data_UD2
#
_chem_comp.id UD2
_chem_comp.name URIDINE-DIPHOSPHATE-N-ACETYLGALACTOSAMINE
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C17 H27 N3 O17 P2"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms
;(2R,3R,4R,5R,6R)-3-(acetylamino)-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-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
;
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2001-02-21
_chem_comp.pdbx_modified_date 2020-06-17
_chem_comp.pdbx_ambiguous_flag ?
_chem_comp.pdbx_release_status REL
_chem_comp.pdbx_replaced_by ?
_chem_comp.pdbx_replaces ?
_chem_comp.formula_weight 607.354
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code UD2
_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 1OMZ
_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
UD2 "C1'" "C1'" C 0 1 N N R N N N -21.840 -55.954 -41.771 4.577 0.429 -0.412 "C1'" UD2 1
UD2 "C2'" "C2'" C 0 1 N N R N N N -22.855 -56.648 -40.824 5.330 0.789 0.871 "C2'" UD2 2
UD2 "C3'" "C3'" C 0 1 N N R N N N -23.963 -57.332 -41.660 4.496 1.788 1.679 "C3'" UD2 3
UD2 "C4'" "C4'" C 0 1 N N R N N N -24.679 -56.265 -42.531 4.208 3.016 0.811 "C4'" UD2 4
UD2 "C5'" "C5'" C 0 1 N N R N N N -23.627 -55.592 -43.464 3.498 2.570 -0.470 "C5'" UD2 5
UD2 "C6'" "C6'" C 0 1 N N N N N N -24.204 -54.489 -44.350 3.260 3.784 -1.370 "C6'" UD2 6
UD2 "C7'" "C7'" C 0 1 N N N N N N -21.395 -57.257 -38.911 6.614 -1.209 1.416 "C7'" UD2 7
UD2 "C8'" "C8'" C 0 1 N N N N N N -21.163 -58.317 -37.842 6.840 -2.454 2.233 "C8'" UD2 8
UD2 "N2'" "N2'" N 0 1 N N N N N N -22.149 -57.621 -39.965 5.549 -0.422 1.666 "N2'" UD2 9
UD2 "O1'" "O1'" O 0 1 N N N N N N -20.989 -56.938 -42.384 3.342 -0.207 -0.078 "O1'" UD2 10
UD2 "O3'" "O3'" O 0 1 N N N N N N -24.901 -57.956 -40.798 5.224 2.186 2.843 "O3'" UD2 11
UD2 "O4'" "O4'" O 0 1 N N N N N N -25.295 -55.274 -41.693 5.437 3.663 0.476 "O4'" UD2 12
UD2 "O5'" "O5'" O 0 1 N N N N N N -22.515 -55.015 -42.683 4.313 1.619 -1.158 "O5'" UD2 13
UD2 "O6'" "O6'" O 0 1 N N N N N N -23.546 -54.430 -45.610 2.497 3.389 -2.512 "O6'" UD2 14
UD2 "O7'" "O7'" O 0 1 N N N N N N -20.885 -56.129 -38.777 7.391 -0.914 0.532 "O7'" UD2 15
UD2 N1 N1 N 0 1 N N N N N N -24.294 -60.063 -48.284 -5.477 1.043 0.383 N1 UD2 16
UD2 C2 C2 C 0 1 N N N N N N -25.218 -60.200 -49.343 -6.056 1.956 1.183 C2 UD2 17
UD2 N3 N3 N 0 1 N N N N N N -24.855 -59.492 -50.500 -6.384 3.176 0.718 N3 UD2 18
UD2 C4 C4 C 0 1 N N N N N N -23.699 -58.694 -50.685 -6.133 3.503 -0.566 C4 UD2 19
UD2 C5 C5 C 0 1 N N N N N N -22.811 -58.610 -49.547 -5.523 2.552 -1.419 C5 UD2 20
UD2 C6 C6 C 0 1 N N N N N N -23.120 -59.272 -48.422 -5.201 1.338 -0.925 C6 UD2 21
UD2 O2 O2 O 0 1 N N N N N N -26.246 -60.869 -49.273 -6.288 1.675 2.343 O2 UD2 22
UD2 O4 O4 O 0 1 N N N N N N -23.498 -58.130 -51.747 -6.429 4.607 -0.988 O4 UD2 23
UD2 C1B C1* C 0 1 N N R N N N -24.595 -60.780 -47.012 -5.132 -0.276 0.918 C1B UD2 24
UD2 C2B C2* C 0 1 N N R N N N -23.456 -61.744 -46.672 -5.967 -1.382 0.224 C2B UD2 25
UD2 "O2'" O2* O 0 1 N N N N N N -23.578 -63.019 -47.276 -7.226 -1.556 0.877 "O2'" UD2 26
UD2 C3B C3* C 0 1 N N S N N N -23.463 -61.792 -45.152 -5.071 -2.631 0.410 C3B UD2 27
UD2 C4B C4* C 0 1 N N R N N N -24.008 -60.427 -44.741 -3.667 -2.052 0.669 C4B UD2 28
UD2 O4B O4* O 0 1 N N N N N N -24.699 -59.859 -45.902 -3.771 -0.622 0.581 O4B UD2 29
UD2 O3B O3* O 0 1 N N N N N N -24.318 -62.812 -44.594 -5.511 -3.398 1.532 O3B UD2 30
UD2 C5B C5* C 0 1 N N N N N N -22.901 -59.489 -44.304 -2.688 -2.569 -0.388 C5B UD2 31
UD2 O5B O5* O 0 1 N N N N N N -21.944 -59.321 -45.336 -1.368 -2.122 -0.073 O5B UD2 32
UD2 PA PA P 0 1 N N S N N N -20.393 -59.122 -45.021 -0.083 -2.481 -0.975 PA UD2 33
UD2 O1A O1A O 0 1 N N N N N N -19.947 -59.871 -43.811 0.177 -4.069 -0.930 O1A UD2 34
UD2 O2A O2A O 0 1 N N N N N N -19.612 -59.327 -46.241 -0.328 -2.060 -2.372 O2A UD2 35
UD2 O3A O3A O 0 1 N N N N N N -20.222 -57.590 -44.680 1.208 -1.709 -0.400 O3A UD2 36
UD2 PB PB P 0 1 N N R N N N -19.783 -56.724 -43.442 2.638 -1.306 -1.021 PB UD2 37
UD2 O1B O1B O 0 1 N N N N N N -18.642 -57.385 -42.803 3.572 -2.615 -1.110 O1B UD2 38
UD2 O2B O2B O 0 1 N N N N N N -19.775 -55.288 -43.869 2.447 -0.744 -2.376 O2B UD2 39
UD2 "H1'" "H1'" H 0 1 N N N N N N -21.158 -55.307 -41.200 5.184 -0.249 -1.012 "H1'" UD2 40
UD2 "H2'" "H2'" H 0 1 N N N N N N -23.331 -55.900 -40.173 6.290 1.236 0.616 "H2'" UD2 41
UD2 "H3'" "H3'" H 0 1 N N N N N N -23.513 -58.096 -42.310 3.557 1.322 1.978 "H3'" UD2 42
UD2 "H4'" "H4'" H 0 1 N N N N N N -25.462 -56.746 -43.135 3.570 3.709 1.360 "H4'" UD2 43
UD2 "H5'" "H5'" H 0 1 N N N N N N -23.271 -56.403 -44.116 2.542 2.113 -0.216 "H5'" UD2 44
UD2 "H6'1" "1H6'" H 0 0 N N N N N N -24.078 -53.523 -43.839 2.714 4.547 -0.815 "H6'1" UD2 45
UD2 "H6'2" "2H6'" H 0 0 N N N N N N -25.267 -54.709 -44.526 4.219 4.188 -1.696 "H6'2" UD2 46
UD2 "H8'1" "1H8'" H 0 0 N N N N N N -21.107 -59.309 -38.314 7.743 -2.957 1.888 "H8'1" UD2 47
UD2 "H8'2" "2H8'" H 0 0 N N N N N N -20.219 -58.107 -37.317 6.952 -2.184 3.283 "H8'2" UD2 48
UD2 "H8'3" "3H8'" H 0 0 N N N N N N -21.995 -58.300 -37.123 5.986 -3.123 2.120 "H8'3" UD2 49
UD2 "HN2'" "HN2'" H 0 0 N N N N N N -22.235 -58.595 -40.176 4.927 -0.658 2.372 "HN2'" UD2 50
UD2 "HO3'" "HO3'" H 0 0 N N N N N N -24.505 -58.095 -39.946 4.754 2.819 3.403 "HO3'" UD2 51
UD2 "HO4'" "HO4'" H 0 0 N N N N N N -25.431 -55.633 -40.824 5.330 4.451 -0.075 "HO4'" UD2 52
UD2 "HO6'" "HO6'" H 0 0 N N N N N N -24.193 -54.417 -46.305 2.308 4.110 -3.128 "HO6'" UD2 53
UD2 HN3 HN3 H 0 1 N N N N N N -25.480 -59.558 -51.278 -6.802 3.822 1.308 HN3 UD2 54
UD2 H5 H5 H 0 1 N N N N N N -21.908 -58.020 -49.602 -5.315 2.796 -2.450 H5 UD2 55
UD2 H6 H6 H 0 1 N N N N N N -22.446 -59.201 -47.581 -4.734 0.600 -1.561 H6 UD2 56
UD2 H1B H1* H 0 1 N N N N N N -25.547 -61.311 -47.161 -5.281 -0.303 1.997 H1B UD2 57
UD2 H2B H2* H 0 1 N N N N N N -22.494 -61.396 -47.076 -6.107 -1.158 -0.834 H2B UD2 58
UD2 "HO2'" HO2* H 0 0 N N N N N N -23.605 -62.921 -48.221 -7.785 -2.237 0.479 "HO2'" UD2 59
UD2 H3B H3* H 0 1 N N N N N N -22.453 -62.026 -44.785 -5.073 -3.240 -0.494 H3B UD2 60
UD2 H4B H4* H 0 1 N N N N N N -24.689 -60.551 -43.886 -3.325 -2.341 1.663 H4B UD2 61
UD2 HO3A HO3* H 0 0 N N N N N N -24.506 -63.466 -45.257 -6.412 -3.738 1.448 HO3A UD2 62
UD2 "H5'1" 1H5* H 0 0 N N N N N N -22.403 -59.911 -43.419 -2.710 -3.659 -0.401 "H5'1" UD2 63
UD2 "H5'2" 2H5* H 0 0 N N N N N N -23.342 -58.509 -44.069 -2.977 -2.188 -1.367 "H5'2" UD2 64
UD2 HOA2 HO1A H 0 0 N N N N N N -19.852 -60.792 -44.025 0.346 -4.415 -0.043 HOA2 UD2 65
UD2 HOB2 HO1B H 0 0 N N N N N N -17.957 -57.528 -43.446 3.740 -3.036 -0.256 HOB2 UD2 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
UD2 O4 C4 DOUB N N 1
UD2 C4 N3 SING N N 2
UD2 C4 C5 SING N N 3
UD2 N3 C2 SING N N 4
UD2 C5 C6 DOUB N N 5
UD2 C2 O2 DOUB N N 6
UD2 C2 N1 SING N N 7
UD2 C6 N1 SING N N 8
UD2 N1 C1B SING N N 9
UD2 "O2'" C2B SING N N 10
UD2 C1B C2B SING N N 11
UD2 C1B O4B SING N N 12
UD2 C2B C3B SING N N 13
UD2 O2A PA DOUB N N 14
UD2 O4B C4B SING N N 15
UD2 "O6'" "C6'" SING N N 16
UD2 O5B PA SING N N 17
UD2 O5B C5B SING N N 18
UD2 C3B C4B SING N N 19
UD2 C3B O3B SING N N 20
UD2 PA O3A SING N N 21
UD2 PA O1A SING N N 22
UD2 C4B C5B SING N N 23
UD2 O3A PB SING N N 24
UD2 "C6'" "C5'" SING N N 25
UD2 O2B PB DOUB N N 26
UD2 "C5'" "O5'" SING N N 27
UD2 "C5'" "C4'" SING N N 28
UD2 PB O1B SING N N 29
UD2 PB "O1'" SING N N 30
UD2 "O5'" "C1'" SING N N 31
UD2 "C4'" "O4'" SING N N 32
UD2 "C4'" "C3'" SING N N 33
UD2 "O1'" "C1'" SING N N 34
UD2 "C1'" "C2'" SING N N 35
UD2 "C3'" "C2'" SING N N 36
UD2 "C3'" "O3'" SING N N 37
UD2 "C2'" "N2'" SING N N 38
UD2 "N2'" "C7'" SING N N 39
UD2 "C7'" "O7'" DOUB N N 40
UD2 "C7'" "C8'" SING N N 41
UD2 "C1'" "H1'" SING N N 42
UD2 "C2'" "H2'" SING N N 43
UD2 "C3'" "H3'" SING N N 44
UD2 "C4'" "H4'" SING N N 45
UD2 "C5'" "H5'" SING N N 46
UD2 "C6'" "H6'1" SING N N 47
UD2 "C6'" "H6'2" SING N N 48
UD2 "C8'" "H8'1" SING N N 49
UD2 "C8'" "H8'2" SING N N 50
UD2 "C8'" "H8'3" SING N N 51
UD2 "N2'" "HN2'" SING N N 52
UD2 "O3'" "HO3'" SING N N 53
UD2 "O4'" "HO4'" SING N N 54
UD2 "O6'" "HO6'" SING N N 55
UD2 N3 HN3 SING N N 56
UD2 C5 H5 SING N N 57
UD2 C6 H6 SING N N 58
UD2 C1B H1B SING N N 59
UD2 C2B H2B SING N N 60
UD2 "O2'" "HO2'" SING N N 61
UD2 C3B H3B SING N N 62
UD2 C4B H4B SING N N 63
UD2 O3B HO3A SING N N 64
UD2 C5B "H5'1" SING N N 65
UD2 C5B "H5'2" SING N N 66
UD2 O1A HOA2 SING N N 67
UD2 O1B HOB2 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
UD2 SMILES ACDLabs 10.04 O=P(OC1OC(C(O)C(O)C1NC(=O)C)CO)(O)OP(=O)(O)OCC3OC(N2C=CC(=O)NC2=O)C(O)C3O
UD2 SMILES_CANONICAL CACTVS 3.341 CC(=O)N[C@@H]1[C@@H](O)[C@@H](O)[C@@H](CO)O[C@@H]1O[P@](O)(=O)O[P@](O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)N3C=CC(=O)NC3=O
UD2 SMILES CACTVS 3.341 CC(=O)N[CH]1[CH](O)[CH](O)[CH](CO)O[CH]1O[P](O)(=O)O[P](O)(=O)OC[CH]2O[CH]([CH](O)[CH]2O)N3C=CC(=O)NC3=O
UD2 SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 CC(=O)N[C@@H]1[C@H]([C@H]([C@H](O[C@@H]1O[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)CO)O)O
UD2 SMILES "OpenEye OEToolkits" 1.5.0 CC(=O)NC1C(C(C(OC1OP(=O)(O)OP(=O)(O)OCC2C(C(C(O2)N3C=CC(=O)NC3=O)O)O)CO)O)O
UD2 InChI InChI 1.03 InChI=1S/C17H27N3O17P2/c1-6(22)18-10-13(26)11(24)7(4-21)35-16(10)36-39(31,32)37-38(29,30)33-5-8-12(25)14(27)15(34-8)20-3-2-9(23)19-17(20)28/h2-3,7-8,10-16,21,24-27H,4-5H2,1H3,(H,18,22)(H,29,30)(H,31,32)(H,19,23,28)/t7-,8-,10-,11+,12-,13-,14-,15-,16-/m1/s1
UD2 InChIKey InChI 1.03 LFTYTUAZOPRMMI-NESSUJCYSA-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
UD2 "SYSTEMATIC NAME" ACDLabs 10.04 "(2R,3R,4R,5R,6R)-3-(acetylamino)-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-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)"
UD2 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[[(2R,3R,4R,5R,6R)-3-acetamido-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy-hydroxy-phosphoryl] [(2R,3S,4R,5R)-5-(2,4-dioxopyrimidin-1-yl)-3,4-dihydroxy-oxolan-2-yl]methyl 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
UD2 'Create component' 2001-02-21 RCSB
UD2 'Modify descriptor' 2011-06-04 RCSB
UD2 'Modify synonyms' 2020-06-05 PDBE
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id UD2
_pdbx_chem_comp_synonyms.name
"(2R,3R,4R,5R,6R)-3-(acetylamino)-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-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"
_pdbx_chem_comp_synonyms.provenance ?
_pdbx_chem_comp_synonyms.type ?
#
_pdbe_chem_comp_drugbank_details.comp_id UD2
_pdbe_chem_comp_drugbank_details.drugbank_id DB02196
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name Uridine-Diphosphate-N-Acetylgalactosamine
_pdbe_chem_comp_drugbank_details.description ?
_pdbe_chem_comp_drugbank_details.cas_number ?
_pdbe_chem_comp_drugbank_details.mechanism_of_action ?
#
_pdbe_chem_comp_synonyms.comp_id UD2
_pdbe_chem_comp_synonyms.name
'(2R,3R,4R,5R,6R)-3-(acetylamino)-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-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'
_pdbe_chem_comp_synonyms.provenance wwPDB
_pdbe_chem_comp_synonyms.type ?
#
_pdbe_chem_comp_drugbank_classification.comp_id UD2
_pdbe_chem_comp_drugbank_classification.drugbank_id DB02196
_pdbe_chem_comp_drugbank_classification.parent 'Pyrimidine nucleotide sugars'
_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 nucleotide sugars. These are pyrimidine nucleotides bound to a saccharide derivative through the terminal phosphate group.'
#
loop_
_pdbe_chem_comp_drugbank_targets.comp_id
_pdbe_chem_comp_drugbank_targets.drugbank_id
_pdbe_chem_comp_drugbank_targets.name
_pdbe_chem_comp_drugbank_targets.organism
_pdbe_chem_comp_drugbank_targets.uniprot_id
_pdbe_chem_comp_drugbank_targets.pharmacologically_active
_pdbe_chem_comp_drugbank_targets.ordinal
UD2 DB02196 'UDP-N-acetylhexosamine pyrophosphorylase' Humans Q16222 unknown 1
UD2 DB02196 'UDP-glucose 4-epimerase' Humans Q14376 unknown 2
UD2 DB02196 'UDP-N-acetylglucosamine 2-epimerase' 'Escherichia coli (strain K12)' P27828 unknown 3
UD2 DB02196 'Histo-blood group ABO system transferase' Humans P16442 unknown 4
UD2 DB02196 'UDP-N-acetylglucosamine--N-acetylmuramyl-(pentapeptide) pyrophosphoryl-undecaprenol N-acetylglucosamine transferase' 'Escherichia coli (strain K12)' P17443 unknown 5
UD2 DB02196 'Exostosin-like 2' Humans Q9UBQ6 unknown 6
UD2 DB02196 WbpP 'Pseudomonas aeruginosa' Q8KN66 unknown 7
#
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
UD2 "C1'" C 7.702 -3.606 1
UD2 "C2'" C 7.702 -5.106 2
UD2 "C3'" C 6.404 -5.856 3
UD2 "C4'" C 5.104 -5.106 4
UD2 "C5'" C 5.104 -3.606 5
UD2 "C6'" C 3.805 -2.856 6
UD2 "C7'" C 10.301 -5.106 7
UD2 "C8'" C 11.600 -5.856 8
UD2 "N2'" N 9.002 -5.856 9
UD2 "O1'" O 9.002 -2.856 10
UD2 "O3'" O 6.404 -7.356 11
UD2 "O4'" O 3.805 -5.856 12
UD2 "O5'" O 6.404 -2.856 13
UD2 "O6'" O 3.805 -1.356 14
UD2 "O7'" O 10.301 -3.606 15
UD2 N1 N 16.765 4.242 16
UD2 C2 C 17.375 2.872 17
UD2 N3 N 18.866 2.715 18
UD2 C4 C 19.748 3.929 19
UD2 C5 C 19.138 5.299 20
UD2 C6 C 17.646 5.456 21
UD2 O2 O 16.493 1.658 22
UD2 O4 O 21.240 3.772 23
UD2 C1B C 15.273 4.399 24
UD2 C2B C 14.523 5.698 25
UD2 "O2'" O 15.133 7.068 26
UD2 C3B C 13.055 5.386 27
UD2 C4B C 12.899 3.894 28
UD2 O4B O 14.269 3.284 29
UD2 O3B O 11.941 6.390 30
UD2 C5B C 11.600 3.144 31
UD2 O5B O 11.600 1.644 32
UD2 PA P 10.301 0.894 33
UD2 O1A O 11.051 -0.405 34
UD2 O2A O 9.551 2.193 35
UD2 O3A O 9.002 0.144 36
UD2 PB P 9.002 -1.356 37
UD2 O1B O 7.502 -1.356 38
UD2 O2B O 10.502 -1.356 39
#
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
UD2 O4 C4 DOUBLE NONE 1
UD2 C4 N3 SINGLE NONE 2
UD2 C4 C5 SINGLE NONE 3
UD2 N3 C2 SINGLE NONE 4
UD2 C5 C6 DOUBLE NONE 5
UD2 C2 O2 DOUBLE NONE 6
UD2 C2 N1 SINGLE NONE 7
UD2 C6 N1 SINGLE NONE 8
UD2 C1B N1 SINGLE BEGINDASH 9
UD2 C2B "O2'" SINGLE BEGINWEDGE 10
UD2 C1B C2B SINGLE NONE 11
UD2 C1B O4B SINGLE NONE 12
UD2 C2B C3B SINGLE NONE 13
UD2 O2A PA DOUBLE NONE 14
UD2 O4B C4B SINGLE NONE 15
UD2 "O6'" "C6'" SINGLE NONE 16
UD2 O5B PA SINGLE NONE 17
UD2 O5B C5B SINGLE NONE 18
UD2 C3B C4B SINGLE NONE 19
UD2 C3B O3B SINGLE BEGINWEDGE 20
UD2 PA O3A SINGLE NONE 21
UD2 PA O1A SINGLE BEGINWEDGE 22
UD2 C4B C5B SINGLE BEGINDASH 23
UD2 O3A PB SINGLE NONE 24
UD2 "C5'" "C6'" SINGLE BEGINWEDGE 25
UD2 O2B PB DOUBLE NONE 26
UD2 "C5'" "O5'" SINGLE NONE 27
UD2 "C5'" "C4'" SINGLE NONE 28
UD2 PB O1B SINGLE BEGINDASH 29
UD2 PB "O1'" SINGLE NONE 30
UD2 "O5'" "C1'" SINGLE NONE 31
UD2 "C4'" "O4'" SINGLE BEGINWEDGE 32
UD2 "C4'" "C3'" SINGLE NONE 33
UD2 "C1'" "O1'" SINGLE BEGINDASH 34
UD2 "C1'" "C2'" SINGLE NONE 35
UD2 "C3'" "C2'" SINGLE NONE 36
UD2 "C3'" "O3'" SINGLE BEGINWEDGE 37
UD2 "C2'" "N2'" SINGLE BEGINDASH 38
UD2 "N2'" "C7'" SINGLE NONE 39
UD2 "C7'" "O7'" DOUBLE NONE 40
UD2 "C7'" "C8'" SINGLE NONE 41
#
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
UD2 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
UD2 amide F1 fragment CC(N)=O InChI=1S/C2H5NO/c1-2(3)4/h1H3,(H2,3,4) DLFVBJFMPXGRIB-UHFFFAOYSA-N
UD2 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
UD2 pyranose F3 fragment OC1CCCCO1 InChI=1S/C5H10O2/c6-5-3-1-2-4-7-5/h5-6H,1-4H2 CELWCAITJAEQNL-UHFFFAOYSA-N
UD2 pyrimidine F4 fragment c1cncnc1 InChI=1S/C4H4N2/c1-2-5-4-6-3-1/h1-4H CZPWVGJYEJSRLH-UHFFFAOYSA-N
UD2 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
UD2 "C1'" S1 1
UD2 "C2'" S1 1
UD2 "C3'" S1 1
UD2 "C4'" S1 1
UD2 "C5'" S1 1
UD2 "O1'" S1 1
UD2 "O5'" S1 1
UD2 N1 S1 1
UD2 C2 S1 1
UD2 N3 S1 1
UD2 C4 S1 1
UD2 C5 S1 1
UD2 C6 S1 1
UD2 O2 S1 1
UD2 O4 S1 1
UD2 C1B S1 1
UD2 C2B S1 1
UD2 C3B S1 1
UD2 C4B S1 1
UD2 O4B S1 1
UD2 C5B S1 1
UD2 O5B S1 1
UD2 PA S1 1
UD2 O2A S1 1
UD2 O3A S1 1
UD2 PB S1 1
UD2 O2B S1 1
UD2 "N2'" F1 1
UD2 "C7'" F1 1
UD2 "O7'" F1 1
UD2 "C8'" F1 1
UD2 "O1'" F2 1
UD2 PB F2 1
UD2 O2B F2 1
UD2 O3A F2 1
UD2 O1B F2 1
UD2 O5B F2 2
UD2 PA F2 2
UD2 O2A F2 2
UD2 O3A F2 2
UD2 O1A F2 2
UD2 "C4'" F3 1
UD2 "C5'" F3 1
UD2 "O5'" F3 1
UD2 "C1'" F3 1
UD2 "C2'" F3 1
UD2 "C3'" F3 1
UD2 "O1'" F3 1
UD2 C5 F4 1
UD2 C4 F4 1
UD2 N3 F4 1
UD2 C2 F4 1
UD2 N1 F4 1
UD2 C6 F4 1
UD2 C2B F5 1
UD2 C3B F5 1
UD2 C4B F5 1
UD2 O4B F5 1
UD2 C1B F5 1
UD2 C5B F5 1
UD2 O5B F5 1
UD2 O3B F5 1
UD2 "O2'" F5 1
#
_pdbe_chem_comp_rdkit_properties.comp_id UD2
_pdbe_chem_comp_rdkit_properties.exactmw 607.082
_pdbe_chem_comp_rdkit_properties.amw 607.355
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 20
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 9
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 18
_pdbe_chem_comp_rdkit_properties.NumHBD 9
_pdbe_chem_comp_rdkit_properties.NumHBA 18
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 39
_pdbe_chem_comp_rdkit_properties.NumAtoms 66
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 22
_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 255.731
_pdbe_chem_comp_rdkit_properties.tpsa 305.860
_pdbe_chem_comp_rdkit_properties.CrippenClogP -2.850
_pdbe_chem_comp_rdkit_properties.CrippenMR 120.600
_pdbe_chem_comp_rdkit_properties.chi0v 19.465
_pdbe_chem_comp_rdkit_properties.chi1v 11.805
_pdbe_chem_comp_rdkit_properties.chi2v 5.943
_pdbe_chem_comp_rdkit_properties.chi3v 5.943
_pdbe_chem_comp_rdkit_properties.chi4v 3.998
_pdbe_chem_comp_rdkit_properties.chi0n 44.676
_pdbe_chem_comp_rdkit_properties.chi1n 21.636
_pdbe_chem_comp_rdkit_properties.chi2n 3.638
_pdbe_chem_comp_rdkit_properties.chi3n 3.638
_pdbe_chem_comp_rdkit_properties.chi4n 2.230
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.870
_pdbe_chem_comp_rdkit_properties.kappa1 11.083
_pdbe_chem_comp_rdkit_properties.kappa2 12.332
_pdbe_chem_comp_rdkit_properties.kappa3 7.659
_pdbe_chem_comp_rdkit_properties.Phi 3.505
#
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
UD2 UniChem DrugBank DB02196
UD2 UniChem PDBe UD2
UD2 UniChem 'Guide to Pharmacology' 4741
UD2 UniChem ChEBI 67168
UD2 UniChem ZINC ZINC000008551132
UD2 UniChem HMDB HMDB0060522
UD2 UniChem 'PubChem TPHARMA' 16188595
UD2 UniChem NMRShiftDB 60022132
UD2 UniChem MetaboLights MTBLC67168
UD2 UniChem BRENDA 1010
UD2 UniChem BRENDA 1308
UD2 UniChem BRENDA 14390
UD2 UniChem BRENDA 194345
UD2 UniChem BRENDA 195915
UD2 UniChem BRENDA 197320
UD2 UniChem BRENDA 356
UD2 UniChem BRENDA 40055
UD2 UniChem BRENDA 550
UD2 UniChem 'Probes And Drugs' PD008141
UD2 UniChem Nikkaji J443.675J
UD2 UniChem PubChem 23700
#
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
UD2 "C1'" -2.671 0.279 1.068 ETKDGv3 1
UD2 "C2'" -3.493 -0.486 -0.002 ETKDGv3 2
UD2 "C3'" -4.548 -1.416 0.661 ETKDGv3 3
UD2 "C4'" -4.881 -0.977 2.105 ETKDGv3 4
UD2 "C5'" -4.771 0.564 2.210 ETKDGv3 5
UD2 "C6'" -5.222 1.071 3.587 ETKDGv3 6
UD2 "C7'" -4.635 0.047 -2.209 ETKDGv3 7
UD2 "C8'" -5.238 1.056 -3.130 ETKDGv3 8
UD2 "N2'" -4.142 0.455 -0.926 ETKDGv3 9
UD2 "O1'" -1.750 1.138 0.418 ETKDGv3 10
UD2 "O3'" -4.094 -2.747 0.661 ETKDGv3 11
UD2 "O4'" -4.011 -1.584 3.029 ETKDGv3 12
UD2 "O5'" -3.473 1.083 1.928 ETKDGv3 13
UD2 "O6'" -4.297 0.702 4.573 ETKDGv3 14
UD2 "O7'" -4.530 -1.153 -2.582 ETKDGv3 15
UD2 N1 5.096 0.913 0.342 ETKDGv3 16
UD2 C2 6.223 1.537 0.991 ETKDGv3 17
UD2 N3 6.117 1.937 2.358 ETKDGv3 18
UD2 C4 4.907 1.676 3.070 ETKDGv3 19
UD2 C5 3.799 0.991 2.394 ETKDGv3 20
UD2 C6 3.906 0.632 1.111 ETKDGv3 21
UD2 O2 7.302 1.732 0.368 ETKDGv3 22
UD2 O4 4.793 2.026 4.275 ETKDGv3 23
UD2 C1B 5.181 0.473 -1.060 ETKDGv3 24
UD2 C2B 5.474 -1.015 -1.144 ETKDGv3 25
UD2 "O2'" 6.857 -1.259 -1.111 ETKDGv3 26
UD2 C3B 4.852 -1.392 -2.465 ETKDGv3 27
UD2 C4B 3.738 -0.346 -2.625 ETKDGv3 28
UD2 O4B 3.967 0.726 -1.731 ETKDGv3 29
UD2 O3B 5.789 -1.264 -3.504 ETKDGv3 30
UD2 C5B 2.356 -0.946 -2.346 ETKDGv3 31
UD2 O5B 1.374 0.042 -2.555 ETKDGv3 32
UD2 PA -0.141 -0.592 -2.090 ETKDGv3 33
UD2 O1A -1.352 0.542 -2.436 ETKDGv3 34
UD2 O2A -0.432 -1.848 -2.881 ETKDGv3 35
UD2 O3A -0.128 -0.982 -0.431 ETKDGv3 36
UD2 PB -0.175 0.475 0.451 ETKDGv3 37
UD2 O1B 0.271 0.153 2.052 ETKDGv3 38
UD2 O2B 0.799 1.485 -0.117 ETKDGv3 39
UD2 "H1'" -2.169 -0.480 1.714 ETKDGv3 40
UD2 "H2'" -2.780 -1.106 -0.587 ETKDGv3 41
UD2 "H3'" -5.499 -1.367 0.079 ETKDGv3 42
UD2 "H4'" -5.934 -1.272 2.330 ETKDGv3 43
UD2 "H5'" -5.481 1.002 1.473 ETKDGv3 44
UD2 "H6'1" -6.227 0.659 3.833 ETKDGv3 45
UD2 "H6'2" -5.301 2.181 3.553 ETKDGv3 46
UD2 "H8'1" -4.439 1.711 -3.534 ETKDGv3 47
UD2 "H8'2" -5.975 1.675 -2.577 ETKDGv3 48
UD2 "H8'3" -5.757 0.553 -3.974 ETKDGv3 49
UD2 "HN2'" -4.195 1.470 -0.680 ETKDGv3 50
UD2 "HO3'" -4.188 -3.084 -0.268 ETKDGv3 51
UD2 "HO4'" -4.395 -2.472 3.252 ETKDGv3 52
UD2 "HO6'" -4.654 1.055 5.430 ETKDGv3 53
UD2 HN3 6.919 2.407 2.835 ETKDGv3 54
UD2 H5 2.892 0.768 2.941 ETKDGv3 55
UD2 H6 3.077 0.112 0.650 ETKDGv3 56
UD2 H1B 5.975 1.041 -1.596 ETKDGv3 57
UD2 H2B 4.960 -1.559 -0.317 ETKDGv3 58
UD2 "HO2'" 6.965 -2.241 -1.021 ETKDGv3 59
UD2 H3B 4.470 -2.440 -2.422 ETKDGv3 60
UD2 H4B 3.736 0.053 -3.664 ETKDGv3 61
UD2 HO3A 5.392 -1.709 -4.298 ETKDGv3 62
UD2 "H5'1" 2.339 -1.318 -1.296 ETKDGv3 63
UD2 "H5'2" 2.192 -1.797 -3.045 ETKDGv3 64
UD2 HOA2 -0.886 1.415 -2.471 ETKDGv3 65
UD2 HOB2 0.145 1.012 2.528 ETKDGv3 66
#