data_TRH
#
_chem_comp.id TRH
_chem_comp.name "2'-DEOXY-THYMIDINE-BETA-L-RHAMNOSE"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C16 H26 N2 O15 P2"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2000-11-28
_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 548.330
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code TRH
_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 1G3L
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site EBI
#
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
TRH O4P O4P O 0 1 N N N N N N 14.715 62.773 52.230 0.500 1.102 -2.566 O4P TRH 1
TRH P2 P2 P 0 1 N N S N N N 15.585 61.713 53.006 -0.506 -0.139 -2.753 P2 TRH 2
TRH O3P O3P O 0 1 N N N N N N 16.478 60.604 52.238 -1.839 0.361 -3.155 O3P TRH 3
TRH O1 O1 O 0 1 N N N N N N 16.412 62.544 54.070 0.063 -1.124 -3.892 O1 TRH 4
TRH C1 C1 C 0 1 N N R N N N 17.700 62.115 54.383 0.151 -0.358 -5.095 C1 TRH 5
TRH C2 C2 C 0 1 N N R N N N 17.672 61.865 55.846 -0.061 -1.277 -6.300 C2 TRH 6
TRH O2 O2 O 0 1 N N N N N N 16.989 62.991 56.379 0.961 -2.275 -6.326 O2 TRH 7
TRH C3 C3 C 0 1 N N R N N N 19.102 61.771 56.403 0.002 -0.442 -7.583 C3 TRH 8
TRH O3 O3 O 0 1 N N N N N N 19.098 61.829 57.821 -0.046 -1.306 -8.720 O3 TRH 9
TRH C4 C4 C 0 1 N N R N N N 19.938 62.867 55.797 1.315 0.347 -7.588 C4 TRH 10
TRH O4 O4 O 0 1 N N N N N N 21.258 62.474 56.124 1.330 1.244 -8.701 O4 TRH 11
TRH C5 C5 C 0 1 N N S N N N 19.623 62.900 54.277 1.423 1.145 -6.287 C5 TRH 12
TRH O5 O5 O 0 1 N N N N N N 18.251 63.358 54.057 1.437 0.253 -5.174 O5 TRH 13
TRH C6 C6 C 0 1 N N N N N N 20.675 63.684 53.489 2.714 1.965 -6.298 C6 TRH 14
TRH OPP OPP O 0 1 N N N N N N 14.621 60.856 53.950 -0.631 -0.942 -1.363 OPP TRH 15
TRH P P P 0 1 N N S N N N 14.283 59.294 53.688 -1.203 0.097 -0.275 P TRH 16
TRH O1P O1P O 0 1 N N N N N N 12.937 59.154 54.505 -2.642 0.638 -0.754 O1P TRH 17
TRH O2P O2P O 0 1 N N N N N N 15.539 58.321 53.947 -0.267 1.235 -0.141 O2P TRH 18
TRH "O5'" "O5'" O 0 1 N N N N N N 13.978 59.217 52.141 -1.354 -0.642 1.146 "O5'" TRH 19
TRH "C5'" "C5'" C 0 1 N N N N N N 12.896 60.016 51.674 -1.863 0.326 2.064 "C5'" TRH 20
TRH "C4'" "C4'" C 0 1 N N R N N N 11.959 59.134 50.855 -2.031 -0.315 3.443 "C4'" TRH 21
TRH "O4'" "O4'" O 0 1 N N N N N N 12.933 58.403 50.168 -0.753 -0.729 3.970 "O4'" TRH 22
TRH "C3'" "C3'" C 0 1 N N S N N N 11.254 57.974 51.475 -2.531 0.728 4.474 "C3'" TRH 23
TRH "O3'" "O3'" O 0 1 N N N N N N 9.914 57.927 51.018 -3.956 0.827 4.459 "O3'" TRH 24
TRH "C2'" "C2'" C 0 1 N N N N N N 11.980 56.747 50.926 -2.032 0.125 5.811 "C2'" TRH 25
TRH "C1'" "C1'" C 0 1 N N R N N N 12.576 57.173 49.604 -0.901 -0.835 5.396 "C1'" TRH 26
TRH N11 N11 N 0 1 N N N N N N 13.697 56.328 49.213 0.348 -0.453 6.057 N11 TRH 27
TRH C21 C21 C 0 1 N N N N N N 13.518 55.498 48.159 0.865 0.771 5.847 C21 TRH 28
TRH O21 O21 O 0 1 N N N N N N 12.337 55.398 47.567 0.286 1.549 5.115 O21 TRH 29
TRH N31 N31 N 0 1 N N N N N N 14.514 54.743 47.743 2.010 1.150 6.445 N31 TRH 30
TRH C41 C41 C 0 1 N N N N N N 15.702 54.823 48.330 2.665 0.299 7.261 C41 TRH 31
TRH O41 O41 O 0 1 N N N N N N 16.686 54.068 47.883 3.703 0.639 7.798 O41 TRH 32
TRH C51 C51 C 0 1 N N N N N N 15.917 55.673 49.381 2.135 -0.994 7.485 C51 TRH 33
TRH C5A C5A C 0 1 N N N N N N 17.288 55.714 50.013 2.847 -1.964 8.392 C5A TRH 34
TRH C61 C61 C 0 1 N N N N N N 14.875 56.446 49.831 0.982 -1.346 6.877 C61 TRH 35
TRH H4PO OH4P H 0 0 N N N N N N 14.190 63.424 52.681 1.355 0.733 -2.305 H4PO TRH 36
TRH HC1 HC1 H 0 1 N N N N N N 18.178 61.219 53.923 -0.617 0.414 -5.089 HC1 TRH 37
TRH HC2 HC2 H 0 1 N N N N N N 17.172 60.904 56.110 -1.036 -1.757 -6.224 HC2 TRH 38
TRH HO2 HO2 H 0 1 N N N N N N 16.971 62.831 57.315 0.889 -2.771 -5.499 HO2 TRH 39
TRH HC3 HC3 H 0 1 N N N N N N 19.549 60.788 56.125 -0.841 0.248 -7.612 HC3 TRH 40
TRH HO3 HO3 H 0 1 N N N N N N 19.981 61.770 58.165 -0.881 -1.790 -8.668 HO3 TRH 41
TRH HC4 HC4 H 0 1 N N N N N N 19.754 63.904 56.161 2.156 -0.342 -7.665 HC4 TRH 42
TRH HO4 HO4 H 0 1 N N N N N N 21.785 63.165 55.741 2.171 1.719 -8.666 HO4 TRH 43
TRH HC5 HC5 H 0 1 N N N N N N 19.684 61.862 53.872 0.568 1.816 -6.202 HC5 TRH 44
TRH HC61 1HC6 H 0 0 N N N N N N 20.448 63.707 52.397 2.791 2.535 -5.372 HC61 TRH 45
TRH HC62 2HC6 H 0 0 N N N N N N 20.802 64.713 53.897 3.570 1.294 -6.383 HC62 TRH 46
TRH HC63 3HC6 H 0 0 N N N N N N 21.700 63.290 53.680 2.703 2.649 -7.146 HC63 TRH 47
TRH H1PO OH1P H 0 0 N N N N N N 12.738 58.237 54.351 -3.220 -0.133 -0.829 H1PO TRH 48
TRH "H5'1" "1H5'" H 0 0 N N N N N N 12.369 60.547 52.500 -1.165 1.161 2.135 "H5'1" TRH 49
TRH "H5'2" "2H5'" H 0 0 N N N N N N 13.240 60.913 51.109 -2.829 0.689 1.712 "H5'2" TRH 50
TRH "H4'C" "CH4'" H 0 0 N N N N N N 11.179 59.805 50.426 -2.717 -1.160 3.390 "H4'C" TRH 51
TRH "H3'C" "CH3'" H 0 0 N N N N N N 11.252 58.033 52.588 -2.073 1.701 4.291 "H3'C" TRH 52
TRH "H3'O" "OH3'" H 0 0 N N N N N N 9.465 57.188 51.412 -4.203 1.420 5.181 "H3'O" TRH 53
TRH "H2'1" "1H2'" H 0 0 N N N N N N 12.727 56.318 51.633 -2.836 -0.422 6.303 "H2'1" TRH 54
TRH "H2'2" "2H2'" H 0 0 N N N N N N 11.331 55.842 50.851 -1.647 0.908 6.465 "H2'2" TRH 55
TRH "H1'C" "CH1'" H 0 0 N N N N N N 11.985 57.156 48.658 -1.165 -1.857 5.666 "H1'C" TRH 56
TRH H31N NH31 H 0 0 N N N N N N 14.365 54.097 46.967 2.367 2.038 6.286 H31N TRH 57
TRH HCA1 1HCA H 0 0 N N N N N N 17.463 56.406 50.869 3.751 -1.498 8.784 HCA1 TRH 58
TRH HCA2 2HCA H 0 0 N N N N N N 17.574 54.681 50.320 2.191 -2.239 9.218 HCA2 TRH 59
TRH HCA3 3HCA H 0 0 N N N N N N 18.044 55.921 49.220 3.115 -2.858 7.828 HCA3 TRH 60
TRH H61C CH61 H 0 0 N N N N N N 14.982 57.149 50.673 0.562 -2.328 7.036 H61C TRH 61
#
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
TRH O4P P2 SING N N 1
TRH O4P H4PO SING N N 2
TRH P2 O3P DOUB N N 3
TRH P2 O1 SING N N 4
TRH P2 OPP SING N N 5
TRH O1 C1 SING N N 6
TRH C1 C2 SING N N 7
TRH C1 O5 SING N N 8
TRH C1 HC1 SING N N 9
TRH C2 O2 SING N N 10
TRH C2 C3 SING N N 11
TRH C2 HC2 SING N N 12
TRH O2 HO2 SING N N 13
TRH C3 O3 SING N N 14
TRH C3 C4 SING N N 15
TRH C3 HC3 SING N N 16
TRH O3 HO3 SING N N 17
TRH C4 O4 SING N N 18
TRH C4 C5 SING N N 19
TRH C4 HC4 SING N N 20
TRH O4 HO4 SING N N 21
TRH C5 O5 SING N N 22
TRH C5 C6 SING N N 23
TRH C5 HC5 SING N N 24
TRH C6 HC61 SING N N 25
TRH C6 HC62 SING N N 26
TRH C6 HC63 SING N N 27
TRH OPP P SING N N 28
TRH P O1P SING N N 29
TRH P O2P DOUB N N 30
TRH P "O5'" SING N N 31
TRH O1P H1PO SING N N 32
TRH "O5'" "C5'" SING N N 33
TRH "C5'" "C4'" SING N N 34
TRH "C5'" "H5'1" SING N N 35
TRH "C5'" "H5'2" SING N N 36
TRH "C4'" "O4'" SING N N 37
TRH "C4'" "C3'" SING N N 38
TRH "C4'" "H4'C" SING N N 39
TRH "O4'" "C1'" SING N N 40
TRH "C3'" "O3'" SING N N 41
TRH "C3'" "C2'" SING N N 42
TRH "C3'" "H3'C" SING N N 43
TRH "O3'" "H3'O" SING N N 44
TRH "C2'" "C1'" SING N N 45
TRH "C2'" "H2'1" SING N N 46
TRH "C2'" "H2'2" SING N N 47
TRH "C1'" N11 SING N N 48
TRH "C1'" "H1'C" SING N N 49
TRH N11 C21 SING N N 50
TRH N11 C61 SING N N 51
TRH C21 O21 DOUB N N 52
TRH C21 N31 SING N N 53
TRH N31 C41 SING N N 54
TRH N31 H31N SING N N 55
TRH C41 O41 DOUB N N 56
TRH C41 C51 SING N N 57
TRH C51 C5A SING N N 58
TRH C51 C61 DOUB N N 59
TRH C5A HCA1 SING N N 60
TRH C5A HCA2 SING N N 61
TRH C5A HCA3 SING N N 62
TRH C61 H61C SING N N 63
#
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
TRH SMILES ACDLabs 10.04 O=P(OC1OC(C(O)C(O)C1O)C)(O)OP(=O)(O)OCC3OC(N2C=C(C(=O)NC2=O)C)CC3O
TRH 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[C@@H]2O)N3C=C(C)C(=O)NC3=O)[C@H](O)[C@H](O)[C@H]1O
TRH SMILES CACTVS 3.341 C[CH]1O[CH](O[P](O)(=O)O[P](O)(=O)OC[CH]2O[CH](C[CH]2O)N3C=C(C)C(=O)NC3=O)[CH](O)[CH](O)[CH]1O
TRH 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[C@@H](O2)N3C=C(C(=O)NC3=O)C)O)O)O)O
TRH SMILES "OpenEye OEToolkits" 1.5.0 CC1C(C(C(C(O1)OP(=O)(O)OP(=O)(O)OCC2C(CC(O2)N3C=C(C(=O)NC3=O)C)O)O)O)O
TRH InChI InChI 1.03 InChI=1S/C16H26N2O15P2/c1-6-4-18(16(24)17-14(6)23)10-3-8(19)9(31-10)5-29-34(25,26)33-35(27,28)32-15-13(22)12(21)11(20)7(2)30-15/h4,7-13,15,19-22H,3,5H2,1-2H3,(H,25,26)(H,27,28)(H,17,23,24)/t7-,8-,9+,10+,11-,12+,13+,15+/m0/s1
TRH InChIKey InChI 1.03 ZOSQFDVXNQFKBY-CGAXJHMRSA-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
TRH "SYSTEMATIC NAME" ACDLabs 10.04 "[(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)tetrahydrofuran-2-yl]methyl (2R,3R,4R,5R,6S)-3,4,5-trihydroxy-6-methyltetrahydro-2H-pyran-2-yl dihydrogen diphosphate (non-preferred name)"
TRH "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[hydroxy-[[(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-pyrimidin-1-yl)oxolan-2-yl]methoxy]phosphoryl] [(2R,3R,4R,5R,6S)-3,4,5-trihydroxy-6-methyl-oxan-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
TRH 'Create component' 2000-11-28 EBI
TRH 'Modify descriptor' 2011-06-04 RCSB
#
_pdbe_chem_comp_drugbank_details.comp_id TRH
_pdbe_chem_comp_drugbank_details.drugbank_id DB03723
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name "2'-Deoxy-thymidine-beta-L-rhamnose"
_pdbe_chem_comp_drugbank_details.description ?
_pdbe_chem_comp_drugbank_details.cas_number 2147-59-3
_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
TRH "2'-Deoxy-thymidine-beta-L-rhamnose" DrugBank ?
TRH dTDP-6-deoxy-L-mannose DrugBank ?
TRH 'dTDP-6-deoxy-β-L-mannose' DrugBank ?
TRH dTDP-L-rhamnose DrugBank ?
TRH 'dTDP-β-L-rhamnose' DrugBank ?
TRH 'Thymidine diphosphate-L-rhamnose' DrugBank ?
#
_pdbe_chem_comp_drugbank_classification.comp_id TRH
_pdbe_chem_comp_drugbank_classification.drugbank_id DB03723
_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
TRH DB03723 'dTDP-4-dehydrorhamnose reductase' 'Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)' P26392 unknown 1
TRH DB03723 'Glucose-1-phosphate thymidylyltransferase' 'Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228)' Q9HU22 unknown 2
#
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
TRH O4P O 10.502 -1.095 1
TRH P2 P 9.002 -1.095 2
TRH O3P O 7.502 -1.095 3
TRH O1 O 9.002 -2.595 4
TRH C1 C 7.702 -3.345 5
TRH C2 C 7.702 -4.845 6
TRH O2 O 9.002 -5.595 7
TRH C3 C 6.404 -5.595 8
TRH O3 O 6.404 -7.095 9
TRH C4 C 5.104 -4.845 10
TRH O4 O 3.805 -5.595 11
TRH C5 C 5.104 -3.345 12
TRH O5 O 6.404 -2.595 13
TRH C6 C 3.805 -2.595 14
TRH OPP O 9.002 0.405 15
TRH P P 10.301 1.155 16
TRH O1P O 9.551 2.454 17
TRH O2P O 11.051 -0.144 18
TRH "O5'" O 11.600 1.905 19
TRH "C5'" C 11.600 3.405 20
TRH "C4'" C 12.899 4.155 21
TRH "O4'" O 14.269 3.545 22
TRH "C3'" C 13.055 5.647 23
TRH "O3'" O 11.941 6.650 24
TRH "C2'" C 14.523 5.959 25
TRH "C1'" C 15.273 4.660 26
TRH N11 N 16.765 4.503 27
TRH C21 C 17.375 3.132 28
TRH O21 O 16.493 1.919 29
TRH N31 N 18.866 2.976 30
TRH C41 C 19.748 4.189 31
TRH O41 O 21.240 4.032 32
TRH C51 C 19.138 5.559 33
TRH C5A C 20.020 6.773 34
TRH C61 C 17.646 5.716 35
#
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
TRH P2 O4P SINGLE BEGINDASH 1
TRH P2 O3P DOUBLE NONE 2
TRH P2 O1 SINGLE NONE 3
TRH P2 OPP SINGLE NONE 4
TRH C1 O1 SINGLE BEGINDASH 5
TRH C1 C2 SINGLE NONE 6
TRH C1 O5 SINGLE NONE 7
TRH C2 O2 SINGLE BEGINDASH 8
TRH C2 C3 SINGLE NONE 9
TRH C3 O3 SINGLE BEGINDASH 10
TRH C3 C4 SINGLE NONE 11
TRH C4 O4 SINGLE BEGINWEDGE 12
TRH C4 C5 SINGLE NONE 13
TRH C5 O5 SINGLE NONE 14
TRH C5 C6 SINGLE BEGINDASH 15
TRH OPP P SINGLE NONE 16
TRH P O1P SINGLE BEGINDASH 17
TRH P O2P DOUBLE NONE 18
TRH P "O5'" SINGLE NONE 19
TRH "O5'" "C5'" SINGLE NONE 20
TRH "C4'" "C5'" SINGLE BEGINDASH 21
TRH "C4'" "O4'" SINGLE NONE 22
TRH "C4'" "C3'" SINGLE NONE 23
TRH "O4'" "C1'" SINGLE NONE 24
TRH "C3'" "O3'" SINGLE BEGINWEDGE 25
TRH "C3'" "C2'" SINGLE NONE 26
TRH "C2'" "C1'" SINGLE NONE 27
TRH "C1'" N11 SINGLE BEGINDASH 28
TRH N11 C21 SINGLE NONE 29
TRH N11 C61 SINGLE NONE 30
TRH C21 O21 DOUBLE NONE 31
TRH C21 N31 SINGLE NONE 32
TRH N31 C41 SINGLE NONE 33
TRH C41 O41 DOUBLE NONE 34
TRH C41 C51 SINGLE NONE 35
TRH C51 C5A SINGLE NONE 36
TRH C51 C61 DOUBLE NONE 37
#
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
TRH 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
TRH 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
TRH 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
TRH pyranose F3 fragment OC1CCCCO1 InChI=1S/C5H10O2/c6-5-3-1-2-4-7-5/h5-6H,1-4H2 CELWCAITJAEQNL-UHFFFAOYSA-N
TRH pyrimidine F4 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
TRH P2 S1 1
TRH O3P S1 1
TRH O1 S1 1
TRH C1 S1 1
TRH C2 S1 1
TRH C3 S1 1
TRH C4 S1 1
TRH C5 S1 1
TRH O5 S1 1
TRH OPP S1 1
TRH P S1 1
TRH O2P S1 1
TRH "O5'" S1 1
TRH "C5'" S1 1
TRH "C4'" S1 1
TRH "O4'" S1 1
TRH "C3'" S1 1
TRH "C2'" S1 1
TRH "C1'" S1 1
TRH N11 S1 1
TRH C21 S1 1
TRH O21 S1 1
TRH N31 S1 1
TRH C41 S1 1
TRH O41 S1 1
TRH C51 S1 1
TRH C61 S1 1
TRH "C1'" F1 1
TRH "C2'" F1 1
TRH "C3'" F1 1
TRH "O3'" F1 1
TRH "C4'" F1 1
TRH "O4'" F1 1
TRH "C5'" F1 1
TRH "O5'" F1 1
TRH O4P F2 1
TRH P2 F2 1
TRH O3P F2 1
TRH O1 F2 1
TRH OPP F2 1
TRH OPP F2 2
TRH P F2 2
TRH O2P F2 2
TRH O1P F2 2
TRH "O5'" F2 2
TRH C4 F3 1
TRH C5 F3 1
TRH O5 F3 1
TRH C1 F3 1
TRH C2 F3 1
TRH C3 F3 1
TRH O1 F3 1
TRH C51 F4 1
TRH C41 F4 1
TRH N31 F4 1
TRH C21 F4 1
TRH N11 F4 1
TRH C61 F4 1
#
_pdbe_chem_comp_rdkit_properties.comp_id TRH
_pdbe_chem_comp_rdkit_properties.exactmw 548.081
_pdbe_chem_comp_rdkit_properties.amw 548.331
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 17
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 7
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 16
_pdbe_chem_comp_rdkit_properties.NumHBD 7
_pdbe_chem_comp_rdkit_properties.NumHBA 16
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 35
_pdbe_chem_comp_rdkit_properties.NumAtoms 61
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 19
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.750
_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 233.311
_pdbe_chem_comp_rdkit_properties.tpsa 256.530
_pdbe_chem_comp_rdkit_properties.CrippenClogP -0.683
_pdbe_chem_comp_rdkit_properties.CrippenMR 110.672
_pdbe_chem_comp_rdkit_properties.chi0v 17.701
_pdbe_chem_comp_rdkit_properties.chi1v 10.949
_pdbe_chem_comp_rdkit_properties.chi2v 5.602
_pdbe_chem_comp_rdkit_properties.chi3v 5.602
_pdbe_chem_comp_rdkit_properties.chi4v 3.693
_pdbe_chem_comp_rdkit_properties.chi0n 41.913
_pdbe_chem_comp_rdkit_properties.chi1n 20.425
_pdbe_chem_comp_rdkit_properties.chi2n 3.298
_pdbe_chem_comp_rdkit_properties.chi3n 3.298
_pdbe_chem_comp_rdkit_properties.chi4n 1.928
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.300
_pdbe_chem_comp_rdkit_properties.kappa1 9.466
_pdbe_chem_comp_rdkit_properties.kappa2 10.591
_pdbe_chem_comp_rdkit_properties.kappa3 6.724
_pdbe_chem_comp_rdkit_properties.Phi 2.864
#
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
TRH UniChem ChEBI CHEBI:15774
TRH UniChem BRENDA 10649
TRH UniChem BRENDA 112019
TRH UniChem BRENDA 11552
TRH UniChem BRENDA 157525
TRH UniChem BRENDA 178391
TRH UniChem BRENDA 67139
TRH UniChem BRENDA 96467
TRH UniChem MolPort Molport-047-919-092
TRH UniChem SureChEMBL 1533809
TRH UniChem 'EPA CompTox Dashboard' DTXSID50175752
TRH UniChem HMDB HMDB0006354
TRH UniChem PubChem 121966
TRH UniChem 'Probes And Drugs' PD059501
TRH UniChem DrugBank DB03723
#
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
TRH O4P -1.762 -2.886 -2.857 ETKDGv3 1
TRH P2 -2.678 -1.828 -1.906 ETKDGv3 2
TRH O3P -3.722 -1.161 -2.776 ETKDGv3 3
TRH O1 -3.453 -2.744 -0.690 ETKDGv3 4
TRH C1 -4.132 -1.876 0.192 ETKDGv3 5
TRH C2 -4.552 -2.680 1.440 ETKDGv3 6
TRH O2 -5.250 -3.852 1.090 ETKDGv3 7
TRH C3 -5.379 -1.793 2.396 ETKDGv3 8
TRH O3 -5.948 -2.573 3.416 ETKDGv3 9
TRH C4 -6.491 -1.040 1.639 ETKDGv3 10
TRH O4 -7.044 -0.054 2.473 ETKDGv3 11
TRH C5 -5.908 -0.376 0.371 ETKDGv3 12
TRH O5 -5.281 -1.345 -0.451 ETKDGv3 13
TRH C6 -7.012 0.299 -0.444 ETKDGv3 14
TRH OPP -1.656 -0.670 -1.183 ETKDGv3 15
TRH P -0.999 0.301 -2.420 ETKDGv3 16
TRH O1P -2.228 1.186 -3.175 ETKDGv3 17
TRH O2P -0.289 -0.547 -3.453 ETKDGv3 18
TRH "O5'" 0.111 1.406 -1.746 ETKDGv3 19
TRH "C5'" 1.042 0.685 -0.972 ETKDGv3 20
TRH "C4'" 2.114 1.640 -0.437 ETKDGv3 21
TRH "O4'" 2.984 0.934 0.414 ETKDGv3 22
TRH "C3'" 2.952 2.261 -1.553 ETKDGv3 23
TRH "O3'" 2.428 3.499 -1.957 ETKDGv3 24
TRH "C2'" 4.303 2.443 -0.908 ETKDGv3 25
TRH "C1'" 4.229 1.595 0.362 ETKDGv3 26
TRH N11 5.327 0.616 0.408 ETKDGv3 27
TRH C21 5.328 -0.554 -0.437 ETKDGv3 28
TRH O21 4.375 -0.781 -1.230 ETKDGv3 29
TRH N31 6.429 -1.460 -0.382 ETKDGv3 30
TRH C41 7.526 -1.183 0.489 ETKDGv3 31
TRH O41 8.507 -1.974 0.527 ETKDGv3 32
TRH C51 7.506 0.032 1.331 ETKDGv3 33
TRH C5A 8.684 0.361 2.206 ETKDGv3 34
TRH C61 6.466 0.879 1.254 ETKDGv3 35
TRH H4PO -1.094 -3.269 -2.234 ETKDGv3 36
TRH HC1 -3.448 -1.062 0.536 ETKDGv3 37
TRH HC2 -3.628 -2.990 1.975 ETKDGv3 38
TRH HO2 -6.033 -3.594 0.539 ETKDGv3 39
TRH HC3 -4.698 -1.033 2.847 ETKDGv3 40
TRH HO3 -5.207 -2.827 4.027 ETKDGv3 41
TRH HC4 -7.284 -1.762 1.331 ETKDGv3 42
TRH HO4 -7.672 -0.516 3.089 ETKDGv3 43
TRH HC5 -5.184 0.421 0.662 ETKDGv3 44
TRH HC61 -6.575 0.759 -1.356 ETKDGv3 45
TRH HC62 -7.777 -0.444 -0.754 ETKDGv3 46
TRH HC63 -7.501 1.101 0.149 ETKDGv3 47
TRH H1PO -2.663 1.689 -2.441 ETKDGv3 48
TRH "H5'1" 1.539 -0.114 -1.570 ETKDGv3 49
TRH "H5'2" 0.533 0.220 -0.097 ETKDGv3 50
TRH "H4'C" 1.616 2.441 0.157 ETKDGv3 51
TRH "H3'C" 3.056 1.567 -2.421 ETKDGv3 52
TRH "H3'O" 1.726 3.305 -2.631 ETKDGv3 53
TRH "H2'1" 4.484 3.508 -0.641 ETKDGv3 54
TRH "H2'2" 5.112 2.109 -1.595 ETKDGv3 55
TRH "H1'C" 4.284 2.269 1.247 ETKDGv3 56
TRH H31N 6.438 -2.314 -0.984 ETKDGv3 57
TRH HCA1 9.472 0.850 1.596 ETKDGv3 58
TRH HCA2 8.396 1.041 3.036 ETKDGv3 59
TRH HCA3 9.099 -0.565 2.659 ETKDGv3 60
TRH H61C 6.481 1.786 1.848 ETKDGv3 61
#