data_UD4
#
_chem_comp.id UD4
_chem_comp.name UDP-2-acetamido-4-amino-2,4,6-trideoxy-alpha-D-glucopyranose
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C17 H28 N4 O15 P2"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms (2R,3R,4S,5S,6R)-3-(acetylamino)-5-amino-4-hydroxy-6-methyltetrahydro-2H-pyran-2-yl
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2008-05-21
_chem_comp.pdbx_modified_date 2021-03-13
_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 590.370
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code UD4
_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 3BSS
_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
UD4 N3 N3 N 0 1 N N N N N N 3.991 -39.279 -11.483 -6.747 -2.999 -0.873 N3 UD4 1
UD4 C2 C2 C 0 1 N N N N N N 4.357 -38.129 -12.070 -6.271 -1.808 -1.279 C2 UD4 2
UD4 N1 N1 N 0 1 N N N N N N 3.592 -37.631 -13.145 -5.643 -0.985 -0.420 N1 UD4 3
UD4 C4 C4 C 0 1 N N N N N N 2.914 -39.964 -11.916 -6.606 -3.385 0.412 C4 UD4 4
UD4 C5 C5 C 0 1 N N N N N N 2.139 -39.500 -12.976 -5.946 -2.529 1.326 C5 UD4 5
UD4 C6 C6 C 0 1 N N N N N N 2.508 -38.303 -13.590 -5.473 -1.342 0.890 C6 UD4 6
UD4 "O7'" "O7'" O 0 1 N N N N N N -3.400 -31.496 -20.671 7.161 1.208 -1.675 "O7'" UD4 7
UD4 "C7'" "C7'" C 0 1 N N N N N N -2.254 -31.292 -20.283 6.166 1.044 -2.350 "C7'" UD4 8
UD4 "C8'" "C8'" C 0 1 N N N N N N -1.042 -31.645 -21.120 5.894 1.950 -3.524 "C8'" UD4 9
UD4 "N2'" "N2'" N 0 1 N N N N N N -2.006 -30.730 -19.096 5.305 0.052 -2.051 "N2'" UD4 10
UD4 "C2'" "C2'" C 0 1 N N R N N N -3.047 -30.367 -18.143 5.569 -0.828 -0.910 "C2'" UD4 11
UD4 "C3'" "C3'" C 0 1 N N S N N N -3.181 -28.839 -18.026 4.869 -2.173 -1.128 "C3'" UD4 12
UD4 "O3'" "O3'" O 0 1 N N N N N N -3.634 -28.286 -19.274 5.417 -2.816 -2.280 "O3'" UD4 13
UD4 "C4'" "C4'" C 0 1 N N S N N N -4.127 -28.423 -16.877 5.087 -3.056 0.105 "C4'" UD4 14
UD4 N4A N4A N 0 1 N N N N N N -4.114 -26.963 -16.726 4.358 -4.320 -0.062 N4A UD4 15
UD4 "C5'" "C5'" C 0 1 N N R N N N -3.726 -29.125 -15.571 4.568 -2.325 1.345 "C5'" UD4 16
UD4 "C6'" "C6'" C 0 1 N N N N N N -4.719 -28.910 -14.423 4.837 -3.174 2.589 "C6'" UD4 17
UD4 "O5'" "O5'" O 0 1 N N N N N N -3.617 -30.546 -15.773 5.238 -1.069 1.472 "O5'" UD4 18
UD4 "C1'" "C1'" C 0 1 N N R N N N -2.713 -30.984 -16.788 5.031 -0.183 0.370 "C1'" UD4 19
UD4 "O1'" "O1'" O 0 1 N N N N N N -1.403 -30.569 -16.414 3.633 0.075 0.222 "O1'" UD4 20
UD4 PB PB P 0 1 N N R N N N -0.374 -31.617 -15.770 2.883 1.293 0.961 PB UD4 21
UD4 O2B O2B O 0 1 N N N N N N 0.922 -30.891 -15.584 3.125 1.209 2.419 O2B UD4 22
UD4 O1B O1B O 0 1 N N N N N N -1.062 -32.244 -14.577 3.451 2.692 0.402 O1B UD4 23
UD4 O3A O3A O 0 1 N N N N N N -0.402 -32.752 -16.919 1.301 1.203 0.674 O3A UD4 24
UD4 PA PA P 0 1 N N R N N N 0.777 -33.431 -17.798 0.004 1.890 1.334 PA UD4 25
UD4 O2A O2A O 0 1 N N N N N N 0.203 -34.754 -18.202 -0.307 1.198 2.753 O2A UD4 26
UD4 O1A O1A O 0 1 N N N N N N 1.265 -32.397 -18.789 0.259 3.334 1.535 O1A UD4 27
UD4 O5B O5B O 0 1 N N N N N N 1.933 -33.684 -16.709 -1.261 1.700 0.356 O5B UD4 28
UD4 C5B C5B C 0 1 N N N N N N 1.738 -34.497 -15.540 -2.538 2.288 0.611 C5B UD4 29
UD4 C4B C4B C 0 1 N N R N N N 3.094 -34.571 -14.865 -3.507 1.909 -0.511 C4B UD4 30
UD4 O4B O4B O 0 1 N N N N N N 2.966 -35.421 -13.724 -3.764 0.495 -0.477 O4B UD4 31
UD4 C2B C2B C 0 1 N N S N N N 4.126 -35.205 -15.819 -4.856 2.625 -0.302 C2B UD4 32
UD4 O3B O3B O 0 1 N N N N N N 5.347 -34.452 -15.810 -5.153 3.467 -1.418 O3B UD4 33
UD4 C3B C3B C 0 1 N N R N N N 4.318 -36.600 -15.253 -5.885 1.473 -0.203 C3B UD4 34
UD4 "O2'" "O2'" O 0 1 N N N N N N 5.617 -37.151 -15.502 -7.083 1.798 -0.911 "O2'" UD4 35
UD4 C1B C1B C 0 1 N N R N N N 4.018 -36.387 -13.764 -5.134 0.306 -0.892 C1B UD4 36
UD4 O2 O2 O 0 1 N N N N N N 5.361 -37.484 -11.674 -6.411 -1.470 -2.439 O2 UD4 37
UD4 O4 O4 O 0 1 N N N N N N 2.596 -41.038 -11.347 -7.041 -4.461 0.781 O4 UD4 38
UD4 H5 H5 H 0 1 N N N N N N 1.275 -40.053 -13.314 -5.824 -2.821 2.358 H5 UD4 39
UD4 H6 H6 H 0 1 N N N N N N 1.930 -37.916 -14.416 -4.968 -0.676 1.573 H6 UD4 40
UD4 "H8'" "H8'" H 0 1 N N N N N N -1.337 -31.731 -22.176 6.695 2.685 -3.608 "H8'" UD4 41
UD4 "H8'A" "H8'A" H 0 0 N N N N N N -0.282 -30.857 -21.015 5.848 1.357 -4.437 "H8'A" UD4 42
UD4 "H8'B" "H8'B" H 0 0 N N N N N N -0.627 -32.604 -20.777 4.944 2.463 -3.374 "H8'B" UD4 43
UD4 "HN2'" "HN2'" H 0 0 N N N N N N -1.054 -30.549 -18.848 4.509 -0.079 -2.590 "HN2'" UD4 44
UD4 "H2'" "H2'" H 0 1 N N N N N N -4.013 -30.755 -18.497 6.643 -0.988 -0.814 "H2'" UD4 45
UD4 "H3'" "H3'" H 0 1 N N N N N N -2.185 -28.436 -17.789 3.801 -2.009 -1.274 "H3'" UD4 46
UD4 "HO3'" "HO3'" H 0 0 N N N N N N -3.734 -27.345 -19.186 5.019 -3.675 -2.478 "HO3'" UD4 47
UD4 "H4'" "H4'" H 0 1 N N N N N N -5.153 -28.735 -17.121 6.151 -3.262 0.221 "H4'" UD4 48
UD4 HN4A HN4A H 0 0 N N N N N N -4.111 -26.728 -15.754 4.487 -4.920 0.740 HN4A UD4 49
UD4 HN4B HN4B H 0 0 N N N N N N -3.295 -26.590 -17.161 3.378 -4.152 -0.234 HN4B UD4 50
UD4 "H5'" "H5'" H 0 1 N N N N N N -2.762 -28.674 -15.291 3.496 -2.156 1.245 "H5'" UD4 51
UD4 "H6'" "H6'" H 0 1 N N N N N N -4.173 -28.859 -13.470 5.909 -3.342 2.689 "H6'" UD4 52
UD4 "H6'A" "H6'A" H 0 0 N N N N N N -5.266 -27.969 -14.583 4.467 -2.654 3.472 "H6'A" UD4 53
UD4 "H6'B" "H6'B" H 0 0 N N N N N N -5.431 -29.748 -14.392 4.326 -4.133 2.491 "H6'B" UD4 54
UD4 "H1'" "H1'" H 0 1 N N N N N N -2.787 -32.078 -16.881 5.556 0.754 0.553 "H1'" UD4 55
UD4 HO1B HO1B H 0 0 N N N N N N -0.430 -32.375 -13.880 3.327 2.815 -0.549 HO1B UD4 56
UD4 HO2A HO2A H 0 0 N N N N N N 0.081 -34.773 -19.144 -0.484 0.249 2.698 HO2A UD4 57
UD4 H5B H5B H 0 1 N N N N N N 0.992 -34.045 -14.870 -2.922 1.923 1.563 H5B UD4 58
UD4 H5BA H5BA H 0 0 N N N N N N 1.359 -35.496 -15.800 -2.436 3.373 0.652 H5BA UD4 59
UD4 H4B H4B H 0 1 N N N N N N 3.426 -33.560 -14.585 -3.083 2.185 -1.476 H4B UD4 60
UD4 H2B H2B H 0 1 N N N N N N 3.801 -35.223 -16.870 -4.840 3.206 0.620 H2B UD4 61
UD4 HO3B HO3B H 0 0 N N N N N N 5.624 -34.286 -16.703 -5.991 3.943 -1.339 HO3B UD4 62
UD4 H3B H3B H 0 1 N N N N N N 3.667 -37.350 -15.725 -6.103 1.235 0.838 H3B UD4 63
UD4 "HO2'" "HO2'" H 0 0 N N N N N N 5.736 -37.273 -16.437 -7.542 2.579 -0.572 "HO2'" UD4 64
UD4 H1B H1B H 0 1 N N N N N N 4.907 -36.047 -13.213 -5.223 0.379 -1.976 H1B UD4 65
UD4 HN3 HN3 H 0 1 N N N N N N 4.524 -39.632 -10.714 -7.198 -3.580 -1.505 HN3 UD4 66
#
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
UD4 C2 N3 SING N N 1
UD4 C4 N3 SING N N 2
UD4 N1 C2 SING N N 3
UD4 C2 O2 DOUB N N 4
UD4 C1B N1 SING N N 5
UD4 C6 N1 SING N N 6
UD4 C5 C4 SING N N 7
UD4 C4 O4 DOUB N N 8
UD4 C6 C5 DOUB N N 9
UD4 C5 H5 SING N N 10
UD4 C6 H6 SING N N 11
UD4 "O7'" "C7'" DOUB N N 12
UD4 "C8'" "C7'" SING N N 13
UD4 "C7'" "N2'" SING N N 14
UD4 "C8'" "H8'" SING N N 15
UD4 "C8'" "H8'A" SING N N 16
UD4 "C8'" "H8'B" SING N N 17
UD4 "N2'" "C2'" SING N N 18
UD4 "N2'" "HN2'" SING N N 19
UD4 "C2'" "C3'" SING N N 20
UD4 "C2'" "C1'" SING N N 21
UD4 "C2'" "H2'" SING N N 22
UD4 "O3'" "C3'" SING N N 23
UD4 "C3'" "C4'" SING N N 24
UD4 "C3'" "H3'" SING N N 25
UD4 "O3'" "HO3'" SING N N 26
UD4 "C4'" N4A SING N N 27
UD4 "C4'" "C5'" SING N N 28
UD4 "C4'" "H4'" SING N N 29
UD4 N4A HN4A SING N N 30
UD4 N4A HN4B SING N N 31
UD4 "O5'" "C5'" SING N N 32
UD4 "C5'" "C6'" SING N N 33
UD4 "C5'" "H5'" SING N N 34
UD4 "C6'" "H6'" SING N N 35
UD4 "C6'" "H6'A" SING N N 36
UD4 "C6'" "H6'B" SING N N 37
UD4 "C1'" "O5'" SING N N 38
UD4 "C1'" "O1'" SING N N 39
UD4 "C1'" "H1'" SING N N 40
UD4 "O1'" PB SING N N 41
UD4 O3A PB SING N N 42
UD4 PB O2B DOUB N N 43
UD4 PB O1B SING N N 44
UD4 O1B HO1B SING N N 45
UD4 PA O3A SING N N 46
UD4 O1A PA DOUB N N 47
UD4 O2A PA SING N N 48
UD4 PA O5B SING N N 49
UD4 O2A HO2A SING N N 50
UD4 O5B C5B SING N N 51
UD4 C5B C4B SING N N 52
UD4 C5B H5B SING N N 53
UD4 C5B H5BA SING N N 54
UD4 C2B C4B SING N N 55
UD4 C4B O4B SING N N 56
UD4 C4B H4B SING N N 57
UD4 C1B O4B SING N N 58
UD4 C2B O3B SING N N 59
UD4 C2B C3B SING N N 60
UD4 C2B H2B SING N N 61
UD4 O3B HO3B SING N N 62
UD4 "O2'" C3B SING N N 63
UD4 C3B C1B SING N N 64
UD4 C3B H3B SING N N 65
UD4 "O2'" "HO2'" SING N N 66
UD4 C1B H1B SING N N 67
UD4 N3 HN3 SING N N 68
#
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
UD4 SMILES ACDLabs 10.04 O=P(OC1OC(C(N)C(O)C1NC(=O)C)C)(O)OP(=O)(O)OCC3OC(N2C=CC(=O)NC2=O)C(O)C3O
UD4 SMILES_CANONICAL CACTVS 3.341 C[C@H]1O[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](NC(C)=O)[C@@H](O)[C@@H]1N
UD4 SMILES CACTVS 3.341 C[CH]1O[CH](O[P](O)(=O)O[P](O)(=O)OC[CH]2O[CH]([CH](O)[CH]2O)N3C=CC(=O)NC3=O)[CH](NC(C)=O)[CH](O)[CH]1N
UD4 SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 C[C@@H]1[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)NC(=O)C)O)N
UD4 SMILES "OpenEye OEToolkits" 1.5.0 CC1C(C(C(C(O1)OP(=O)(O)OP(=O)(O)OCC2C(C(C(O2)N3C=CC(=O)NC3=O)O)O)NC(=O)C)O)N
UD4 InChI InChI 1.03 InChI=1S/C17H28N4O15P2/c1-6-10(18)13(25)11(19-7(2)22)16(33-6)35-38(30,31)36-37(28,29)32-5-8-12(24)14(26)15(34-8)21-4-3-9(23)20-17(21)27/h3-4,6,8,10-16,24-26H,5,18H2,1-2H3,(H,19,22)(H,28,29)(H,30,31)(H,20,23,27)/t6-,8-,10-,11-,12-,13+,14-,15-,16-/m1/s1
UD4 InChIKey InChI 1.03 FUUMLYWEEZBCQR-UINYWEPJSA-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
UD4 "SYSTEMATIC NAME" ACDLabs 10.04 "(2R,3R,4S,5S,6R)-3-(acetylamino)-5-amino-4-hydroxy-6-methyltetrahydro-2H-pyran-2-yl [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate (non-preferred name)"
UD4 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3R,4S,5S,6R)-3-acetamido-5-amino-4-hydroxy-6-methyl-oxan-2-yl] [[(2R,3S,4R,5R)-5-(2,4-dioxopyrimidin-1-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl] 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
UD4 'Create component' 2008-05-21 RCSB
UD4 'Modify descriptor' 2011-06-04 RCSB
UD4 'Modify synonyms' 2021-03-13 RCSB
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id UD4
_pdbx_chem_comp_synonyms.name (2R,3R,4S,5S,6R)-3-(acetylamino)-5-amino-4-hydroxy-6-methyltetrahydro-2H-pyran-2-yl
_pdbx_chem_comp_synonyms.provenance PDB
_pdbx_chem_comp_synonyms.type ?
#
_pdbe_chem_comp_synonyms.comp_id UD4
_pdbe_chem_comp_synonyms.name (2R,3R,4S,5S,6R)-3-(acetylamino)-5-amino-4-hydroxy-6-methyltetrahydro-2H-pyran-2-yl
_pdbe_chem_comp_synonyms.provenance wwPDB
_pdbe_chem_comp_synonyms.type ?
#
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
UD4 N3 N 18.866 2.715 1
UD4 C2 C 17.375 2.872 2
UD4 N1 N 16.765 4.242 3
UD4 C4 C 19.748 3.929 4
UD4 C5 C 19.138 5.299 5
UD4 C6 C 17.646 5.456 6
UD4 "O7'" O 10.301 -3.606 7
UD4 "C7'" C 10.301 -5.106 8
UD4 "C8'" C 11.600 -5.856 9
UD4 "N2'" N 9.002 -5.856 10
UD4 "C2'" C 7.702 -5.106 11
UD4 "C3'" C 6.404 -5.856 12
UD4 "O3'" O 6.404 -7.356 13
UD4 "C4'" C 5.104 -5.106 14
UD4 N4A N 3.805 -5.856 15
UD4 "C5'" C 5.104 -3.606 16
UD4 "C6'" C 3.805 -2.856 17
UD4 "O5'" O 6.404 -2.856 18
UD4 "C1'" C 7.702 -3.606 19
UD4 "O1'" O 9.002 -2.856 20
UD4 PB P 9.002 -1.356 21
UD4 O2B O 10.502 -1.356 22
UD4 O1B O 7.502 -1.356 23
UD4 O3A O 9.002 0.144 24
UD4 PA P 10.301 0.894 25
UD4 O2A O 11.051 -0.405 26
UD4 O1A O 9.551 2.193 27
UD4 O5B O 11.600 1.644 28
UD4 C5B C 11.600 3.144 29
UD4 C4B C 12.899 3.894 30
UD4 O4B O 14.269 3.284 31
UD4 C2B C 13.055 5.386 32
UD4 O3B O 11.941 6.390 33
UD4 C3B C 14.523 5.698 34
UD4 "O2'" O 15.133 7.068 35
UD4 C1B C 15.273 4.399 36
UD4 O2 O 16.493 1.658 37
UD4 O4 O 21.240 3.772 38
#
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
UD4 C2 N3 SINGLE NONE 1
UD4 C4 N3 SINGLE NONE 2
UD4 N1 C2 SINGLE NONE 3
UD4 C2 O2 DOUBLE NONE 4
UD4 C1B N1 SINGLE BEGINDASH 5
UD4 C6 N1 SINGLE NONE 6
UD4 C5 C4 SINGLE NONE 7
UD4 C4 O4 DOUBLE NONE 8
UD4 C6 C5 DOUBLE NONE 9
UD4 "O7'" "C7'" DOUBLE NONE 10
UD4 "C8'" "C7'" SINGLE NONE 11
UD4 "C7'" "N2'" SINGLE NONE 12
UD4 "C2'" "N2'" SINGLE BEGINDASH 13
UD4 "C2'" "C3'" SINGLE NONE 14
UD4 "C2'" "C1'" SINGLE NONE 15
UD4 "C3'" "O3'" SINGLE BEGINWEDGE 16
UD4 "C3'" "C4'" SINGLE NONE 17
UD4 "C4'" N4A SINGLE BEGINDASH 18
UD4 "C4'" "C5'" SINGLE NONE 19
UD4 "O5'" "C5'" SINGLE NONE 20
UD4 "C5'" "C6'" SINGLE BEGINWEDGE 21
UD4 "C1'" "O5'" SINGLE NONE 22
UD4 "C1'" "O1'" SINGLE BEGINDASH 23
UD4 "O1'" PB SINGLE NONE 24
UD4 O3A PB SINGLE NONE 25
UD4 PB O2B DOUBLE NONE 26
UD4 PB O1B SINGLE BEGINDASH 27
UD4 PA O3A SINGLE NONE 28
UD4 O1A PA DOUBLE NONE 29
UD4 PA O2A SINGLE BEGINDASH 30
UD4 PA O5B SINGLE NONE 31
UD4 O5B C5B SINGLE NONE 32
UD4 C4B C5B SINGLE BEGINDASH 33
UD4 C2B C4B SINGLE NONE 34
UD4 C4B O4B SINGLE NONE 35
UD4 C1B O4B SINGLE NONE 36
UD4 C2B O3B SINGLE BEGINWEDGE 37
UD4 C2B C3B SINGLE NONE 38
UD4 C3B "O2'" SINGLE BEGINWEDGE 39
UD4 C3B C1B SINGLE NONE 40
#
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
UD4 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
UD4 amide F1 fragment CC(N)=O InChI=1S/C2H5NO/c1-2(3)4/h1H3,(H2,3,4) DLFVBJFMPXGRIB-UHFFFAOYSA-N
UD4 phosphate F2 fragment O=P(O)(O)O InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4) NBIIXXVUZAFLBC-UHFFFAOYSA-N
UD4 pyranose F3 fragment OC1CCCCO1 InChI=1S/C5H10O2/c6-5-3-1-2-4-7-5/h5-6H,1-4H2 CELWCAITJAEQNL-UHFFFAOYSA-N
UD4 pyrimidine F4 fragment c1cncnc1 InChI=1S/C4H4N2/c1-2-5-4-6-3-1/h1-4H CZPWVGJYEJSRLH-UHFFFAOYSA-N
UD4 ribose F5 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
UD4 N3 S1 1
UD4 C2 S1 1
UD4 N1 S1 1
UD4 C4 S1 1
UD4 C5 S1 1
UD4 C6 S1 1
UD4 "C2'" S1 1
UD4 "C3'" S1 1
UD4 "C4'" S1 1
UD4 "C5'" S1 1
UD4 "O5'" S1 1
UD4 "C1'" S1 1
UD4 "O1'" S1 1
UD4 PB S1 1
UD4 O2B S1 1
UD4 O3A S1 1
UD4 PA S1 1
UD4 O1A S1 1
UD4 O5B S1 1
UD4 C5B S1 1
UD4 C4B S1 1
UD4 O4B S1 1
UD4 C2B S1 1
UD4 C3B S1 1
UD4 C1B S1 1
UD4 O2 S1 1
UD4 O4 S1 1
UD4 "N2'" F1 1
UD4 "C7'" F1 1
UD4 "O7'" F1 1
UD4 "C8'" F1 1
UD4 "O1'" F2 1
UD4 PB F2 1
UD4 O2B F2 1
UD4 O3A F2 1
UD4 O1B F2 1
UD4 O3A F2 2
UD4 PA F2 2
UD4 O1A F2 2
UD4 O2A F2 2
UD4 O5B F2 2
UD4 "C4'" F3 1
UD4 "C5'" F3 1
UD4 "O5'" F3 1
UD4 "C1'" F3 1
UD4 "C2'" F3 1
UD4 "C3'" F3 1
UD4 "O1'" F3 1
UD4 C5 F4 1
UD4 C4 F4 1
UD4 N3 F4 1
UD4 C2 F4 1
UD4 N1 F4 1
UD4 C6 F4 1
UD4 C3B F5 1
UD4 C2B F5 1
UD4 C4B F5 1
UD4 O4B F5 1
UD4 C1B F5 1
UD4 C5B F5 1
UD4 O5B F5 1
UD4 O3B F5 1
UD4 "O2'" F5 1
#
_pdbe_chem_comp_rdkit_properties.comp_id UD4
_pdbe_chem_comp_rdkit_properties.exactmw 590.103
_pdbe_chem_comp_rdkit_properties.amw 590.372
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 19
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 9
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 17
_pdbe_chem_comp_rdkit_properties.NumHBD 8
_pdbe_chem_comp_rdkit_properties.NumHBA 17
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 38
_pdbe_chem_comp_rdkit_properties.NumAtoms 66
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 21
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 1
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.706
_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 11
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 252.830
_pdbe_chem_comp_rdkit_properties.tpsa 291.420
_pdbe_chem_comp_rdkit_properties.CrippenClogP -1.856
_pdbe_chem_comp_rdkit_properties.CrippenMR 121.157
_pdbe_chem_comp_rdkit_properties.chi0v 19.096
_pdbe_chem_comp_rdkit_properties.chi1v 11.620
_pdbe_chem_comp_rdkit_properties.chi2v 5.868
_pdbe_chem_comp_rdkit_properties.chi3v 5.868
_pdbe_chem_comp_rdkit_properties.chi4v 3.938
_pdbe_chem_comp_rdkit_properties.chi0n 45.307
_pdbe_chem_comp_rdkit_properties.chi1n 22.029
_pdbe_chem_comp_rdkit_properties.chi2n 3.563
_pdbe_chem_comp_rdkit_properties.chi3n 3.563
_pdbe_chem_comp_rdkit_properties.chi4n 2.170
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.830
_pdbe_chem_comp_rdkit_properties.kappa1 10.218
_pdbe_chem_comp_rdkit_properties.kappa2 11.729
_pdbe_chem_comp_rdkit_properties.kappa3 7.218
_pdbe_chem_comp_rdkit_properties.Phi 3.154
#
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
UD4 UniChem PDBe UD4
UD4 UniChem 'KEGG LIGAND' C04630
UD4 UniChem ChEBI 63273
UD4 UniChem ZINC ZINC000056871102
UD4 UniChem PubChem 24856359
UD4 UniChem BRENDA 166203
UD4 UniChem BRENDA 171711
UD4 UniChem BRENDA 28627
UD4 UniChem BRENDA 171534
UD4 UniChem Nikkaji J2.752.432J
UD4 UniChem BRENDA 169631
#
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
UD4 N3 -8.155 -1.226 0.450 ETKDGv3 1
UD4 C2 -6.953 -0.644 -0.058 ETKDGv3 2
UD4 N1 -7.025 0.558 -0.856 ETKDGv3 3
UD4 C4 -9.406 -0.589 0.186 ETKDGv3 4
UD4 C5 -9.438 0.653 -0.595 ETKDGv3 5
UD4 C6 -8.308 1.183 -1.073 ETKDGv3 6
UD4 "O7'" 6.003 -2.754 -2.220 ETKDGv3 7
UD4 "C7'" 6.351 -3.017 -1.037 ETKDGv3 8
UD4 "C8'" 6.900 -4.368 -0.713 ETKDGv3 9
UD4 "N2'" 6.261 -2.017 -0.013 ETKDGv3 10
UD4 "C2'" 5.683 -0.690 -0.257 ETKDGv3 11
UD4 "C3'" 6.087 0.294 0.861 ETKDGv3 12
UD4 "O3'" 7.483 0.473 0.877 ETKDGv3 13
UD4 "C4'" 5.352 1.645 0.693 ETKDGv3 14
UD4 N4A 5.606 2.501 1.858 ETKDGv3 15
UD4 "C5'" 3.832 1.376 0.535 ETKDGv3 16
UD4 "C6'" 3.049 2.668 0.282 ETKDGv3 17
UD4 "O5'" 3.587 0.507 -0.560 ETKDGv3 18
UD4 "C1'" 4.148 -0.782 -0.352 ETKDGv3 19
UD4 "O1'" 3.625 -1.402 0.810 ETKDGv3 20
UD4 PB 2.031 -1.933 0.504 ETKDGv3 21
UD4 O2B 2.065 -3.052 -0.514 ETKDGv3 22
UD4 O1B 1.387 -2.520 1.956 ETKDGv3 23
UD4 O3A 1.100 -0.632 -0.084 ETKDGv3 24
UD4 PA -0.533 -1.115 -0.094 ETKDGv3 25
UD4 O2A -0.715 -2.597 -0.895 ETKDGv3 26
UD4 O1A -1.036 -1.239 1.328 ETKDGv3 27
UD4 O5B -1.427 0.089 -0.906 ETKDGv3 28
UD4 C5B -2.769 -0.332 -0.992 ETKDGv3 29
UD4 C4B -3.606 0.767 -1.658 ETKDGv3 30
UD4 O4B -4.911 0.275 -1.894 ETKDGv3 31
UD4 C2B -3.686 2.034 -0.790 ETKDGv3 32
UD4 O3B -3.450 3.165 -1.591 ETKDGv3 33
UD4 C3B -5.113 2.009 -0.291 ETKDGv3 34
UD4 "O2'" -5.665 3.293 -0.164 ETKDGv3 35
UD4 C1B -5.818 1.220 -1.378 ETKDGv3 36
UD4 O2 -5.845 -1.184 0.203 ETKDGv3 37
UD4 O4 -10.475 -1.088 0.625 ETKDGv3 38
UD4 H5 -10.384 1.147 -0.781 ETKDGv3 39
UD4 H6 -8.369 2.105 -1.638 ETKDGv3 40
UD4 "H8'" 6.706 -5.078 -1.545 ETKDGv3 41
UD4 "H8'A" 6.416 -4.757 0.208 ETKDGv3 42
UD4 "H8'B" 7.994 -4.292 -0.547 ETKDGv3 43
UD4 "HN2'" 6.637 -2.249 0.935 ETKDGv3 44
UD4 "H2'" 6.073 -0.296 -1.224 ETKDGv3 45
UD4 "H3'" 5.791 -0.141 1.841 ETKDGv3 46
UD4 "HO3'" 7.746 0.880 0.010 ETKDGv3 47
UD4 "H4'" 5.728 2.149 -0.227 ETKDGv3 48
UD4 HN4A 6.638 2.569 2.012 ETKDGv3 49
UD4 HN4B 5.308 3.475 1.626 ETKDGv3 50
UD4 "H5'" 3.429 0.941 1.478 ETKDGv3 51
UD4 "H6'" 3.052 3.317 1.182 ETKDGv3 52
UD4 "H6'A" 1.991 2.424 0.049 ETKDGv3 53
UD4 "H6'B" 3.480 3.224 -0.578 ETKDGv3 54
UD4 "H1'" 3.931 -1.393 -1.257 ETKDGv3 55
UD4 HO1B 2.029 -3.212 2.255 ETKDGv3 56
UD4 HO2A -0.428 -2.416 -1.826 ETKDGv3 57
UD4 H5B -3.193 -0.539 0.017 ETKDGv3 58
UD4 H5BA -2.846 -1.249 -1.618 ETKDGv3 59
UD4 H4B -3.139 1.003 -2.641 ETKDGv3 60
UD4 H2B -2.971 2.009 0.068 ETKDGv3 61
UD4 HO3B -3.188 3.902 -0.980 ETKDGv3 62
UD4 H3B -5.162 1.461 0.680 ETKDGv3 63
UD4 "HO2'" -5.275 3.685 0.661 ETKDGv3 64
UD4 H1B -6.093 1.905 -2.213 ETKDGv3 65
UD4 HN3 -8.119 -2.103 1.016 ETKDGv3 66
#