data_UDX
#
_chem_comp.id UDX
_chem_comp.name "URIDINE-5'-DIPHOSPHATE-XYLOPYRANOSE"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C14 H22 N2 O16 P2"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms UDP-ALPHA-D-XYLOPYRANOSE
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 1999-12-13
_chem_comp.pdbx_modified_date 2021-03-01
_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 536.276
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code UDX
_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 1DLI
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site RCSB
#
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
UDX "C1'" "C1'" C 0 1 N N R N N N -16.704 14.729 55.547 -0.186 -0.590 5.370 "C1'" UDX 1
UDX "C2'" "C2'" C 0 1 N N R N N N -17.756 14.850 54.469 -0.246 0.226 6.663 "C2'" UDX 2
UDX "O2'" "O2'" O 0 1 N N N N N N -17.668 16.155 53.934 -1.366 1.113 6.616 "O2'" UDX 3
UDX "C3'" "C3'" C 0 1 N N S N N N -19.160 14.623 55.062 1.047 1.037 6.804 "C3'" UDX 4
UDX "O3'" "O3'" O 0 1 N N N N N N -20.147 14.667 54.040 1.068 1.689 8.075 "O3'" UDX 5
UDX "C4'" "C4'" C 0 1 N N R N N N -19.182 13.257 55.697 2.239 0.081 6.688 "C4'" UDX 6
UDX "O4'" "O4'" O 0 1 N N N N N N -20.488 12.974 56.189 3.454 0.832 6.665 "O4'" UDX 7
UDX "C5'" "C5'" C 0 1 N N N N N N -18.150 13.244 56.818 2.111 -0.725 5.394 "C5'" UDX 8
UDX "O5'" "O5'" O 0 1 N N N N N N -16.842 13.506 56.269 0.912 -1.497 5.423 "O5'" UDX 9
UDX PB PB P 0 1 N N S N N N -15.543 16.266 57.292 -0.739 -0.407 2.999 PB UDX 10
UDX O1B O1B O 0 1 N N N N N N -14.624 15.114 57.402 -2.174 -0.611 3.299 O1B UDX 11
UDX O2B O2B O 0 1 N N N N N N -16.106 16.883 58.529 -0.044 -1.830 2.707 O2B UDX 12
UDX O3B O3B O 0 1 N N N N N N -16.769 15.850 56.371 -0.021 0.292 4.259 O3B UDX 13
UDX O3A O3A O 0 1 N N N N N N -14.807 17.451 56.530 -0.591 0.537 1.704 O3A UDX 14
UDX PA PA P 0 1 N N R N N N -14.523 17.870 55.021 -1.327 -0.219 0.488 PA UDX 15
UDX O1A O1A O 0 1 N N N N N N -14.778 19.330 54.983 -2.752 -0.426 0.827 O1A UDX 16
UDX O2A O2A O 0 1 N N N N N N -15.264 16.969 54.124 -0.622 -1.645 0.239 O2A UDX 17
UDX O5D O5* O 0 1 N N N N N N -12.954 17.628 54.826 -1.217 0.674 -0.845 O5D UDX 18
UDX C5D C5* C 0 1 N N N N N N -12.403 16.317 54.909 -1.885 -0.046 -1.882 C5D UDX 19
UDX C4D C4* C 0 1 N N R N N N -10.889 16.375 54.817 -1.816 0.752 -3.185 C4D UDX 20
UDX O4D O4* O 0 1 N N N N N N -10.505 16.734 53.457 -0.446 0.925 -3.581 O4D UDX 21
UDX C3D C3* C 0 1 N N S N N N -10.336 17.459 55.732 -2.528 -0.020 -4.312 C3D UDX 22
UDX O3D O3* O 0 1 N N N N N N -9.053 17.031 56.212 -3.617 0.739 -4.839 O3D UDX 23
UDX C2D C2* C 0 1 N N R N N N -10.174 18.654 54.803 -1.428 -0.213 -5.389 C2D UDX 24
UDX O2D O2* O 0 1 N N N N N N -9.117 19.488 55.229 -1.959 -0.012 -6.700 O2D UDX 25
UDX C1D C1* C 0 1 N N R N N N -9.773 17.985 53.505 -0.418 0.904 -5.024 C1D UDX 26
UDX N1 N1 N 0 1 N N N N N N -10.084 18.893 52.413 0.923 0.569 -5.509 N1 UDX 27
UDX C6 C6 C 0 1 N N N N N N -11.380 19.132 52.068 1.584 1.443 -6.329 C6 UDX 28
UDX C2 C2 C 0 1 N N N N N N -9.048 19.467 51.754 1.495 -0.590 -5.140 C2 UDX 29
UDX O2 O2 O 0 1 N N N N N N -7.880 19.268 52.071 0.889 -1.352 -4.411 O2 UDX 30
UDX N3 N3 N 0 1 N N N N N N -9.418 20.295 50.715 2.724 -0.924 -5.575 N3 UDX 31
UDX C4 C4 C 0 1 N N N N N N -10.709 20.581 50.316 3.409 -0.091 -6.384 C4 UDX 32
UDX O4 O4 O 0 1 N N N N N N -10.931 21.356 49.395 4.523 -0.390 -6.774 O4 UDX 33
UDX C5 C5 C 0 1 N N N N N N -11.711 19.933 51.076 2.820 1.135 -6.776 C5 UDX 34
UDX "H1'" "H1'" H 0 1 N N N N N N -15.690 14.695 55.083 -1.114 -1.151 5.253 "H1'" UDX 35
UDX "H2'1" "1H2'" H 0 0 N N N N N N -17.587 14.083 53.676 -0.348 -0.445 7.515 "H2'1" UDX 36
UDX "HO'2" "2HO'" H 0 0 N N N N N N -18.329 16.231 53.256 -2.155 0.562 6.522 "HO'2" UDX 37
UDX "H3'1" "1H3'" H 0 0 N N N N N N -19.381 15.420 55.809 1.100 1.782 6.010 "H3'1" UDX 38
UDX "HO'3" "3HO'" H 0 0 N N N N N N -21.012 14.527 54.405 1.897 2.185 8.121 "HO'3" UDX 39
UDX "H4'1" "1H4'" H 0 0 N N N N N N -18.927 12.467 54.952 2.246 -0.597 7.542 "H4'1" UDX 40
UDX "HO'4" "4HO'" H 0 0 N N N N N N -20.501 12.112 56.589 4.177 0.194 6.589 "HO'4" UDX 41
UDX "H5'1" "1H5'" H 0 0 N N N N N N -18.411 13.950 57.640 2.082 -0.043 4.544 "H5'1" UDX 42
UDX "H5'2" "2H5'" H 0 0 N N N N N N -18.178 12.297 57.406 2.968 -1.390 5.295 "H5'2" UDX 43
UDX HOB2 2HOB H 0 0 N N N N N N -16.696 17.623 58.458 0.886 -1.652 2.516 HOB2 UDX 44
UDX HOA2 2HOA H 0 0 N N N N N N -15.094 17.219 53.223 0.302 -1.465 0.021 HOA2 UDX 45
UDX H5A1 1H5* H 0 0 N N N N N N -12.743 15.780 55.824 -1.400 -1.012 -2.023 H5A1 UDX 46
UDX H5A2 2H5* H 0 0 N N N N N N -12.840 15.633 54.144 -2.928 -0.199 -1.604 H5A2 UDX 47
UDX H4A1 1H4* H 0 0 N N N N N N -10.486 15.377 55.111 -2.288 1.725 -3.048 H4A1 UDX 48
UDX H3A1 1H3* H 0 0 N N N N N N -10.977 17.685 56.615 -2.879 -0.986 -3.948 H3A1 UDX 49
UDX HOA3 3HO* H 0 0 N N N N N N -8.707 17.707 56.782 -3.981 0.231 -5.577 HOA3 UDX 50
UDX H2A1 1H2* H 0 0 N N N N N N -11.085 19.293 54.747 -0.967 -1.197 -5.304 H2A1 UDX 51
UDX HOC2 2HO* H 0 0 N N N N N N -9.015 20.233 54.649 -2.577 -0.737 -6.865 HOC2 UDX 52
UDX "H1'1" 1H1* H 0 0 N N N N N N -8.684 17.759 53.424 -0.743 1.862 -5.429 "H1'1" UDX 53
UDX H61 1H6 H 0 1 N N N N N N -12.204 18.651 52.620 1.119 2.374 -6.618 H61 UDX 54
UDX HN3 HN3 H 0 1 N N N N N N -8.663 20.738 50.190 3.120 -1.767 -5.302 HN3 UDX 55
UDX H51 1H5 H 0 1 N N N N N N -12.790 20.056 50.888 3.353 1.815 -7.424 H51 UDX 56
#
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
UDX "C1'" "C2'" SING N N 1
UDX "C1'" "O5'" SING N N 2
UDX "C1'" O3B SING N N 3
UDX "C1'" "H1'" SING N N 4
UDX "C2'" "O2'" SING N N 5
UDX "C2'" "C3'" SING N N 6
UDX "C2'" "H2'1" SING N N 7
UDX "O2'" "HO'2" SING N N 8
UDX "C3'" "O3'" SING N N 9
UDX "C3'" "C4'" SING N N 10
UDX "C3'" "H3'1" SING N N 11
UDX "O3'" "HO'3" SING N N 12
UDX "C4'" "O4'" SING N N 13
UDX "C4'" "C5'" SING N N 14
UDX "C4'" "H4'1" SING N N 15
UDX "O4'" "HO'4" SING N N 16
UDX "C5'" "O5'" SING N N 17
UDX "C5'" "H5'1" SING N N 18
UDX "C5'" "H5'2" SING N N 19
UDX PB O1B DOUB N N 20
UDX PB O2B SING N N 21
UDX PB O3B SING N N 22
UDX PB O3A SING N N 23
UDX O2B HOB2 SING N N 24
UDX O3A PA SING N N 25
UDX PA O1A DOUB N N 26
UDX PA O2A SING N N 27
UDX PA O5D SING N N 28
UDX O2A HOA2 SING N N 29
UDX O5D C5D SING N N 30
UDX C5D C4D SING N N 31
UDX C5D H5A1 SING N N 32
UDX C5D H5A2 SING N N 33
UDX C4D O4D SING N N 34
UDX C4D C3D SING N N 35
UDX C4D H4A1 SING N N 36
UDX O4D C1D SING N N 37
UDX C3D O3D SING N N 38
UDX C3D C2D SING N N 39
UDX C3D H3A1 SING N N 40
UDX O3D HOA3 SING N N 41
UDX C2D O2D SING N N 42
UDX C2D C1D SING N N 43
UDX C2D H2A1 SING N N 44
UDX O2D HOC2 SING N N 45
UDX C1D N1 SING N N 46
UDX C1D "H1'1" SING N N 47
UDX N1 C6 SING N N 48
UDX N1 C2 SING N N 49
UDX C6 C5 DOUB N N 50
UDX C6 H61 SING N N 51
UDX C2 O2 DOUB N N 52
UDX C2 N3 SING N N 53
UDX N3 C4 SING N N 54
UDX N3 HN3 SING N N 55
UDX C4 O4 DOUB N N 56
UDX C4 C5 SING N N 57
UDX C5 H51 SING N N 58
#
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
UDX SMILES ACDLabs 10.04 O=P(OC1OCC(O)C(O)C1O)(O)OP(=O)(O)OCC3OC(N2C=CC(=O)NC2=O)C(O)C3O
UDX SMILES_CANONICAL CACTVS 3.341 O[C@@H]1CO[C@H](O[P@@](O)(=O)O[P@@](O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)N3C=CC(=O)NC3=O)[C@H](O)[C@H]1O
UDX SMILES CACTVS 3.341 O[CH]1CO[CH](O[P](O)(=O)O[P](O)(=O)OC[CH]2O[CH]([CH](O)[CH]2O)N3C=CC(=O)NC3=O)[CH](O)[CH]1O
UDX SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 C1[C@H]([C@@H]([C@H]([C@H](O1)O[P@](=O)(O)O[P@](=O)(O)OC[C@@H]2[C@H]([C@H]([C@@H](O2)N3C=CC(=O)NC3=O)O)O)O)O)O
UDX SMILES "OpenEye OEToolkits" 1.5.0 C1C(C(C(C(O1)OP(=O)(O)OP(=O)(O)OCC2C(C(C(O2)N3C=CC(=O)NC3=O)O)O)O)O)O
UDX InChI InChI 1.03 InChI=1S/C14H22N2O16P2/c17-5-3-28-13(11(22)8(5)19)31-34(26,27)32-33(24,25)29-4-6-9(20)10(21)12(30-6)16-2-1-7(18)15-14(16)23/h1-2,5-6,8-13,17,19-22H,3-4H2,(H,24,25)(H,26,27)(H,15,18,23)/t5-,6-,8+,9-,10-,11-,12-,13-/m1/s1
UDX InChIKey InChI 1.03 DQQDLYVHOTZLOR-OCIMBMBZSA-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
UDX "SYSTEMATIC NAME" ACDLabs 10.04 "[(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3R,4S,5R)-3,4,5-trihydroxytetrahydro-2H-pyran-2-yl dihydrogen diphosphate (non-preferred name)"
UDX "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[[(2R,3S,4R,5R)-5-(2,4-dioxopyrimidin-1-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl] [(2R,3R,4S,5R)-3,4,5-trihydroxyoxan-2-yl] hydrogen 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
UDX 'Create component' 1999-12-13 RCSB
UDX 'Modify descriptor' 2011-06-04 RCSB
UDX 'Modify synonyms' 2021-03-01 PDBE
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id UDX
_pdbx_chem_comp_synonyms.name UDP-ALPHA-D-XYLOPYRANOSE
_pdbx_chem_comp_synonyms.provenance ?
_pdbx_chem_comp_synonyms.type ?
#
_pdbe_chem_comp_drugbank_details.comp_id UDX
_pdbe_chem_comp_drugbank_details.drugbank_id DB01713
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name UDP-alpha-D-xylose
_pdbe_chem_comp_drugbank_details.description
'The decarboxylation product of UDPglucuronic acid, which is used for formation of the xylosides of seryl hydroxyl groups in mucoprotein synthesis. Also forms plant xylans.'
_pdbe_chem_comp_drugbank_details.cas_number 3616-06-6
_pdbe_chem_comp_drugbank_details.mechanism_of_action ?
#
loop_
_pdbe_chem_comp_synonyms.comp_id
_pdbe_chem_comp_synonyms.name
_pdbe_chem_comp_synonyms.provenance
_pdbe_chem_comp_synonyms.type
UDX UDP-ALPHA-D-XYLOPYRANOSE wwPDB ?
UDX UDP-alpha-D-xylose DrugBank ?
UDX UDP-xylose DrugBank ?
UDX "Uridine-5'-diphosphate-xylopyranose" DrugBank ?
#
_pdbe_chem_comp_drugbank_classification.comp_id UDX
_pdbe_chem_comp_drugbank_classification.drugbank_id DB01713
_pdbe_chem_comp_drugbank_classification.parent 'Pyrimidine ribonucleoside diphosphates'
_pdbe_chem_comp_drugbank_classification.kingdom 'Organic compounds'
_pdbe_chem_comp_drugbank_classification.class 'Pyrimidine nucleotides'
_pdbe_chem_comp_drugbank_classification.superclass 'Nucleosides, nucleotides, and analogues'
_pdbe_chem_comp_drugbank_classification.description
'This compound belongs to the class of organic compounds known as pyrimidine ribonucleoside diphosphates. These are pyrimidine ribonucleotides with diphosphate group  linked to the ribose moiety.'
#
_pdbe_chem_comp_drugbank_targets.comp_id UDX
_pdbe_chem_comp_drugbank_targets.drugbank_id DB01713
_pdbe_chem_comp_drugbank_targets.name 'UDP-glucose 6-dehydrogenase'
_pdbe_chem_comp_drugbank_targets.organism 'Streptococcus pyogenes'
_pdbe_chem_comp_drugbank_targets.uniprot_id P0C0F4
_pdbe_chem_comp_drugbank_targets.pharmacologically_active unknown
_pdbe_chem_comp_drugbank_targets.ordinal 1
#
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
UDX "C1'" C 6.404 5.224 1
UDX "C2'" C 5.104 5.974 2
UDX "O2'" O 3.805 5.224 3
UDX "C3'" C 5.104 7.474 4
UDX "O3'" O 3.805 8.224 5
UDX "C4'" C 6.404 8.224 6
UDX "O4'" O 6.404 9.724 7
UDX "C5'" C 7.702 7.474 8
UDX "O5'" O 7.702 5.974 9
UDX PB P 7.702 2.974 10
UDX O1B O 6.952 1.675 11
UDX O2B O 8.453 4.273 12
UDX O3B O 6.404 3.724 13
UDX O3A O 9.002 2.224 14
UDX PA P 9.002 0.724 15
UDX O1A O 10.502 0.724 16
UDX O2A O 7.502 0.724 17
UDX O5D O 9.002 -0.776 18
UDX C5D C 10.301 -1.526 19
UDX C4D C 10.301 -3.026 20
UDX O4D O 11.514 -3.908 21
UDX C3D C 9.087 -3.908 22
UDX O3D O 7.660 -3.444 23
UDX C2D C 9.551 -5.335 24
UDX O2D O 8.669 -6.548 25
UDX C1D C 11.051 -5.335 26
UDX N1 N 11.932 -6.548 27
UDX C6 C 13.424 -6.391 28
UDX C2 C 11.322 -7.918 29
UDX O2 O 9.830 -8.075 30
UDX N3 N 12.204 -9.132 31
UDX C4 C 13.696 -8.975 32
UDX O4 O 14.577 -10.189 33
UDX C5 C 14.306 -7.605 34
#
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
UDX "C1'" "C2'" SINGLE NONE 1
UDX "C1'" "O5'" SINGLE NONE 2
UDX "C1'" O3B SINGLE BEGINDASH 3
UDX "C2'" "O2'" SINGLE BEGINDASH 4
UDX "C2'" "C3'" SINGLE NONE 5
UDX "C3'" "O3'" SINGLE BEGINWEDGE 6
UDX "C3'" "C4'" SINGLE NONE 7
UDX "C4'" "O4'" SINGLE BEGINDASH 8
UDX "C4'" "C5'" SINGLE NONE 9
UDX "C5'" "O5'" SINGLE NONE 10
UDX PB O1B DOUBLE NONE 11
UDX PB O2B SINGLE BEGINWEDGE 12
UDX PB O3B SINGLE NONE 13
UDX PB O3A SINGLE NONE 14
UDX O3A PA SINGLE NONE 15
UDX PA O1A DOUBLE NONE 16
UDX PA O2A SINGLE BEGINDASH 17
UDX PA O5D SINGLE NONE 18
UDX O5D C5D SINGLE NONE 19
UDX C4D C5D SINGLE BEGINWEDGE 20
UDX C4D O4D SINGLE NONE 21
UDX C4D C3D SINGLE NONE 22
UDX O4D C1D SINGLE NONE 23
UDX C3D O3D SINGLE BEGINDASH 24
UDX C3D C2D SINGLE NONE 25
UDX C2D O2D SINGLE BEGINDASH 26
UDX C2D C1D SINGLE NONE 27
UDX C1D N1 SINGLE BEGINWEDGE 28
UDX N1 C6 SINGLE NONE 29
UDX N1 C2 SINGLE NONE 30
UDX C6 C5 DOUBLE NONE 31
UDX C2 O2 DOUBLE NONE 32
UDX C2 N3 SINGLE NONE 33
UDX N3 C4 SINGLE NONE 34
UDX C4 O4 DOUBLE NONE 35
UDX C4 C5 SINGLE NONE 36
#
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
UDX MurckoScaffold S1 scaffold 'O=c1ccn([C@H]2CC[C@@H](CO[PH](=O)O[PH](=O)O[C@@H]3CCCCO3)O2)c(=O)[nH]1' InChI=1S/C14H22N2O9P2/c17-11-6-7-16(14(18)15-11)12-5-4-10(23-12)9-22-26(19)25-27(20)24-13-3-1-2-8-21-13/h6-7,10,12-13,26-27H,1-5,8-9H2,(H,15,17,18)/t10-,12+,13+/m0/s1 AKKVBKIXAFLMCT-CYZMBNFOSA-N
UDX phosphate F1 fragment O=P(O)(O)O InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4) NBIIXXVUZAFLBC-UHFFFAOYSA-N
UDX pyranose F2 fragment OC1CCCCO1 InChI=1S/C5H10O2/c6-5-3-1-2-4-7-5/h5-6H,1-4H2 CELWCAITJAEQNL-UHFFFAOYSA-N
UDX pyrimidine F3 fragment c1cncnc1 InChI=1S/C4H4N2/c1-2-5-4-6-3-1/h1-4H CZPWVGJYEJSRLH-UHFFFAOYSA-N
UDX ribose F4 fragment OCC1OCC(O)C1O InChI=1S/C5H10O4/c6-1-4-5(8)3(7)2-9-4/h3-8H,1-2H2 KZVAAIRBJJYZOW-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
UDX "C1'" S1 1
UDX "C2'" S1 1
UDX "C3'" S1 1
UDX "C4'" S1 1
UDX "C5'" S1 1
UDX "O5'" S1 1
UDX PB S1 1
UDX O1B S1 1
UDX O3B S1 1
UDX O3A S1 1
UDX PA S1 1
UDX O1A S1 1
UDX O5D S1 1
UDX C5D S1 1
UDX C4D S1 1
UDX O4D S1 1
UDX C3D S1 1
UDX C2D S1 1
UDX C1D S1 1
UDX N1 S1 1
UDX C6 S1 1
UDX C2 S1 1
UDX O2 S1 1
UDX N3 S1 1
UDX C4 S1 1
UDX O4 S1 1
UDX C5 S1 1
UDX O2B F1 1
UDX PB F1 1
UDX O1B F1 1
UDX O3B F1 1
UDX O3A F1 1
UDX O3A F1 2
UDX PA F1 2
UDX O1A F1 2
UDX O2A F1 2
UDX O5D F1 2
UDX "C4'" F2 1
UDX "C5'" F2 1
UDX "O5'" F2 1
UDX "C1'" F2 1
UDX "C2'" F2 1
UDX "C3'" F2 1
UDX O3B F2 1
UDX C5 F3 1
UDX C6 F3 1
UDX N1 F3 1
UDX C2 F3 1
UDX N3 F3 1
UDX C4 F3 1
UDX C2D F4 1
UDX C3D F4 1
UDX C4D F4 1
UDX O4D F4 1
UDX C1D F4 1
UDX C5D F4 1
UDX O5D F4 1
UDX O3D F4 1
UDX O2D F4 1
#
_pdbe_chem_comp_rdkit_properties.comp_id UDX
_pdbe_chem_comp_rdkit_properties.exactmw 536.044
_pdbe_chem_comp_rdkit_properties.amw 536.276
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 18
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 8
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 15
_pdbe_chem_comp_rdkit_properties.NumHBD 8
_pdbe_chem_comp_rdkit_properties.NumHBA 17
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 34
_pdbe_chem_comp_rdkit_properties.NumAtoms 56
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 20
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.714
_pdbe_chem_comp_rdkit_properties.NumRings 3
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 1
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 2
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 2
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 3
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 2
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 2
_pdbe_chem_comp_rdkit_properties.NumSpiroAtoms 0
_pdbe_chem_comp_rdkit_properties.NumBridgeheadAtoms 0
_pdbe_chem_comp_rdkit_properties.NumAtomStereoCenters 10
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 219.842
_pdbe_chem_comp_rdkit_properties.tpsa 276.760
_pdbe_chem_comp_rdkit_properties.CrippenClogP -2.355
_pdbe_chem_comp_rdkit_properties.CrippenMR 102.995
_pdbe_chem_comp_rdkit_properties.chi0v 17.110
_pdbe_chem_comp_rdkit_properties.chi1v 10.653
_pdbe_chem_comp_rdkit_properties.chi2v 5.455
_pdbe_chem_comp_rdkit_properties.chi3v 5.455
_pdbe_chem_comp_rdkit_properties.chi4v 3.618
_pdbe_chem_comp_rdkit_properties.chi0n 37.321
_pdbe_chem_comp_rdkit_properties.chi1n 18.037
_pdbe_chem_comp_rdkit_properties.chi2n 3.151
_pdbe_chem_comp_rdkit_properties.chi3n 3.151
_pdbe_chem_comp_rdkit_properties.chi4n 1.854
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.340
_pdbe_chem_comp_rdkit_properties.kappa1 10.197
_pdbe_chem_comp_rdkit_properties.kappa2 10.336
_pdbe_chem_comp_rdkit_properties.kappa3 6.256
_pdbe_chem_comp_rdkit_properties.Phi 3.100
#
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
UDX UniChem DrugBank DB01713
UDX UniChem 'Guide to Pharmacology' 4730
UDX UniChem ChEBI 16082
UDX UniChem ZINC ZINC000008551129
UDX UniChem HMDB HMDB0001018
UDX UniChem 'PubChem TPHARMA' 16054072
UDX UniChem NMRShiftDB 60020474
UDX UniChem Nikkaji J923.253B
UDX UniChem MetaboLights MTBLC16082
UDX UniChem BRENDA 1013
UDX UniChem BRENDA 11720
UDX UniChem BRENDA 2438
UDX UniChem BRENDA 27264
UDX UniChem BRENDA 341
UDX UniChem BRENDA 4576
UDX UniChem 'Probes And Drugs' PD048548
UDX UniChem ACTor 21401-20-7
UDX UniChem PubChem 19235
#
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
UDX "C1'" -3.269 -0.980 -0.189 ETKDGv3 1
UDX "C2'" -4.234 -1.876 0.616 ETKDGv3 2
UDX "O2'" -4.717 -2.917 -0.193 ETKDGv3 3
UDX "C3'" -5.416 -1.049 1.150 ETKDGv3 4
UDX "O3'" -6.184 -1.823 2.036 ETKDGv3 5
UDX "C4'" -4.891 0.188 1.888 ETKDGv3 6
UDX "O4'" -5.969 1.020 2.229 ETKDGv3 7
UDX "C5'" -3.907 0.947 0.985 ETKDGv3 8
UDX "O5'" -2.824 0.119 0.598 ETKDGv3 9
UDX PB -2.707 0.059 -2.456 ETKDGv3 10
UDX O1B -2.088 1.306 -1.861 ETKDGv3 11
UDX O2B -3.464 0.464 -3.914 ETKDGv3 12
UDX O3B -3.892 -0.549 -1.387 ETKDGv3 13
UDX O3A -1.534 -1.146 -2.744 ETKDGv3 14
UDX PA -0.218 -0.418 -3.546 ETKDGv3 15
UDX O1A -0.688 0.290 -4.798 ETKDGv3 16
UDX O2A 0.882 -1.625 -3.993 ETKDGv3 17
UDX O5D 0.565 0.703 -2.527 ETKDGv3 18
UDX C5D 0.966 0.029 -1.356 ETKDGv3 19
UDX C4D 1.624 1.023 -0.395 ETKDGv3 20
UDX O4D 1.971 0.366 0.802 ETKDGv3 21
UDX C3D 2.886 1.645 -0.978 ETKDGv3 22
UDX O3D 2.584 2.792 -1.730 ETKDGv3 23
UDX C2D 3.697 1.960 0.261 ETKDGv3 24
UDX O2D 3.546 3.299 0.674 ETKDGv3 25
UDX C1D 3.137 0.985 1.309 ETKDGv3 26
UDX N1 4.141 -0.037 1.650 ETKDGv3 27
UDX C6 4.340 -1.172 0.778 ETKDGv3 28
UDX C2 5.022 0.146 2.779 ETKDGv3 29
UDX O2 4.925 1.164 3.516 ETKDGv3 30
UDX N3 6.020 -0.837 3.061 ETKDGv3 31
UDX C4 6.156 -1.964 2.195 ETKDGv3 32
UDX O4 7.028 -2.841 2.430 ETKDGv3 33
UDX C5 5.278 -2.091 1.025 ETKDGv3 34
UDX "H1'" -2.385 -1.620 -0.413 ETKDGv3 35
UDX "H2'1" -3.683 -2.303 1.488 ETKDGv3 36
UDX "HO'2" -3.973 -3.566 -0.298 ETKDGv3 37
UDX "H3'1" -6.049 -0.711 0.295 ETKDGv3 38
UDX "HO'3" -6.758 -2.413 1.480 ETKDGv3 39
UDX "H4'1" -4.358 -0.141 2.812 ETKDGv3 40
UDX "HO'4" -5.634 1.655 2.915 ETKDGv3 41
UDX "H5'1" -4.428 1.373 0.099 ETKDGv3 42
UDX "H5'2" -3.494 1.806 1.555 ETKDGv3 43
UDX HOB2 -3.827 -0.392 -4.254 ETKDGv3 44
UDX HOA2 0.341 -2.286 -4.494 ETKDGv3 45
UDX H5A1 0.087 -0.411 -0.833 ETKDGv3 46
UDX H5A2 1.691 -0.782 -1.593 ETKDGv3 47
UDX H4A1 0.885 1.822 -0.153 ETKDGv3 48
UDX H3A1 3.434 0.900 -1.603 ETKDGv3 49
UDX HOA3 3.422 3.049 -2.196 ETKDGv3 50
UDX H2A1 4.776 1.776 0.063 ETKDGv3 51
UDX HOC2 2.581 3.464 0.846 ETKDGv3 52
UDX "H1'1" 2.842 1.538 2.228 ETKDGv3 53
UDX H61 3.720 -1.293 -0.101 ETKDGv3 54
UDX HN3 6.651 -0.726 3.887 ETKDGv3 55
UDX H51 5.395 -2.933 0.354 ETKDGv3 56
#