChem BRENDA 110062
UPS UniChem BRENDA 21924
UPS UniChem PubChem 44755087
UPS UniChem Nikkaji J1.063.262E
#
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
UPS OP3 3.603 2.321 1.631 ETKDGv3 1
UPS P 3.349 1.935 0.001 ETKDGv3 2
UPS S1P 2.958 3.376 -0.867 ETKDGv3 3
UPS OP2 4.754 1.260 -0.661 ETKDGv3 4
UPS "O5'" 2.048 0.844 -0.143 ETKDGv3 5
UPS "C5'" 2.365 -0.327 0.572 ETKDGv3 6
UPS "C4'" 1.190 -1.309 0.505 ETKDGv3 7
UPS "O4'" 0.038 -0.707 1.053 ETKDGv3 8
UPS "C1'" -1.052 -1.180 0.300 ETKDGv3 9
UPS N1 -2.163 -0.214 0.322 ETKDGv3 10
UPS C2 -1.944 1.204 0.149 ETKDGv3 11
UPS O2 -0.783 1.665 -0.012 ETKDGv3 12
UPS N3 -3.061 2.094 0.153 ETKDGv3 13
UPS C4 -4.379 1.563 0.292 ETKDGv3 14
UPS O4 -5.375 2.333 0.298 ETKDGv3 15
UPS C5 -4.567 0.113 0.423 ETKDGv3 16
UPS C6 -3.514 -0.710 0.429 ETKDGv3 17
UPS "C2'" -0.572 -1.433 -1.118 ETKDGv3 18
UPS "C3'" 0.889 -1.761 -0.936 ETKDGv3 19
UPS "O3'" 1.092 -3.143 -1.074 ETKDGv3 20
UPS HOP3 4.480 2.782 1.652 ETKDGv3 21
UPS HOP2 5.182 0.771 0.087 ETKDGv3 22
UPS "H5'" 3.262 -0.826 0.139 ETKDGv3 23
UPS "H5'A" 2.556 -0.097 1.645 ETKDGv3 24
UPS "H4'" 1.449 -2.191 1.133 ETKDGv3 25
UPS "H1'" -1.380 -2.147 0.748 ETKDGv3 26
UPS H5 -5.567 -0.294 0.511 ETKDGv3 27
UPS H6 -3.691 -1.775 0.520 ETKDGv3 28
UPS "H2'" -1.142 -2.261 -1.595 ETKDGv3 29
UPS "H2'A" -0.674 -0.516 -1.739 ETKDGv3 30
UPS "H3'" 1.490 -1.211 -1.698 ETKDGv3 31
UPS "HO3'" 2.074 -3.279 -1.114 ETKDGv3 32
UPS HN3 -2.916 3.123 0.044 ETKDGv3 33
#