data_TDX
#
_chem_comp.id TDX
_chem_comp.name "THYMIDINE-5'-DIPHOSPHO-BETA-D-XYLOSE"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C15 H24 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 2001-11-23
_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 534.303
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code TDX
_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 1KEP
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site PDBJ
#
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.alt_atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.charge
_chem_comp_atom.pdbx_align
_chem_comp_atom.pdbx_aromatic_flag
_chem_comp_atom.pdbx_leaving_atom_flag
_chem_comp_atom.pdbx_stereo_config
_chem_comp_atom.pdbx_backbone_atom_flag
_chem_comp_atom.pdbx_n_terminal_atom_flag
_chem_comp_atom.pdbx_c_terminal_atom_flag
_chem_comp_atom.model_Cartn_x
_chem_comp_atom.model_Cartn_y
_chem_comp_atom.model_Cartn_z
_chem_comp_atom.pdbx_model_Cartn_x_ideal
_chem_comp_atom.pdbx_model_Cartn_y_ideal
_chem_comp_atom.pdbx_model_Cartn_z_ideal
_chem_comp_atom.pdbx_component_atom_id
_chem_comp_atom.pdbx_component_comp_id
_chem_comp_atom.pdbx_ordinal
TDX O4 O4 O 0 1 N N N N N N -20.770 -11.286 72.139 3.417 -1.244 -7.574 O4 TDX 1
TDX C4 C4 C 0 1 N N N N N N -20.925 -10.052 72.244 2.512 -0.683 -6.982 C4 TDX 2
TDX N3 N3 N 0 1 N N N N N N -21.942 -9.520 72.946 1.638 -1.396 -6.244 N3 TDX 3
TDX C2 C2 C 0 1 N N N N N N -22.093 -8.214 73.042 0.638 -0.775 -5.591 C2 TDX 4
TDX O2 O2 O 0 1 N N N N N N -23.080 -7.789 73.721 -0.145 -1.431 -4.932 O2 TDX 5
TDX C5 C5 C 0 1 N N N N N N -20.005 -9.162 71.558 2.374 0.723 -7.057 C5 TDX 6
TDX C5M C5M C 0 1 N N N N N N -18.858 -9.722 70.738 3.340 1.543 -7.872 C5M TDX 7
TDX C6 C6 C 0 1 N N N N N N -20.225 -7.828 71.652 1.362 1.320 -6.392 C6 TDX 8
TDX N1 N1 N 0 1 N N N N N N -21.234 -7.378 72.420 0.493 0.560 -5.657 N1 TDX 9
TDX C1B C1* C 0 1 N N R N N N -21.459 -5.943 72.500 -0.605 1.207 -4.935 C1B TDX 10
TDX C2B C2* C 0 1 N N N N N N -20.243 -5.063 72.794 -1.955 0.657 -5.434 C2B TDX 11
TDX C3B C3* C 0 1 N N S N N N -20.580 -3.791 72.001 -2.619 0.073 -4.164 C3B TDX 12
TDX O3B O3* O 0 1 N N N N N N -21.390 -2.833 72.760 -4.015 0.379 -4.131 O3B TDX 13
TDX O4B O4* O 0 1 N N N N N N -21.989 -5.542 71.219 -0.511 0.910 -3.532 O4B TDX 14
TDX C4B C4* C 0 1 N N R N N N -21.433 -4.293 70.814 -1.864 0.815 -3.032 C4B TDX 15
TDX C5B C5* C 0 1 N N N N N N -20.577 -4.457 69.570 -1.907 0.005 -1.734 C5B TDX 16
TDX O5B O5* O 0 1 N N N N N N -19.416 -5.204 69.920 -1.204 0.710 -0.709 O5B TDX 17
TDX PA PA P 0 1 N N S N N N -18.205 -5.389 68.872 -1.290 -0.193 0.619 PA TDX 18
TDX O1A O1A O 0 1 N N N N N N -18.671 -6.235 67.713 -0.662 -1.509 0.362 O1A TDX 19
TDX O2A O2A O 0 1 N N N N N N -17.031 -5.897 69.662 -2.833 -0.405 1.026 O2A TDX 20
TDX O3A O3A O 0 1 N N N N N N -17.969 -3.955 68.184 -0.514 0.544 1.821 O3A TDX 21
TDX PB PB P 0 1 N N R N N N -17.446 -2.563 68.844 -0.639 -0.410 3.112 PB TDX 22
TDX O1B O1B O 0 1 N N N N N N -16.700 -2.712 70.140 -0.022 -1.722 2.816 O1B TDX 23
TDX O2B O2B O 0 1 N N N N N N -18.600 -1.652 68.885 -2.193 -0.618 3.477 O2B TDX 24
TDX "O1'" "O1'" O 0 1 N N N N N N -16.425 -2.104 67.685 0.118 0.270 4.358 "O1'" TDX 25
TDX "C1'" "C1'" C 0 1 N N R N N N -16.783 -2.340 66.319 -0.027 -0.620 5.466 "C1'" TDX 26
TDX "O5'" "O5'" O 0 1 N N N N N N -17.192 -1.108 65.753 1.061 -1.541 5.481 "O5'" TDX 27
TDX "C5'" "C5'" C 0 1 N N N N N N -16.178 -0.077 65.824 2.268 -0.783 5.427 "C5'" TDX 28
TDX "C2'" "C2'" C 0 1 N N R N N N -15.583 -2.864 65.548 -0.040 0.184 6.768 "C2'" TDX 29
TDX "O2'" "O2'" O 0 1 N N N N N N -15.087 -4.055 66.149 -1.149 1.086 6.761 "O2'" TDX 30
TDX "C3'" "C3'" C 0 1 N N S N N N -14.453 -1.824 65.540 1.264 0.978 6.879 "C3'" TDX 31
TDX "O3'" "O3'" O 0 1 N N N N N N -13.326 -2.256 64.740 1.333 1.617 8.155 "O3'" TDX 32
TDX "C4'" "C4'" C 0 1 N N R N N N -14.979 -0.500 64.998 2.441 0.008 6.725 "C4'" TDX 33
TDX "O4'" "O4'" O 0 1 N N N N N N -13.982 0.520 65.058 3.666 0.742 6.678 "O4'" TDX 34
TDX H3 H3 H 0 1 N N N N N N -22.616 -10.123 73.418 1.728 -2.360 -6.185 H3 TDX 35
TDX H5M1 1H5M H 0 0 N N N N N N -19.278 -10.434 69.990 4.080 0.885 -8.329 H5M1 TDX 36
TDX H5M2 2H5M H 0 0 N N N N N N -18.152 -9.039 70.211 2.797 2.076 -8.652 H5M2 TDX 37
TDX H5M3 3H5M H 0 0 N N N N N N -18.263 -10.404 71.390 3.844 2.261 -7.225 H5M3 TDX 38
TDX H6 H6 H 0 1 N N N N N N -19.587 -7.113 71.107 1.238 2.392 -6.440 H6 TDX 39
TDX H1B H1* H 0 1 N N N N N N -22.136 -5.788 73.372 -0.564 2.286 -5.089 H1B TDX 40
TDX "H2'1" 1H2* H 0 0 N N N N N N -19.256 -5.523 72.556 -2.565 1.460 -5.848 "H2'1" TDX 41
TDX "H2'2" 2H2* H 0 0 N N N N N N -20.023 -4.903 73.875 -1.798 -0.124 -6.176 "H2'2" TDX 42
TDX H3B H3* H 0 1 N N N N N N -19.640 -3.261 71.719 -2.457 -1.002 -4.100 H3B TDX 43
TDX "HO3'" *HO3 H 0 0 N N N N N N -21.598 -2.046 72.270 -4.410 -0.035 -4.911 "HO3'" TDX 44
TDX H4B H4* H 0 1 N N N N N N -22.236 -3.564 70.556 -2.284 1.809 -2.877 H4B TDX 45
TDX "H5'1" 1H5* H 0 0 N N N N N N -20.331 -3.483 69.087 -2.944 -0.139 -1.431 "H5'1" TDX 46
TDX "H5'2" 2H5* H 0 0 N N N N N N -21.138 -4.910 68.720 -1.437 -0.964 -1.896 "H5'2" TDX 47
TDX H2A H2A H 0 1 N N N N N N -16.317 -6.006 69.044 -3.203 0.473 1.185 H2A TDX 48
TDX H2B H2B H 0 1 N N N N N N -18.295 -0.839 69.270 -2.557 0.258 3.662 H2B TDX 49
TDX "H1'" "H1'" H 0 1 N N N N N N -17.603 -3.094 66.268 -0.964 -1.168 5.370 "H1'" TDX 50
TDX H5B "1H5'" H 0 1 N N N N N N -15.901 0.173 66.875 3.114 -1.459 5.299 H5B TDX 51
TDX H5D "2H5'" H 0 1 N N N N N N -16.569 0.923 65.522 2.226 -0.093 4.585 H5D TDX 52
TDX "H2'" "H2'" H 0 1 N N N N N N -15.915 -3.073 64.504 -0.128 -0.494 7.616 "H2'" TDX 53
TDX "HO2'" "'HO2" H 0 0 N N N N N N -14.337 -4.383 65.667 -1.948 0.546 6.690 "HO2'" TDX 54
TDX "H3'" "H3'" H 0 1 N N N N N N -14.101 -1.700 66.591 1.304 1.729 6.091 "H3'" TDX 55
TDX HO3A "'HO3" H 0 0 N N N N N N -12.627 -1.613 64.735 2.175 2.092 8.184 HO3A TDX 56
TDX "H4'" "H4'" H 0 1 N N N N N N -15.265 -0.642 63.930 2.461 -0.678 7.572 "H4'" TDX 57
TDX "HO4'" "'HO4" H 0 0 N N N N N N -13.231 0.255 64.540 4.376 0.095 6.574 "HO4'" TDX 58
#
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
TDX O4 C4 DOUB N N 1
TDX C4 N3 SING N N 2
TDX C4 C5 SING N N 3
TDX N3 C2 SING N N 4
TDX N3 H3 SING N N 5
TDX C2 O2 DOUB N N 6
TDX C2 N1 SING N N 7
TDX C5 C5M SING N N 8
TDX C5 C6 DOUB N N 9
TDX C5M H5M1 SING N N 10
TDX C5M H5M2 SING N N 11
TDX C5M H5M3 SING N N 12
TDX C6 N1 SING N N 13
TDX C6 H6 SING N N 14
TDX N1 C1B SING N N 15
TDX C1B C2B SING N N 16
TDX C1B O4B SING N N 17
TDX C1B H1B SING N N 18
TDX C2B C3B SING N N 19
TDX C2B "H2'1" SING N N 20
TDX C2B "H2'2" SING N N 21
TDX C3B O3B SING N N 22
TDX C3B C4B SING N N 23
TDX C3B H3B SING N N 24
TDX O3B "HO3'" SING N N 25
TDX O4B C4B SING N N 26
TDX C4B C5B SING N N 27
TDX C4B H4B SING N N 28
TDX C5B O5B SING N N 29
TDX C5B "H5'1" SING N N 30
TDX C5B "H5'2" SING N N 31
TDX O5B PA SING N N 32
TDX PA O1A DOUB N N 33
TDX PA O2A SING N N 34
TDX PA O3A SING N N 35
TDX O2A H2A SING N N 36
TDX O3A PB SING N N 37
TDX PB O1B DOUB N N 38
TDX PB O2B SING N N 39
TDX PB "O1'" SING N N 40
TDX O2B H2B SING N N 41
TDX "O1'" "C1'" SING N N 42
TDX "C1'" "O5'" SING N N 43
TDX "C1'" "C2'" SING N N 44
TDX "C1'" "H1'" SING N N 45
TDX "O5'" "C5'" SING N N 46
TDX "C5'" "C4'" SING N N 47
TDX "C5'" H5B SING N N 48
TDX "C5'" H5D SING N N 49
TDX "C2'" "O2'" SING N N 50
TDX "C2'" "C3'" SING N N 51
TDX "C2'" "H2'" SING N N 52
TDX "O2'" "HO2'" SING N N 53
TDX "C3'" "O3'" SING N N 54
TDX "C3'" "C4'" SING N N 55
TDX "C3'" "H3'" SING N N 56
TDX "O3'" HO3A SING N N 57
TDX "C4'" "O4'" SING N N 58
TDX "C4'" "H4'" SING N N 59
TDX "O4'" "HO4'" SING N N 60
#
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
TDX SMILES ACDLabs 10.04 O=P(OC1OCC(O)C(O)C1O)(O)OP(=O)(O)OCC3OC(N2C=C(C(=O)NC2=O)C)CC3O
TDX SMILES_CANONICAL CACTVS 3.341 CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P@@](O)(=O)O[P@@](O)(=O)O[C@H]3OC[C@@H](O)[C@H](O)[C@H]3O)O2)C(=O)NC1=O
TDX SMILES CACTVS 3.341 CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(=O)O[P](O)(=O)O[CH]3OC[CH](O)[CH](O)[CH]3O)O2)C(=O)NC1=O
TDX SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)CO[P@](=O)(O)O[P@](=O)(O)O[C@@H]3[C@@H]([C@H]([C@@H](CO3)O)O)O)O
TDX SMILES "OpenEye OEToolkits" 1.5.0 CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(O)OP(=O)(O)OC3C(C(C(CO3)O)O)O)O
TDX InChI InChI 1.03 InChI=1S/C15H24N2O15P2/c1-6-3-17(15(23)16-13(6)22)10-2-7(18)9(30-10)5-29-33(24,25)32-34(26,27)31-14-12(21)11(20)8(19)4-28-14/h3,7-12,14,18-21H,2,4-5H2,1H3,(H,24,25)(H,26,27)(H,16,22,23)/t7-,8+,9+,10+,11-,12+,14+/m0/s1
TDX InChIKey InChI 1.03 AJUADKZRQSBUAK-KDGZBOQCSA-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
TDX "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,4S,5R)-3,4,5-trihydroxytetrahydro-2H-pyran-2-yl dihydrogen diphosphate (non-preferred name)"
TDX "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-pyrimidin-1-yl)oxolan-2-yl]methyl [hydroxy-[(2R,3R,4S,5R)-3,4,5-trihydroxyoxan-2-yl]oxy-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
TDX 'Create component' 2001-11-23 PDBJ
TDX 'Modify descriptor' 2011-06-04 RCSB
#
_pdbe_chem_comp_drugbank_details.comp_id TDX
_pdbe_chem_comp_drugbank_details.drugbank_id DB03161
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name "Thymidine-5'-diphospho-beta-D-xylose"
_pdbe_chem_comp_drugbank_details.description ?
_pdbe_chem_comp_drugbank_details.cas_number ?
_pdbe_chem_comp_drugbank_details.mechanism_of_action ?
#
_pdbe_chem_comp_drugbank_classification.comp_id TDX
_pdbe_chem_comp_drugbank_classification.drugbank_id DB03161
_pdbe_chem_comp_drugbank_classification.parent "Pyrimidine 2'-deoxyribonucleoside 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 2'-deoxyribonucleoside diphosphates. These are pyrimidine nucleotides with a diphosphate group  linked to the ribose moiety lacking a hydroxyl group at position 2."
#
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
TDX DB03161 'dTDP-glucose 4,6-dehydratase' 'Streptococcus mutans serotype c (strain ATCC 700610 / UA159)' P95780 unknown 1
TDX DB03161 'dTDP-4-dehydrorhamnose 3,5-epimerase' 'Streptococcus suis' Q8GIQ0 unknown 2
#
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
TDX O4 O 5.598 8.591 1
TDX C4 C 5.598 7.091 2
TDX N3 N 6.897 6.341 3
TDX C2 C 6.897 4.841 4
TDX O2 O 8.196 4.091 5
TDX C5 C 4.299 6.341 6
TDX C5M C 3.000 7.091 7
TDX C6 C 4.299 4.841 8
TDX N1 N 5.598 4.091 9
TDX C1B C 5.598 2.591 10
TDX C2B C 4.385 1.709 11
TDX C3B C 4.848 0.283 12
TDX O3B O 3.966 -0.931 13
TDX O4B O 6.812 1.709 14
TDX C4B C 6.348 0.283 15
TDX C5B C 7.230 -0.931 16
TDX O5B O 8.722 -0.774 17
TDX PA P 9.603 -1.988 18
TDX O1A O 10.817 -1.106 19
TDX O2A O 8.390 -2.869 20
TDX O3A O 10.485 -3.201 21
TDX PB P 11.977 -3.044 22
TDX O1B O 12.133 -4.536 23
TDX O2B O 11.820 -1.552 24
TDX "O1'" O 13.469 -2.887 25
TDX "C1'" C 14.350 -4.101 26
TDX "O5'" O 13.740 -5.471 27
TDX "C5'" C 14.622 -6.685 28
TDX "C2'" C 15.842 -3.944 29
TDX "O2'" O 16.452 -2.574 30
TDX "C3'" C 16.724 -5.158 31
TDX "O3'" O 18.215 -5.001 32
TDX "C4'" C 16.113 -6.528 33
TDX "O4'" O 16.995 -7.742 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
TDX O4 C4 DOUBLE NONE 1
TDX C4 N3 SINGLE NONE 2
TDX C4 C5 SINGLE NONE 3
TDX N3 C2 SINGLE NONE 4
TDX C2 O2 DOUBLE NONE 5
TDX C2 N1 SINGLE NONE 6
TDX C5 C5M SINGLE NONE 7
TDX C5 C6 DOUBLE NONE 8
TDX C6 N1 SINGLE NONE 9
TDX C1B N1 SINGLE BEGINDASH 10
TDX C1B C2B SINGLE NONE 11
TDX C1B O4B SINGLE NONE 12
TDX C2B C3B SINGLE NONE 13
TDX C3B O3B SINGLE BEGINWEDGE 14
TDX C3B C4B SINGLE NONE 15
TDX O4B C4B SINGLE NONE 16
TDX C4B C5B SINGLE BEGINDASH 17
TDX C5B O5B SINGLE NONE 18
TDX O5B PA SINGLE NONE 19
TDX PA O1A DOUBLE NONE 20
TDX PA O2A SINGLE BEGINDASH 21
TDX PA O3A SINGLE NONE 22
TDX O3A PB SINGLE NONE 23
TDX PB O1B DOUBLE NONE 24
TDX PB O2B SINGLE BEGINWEDGE 25
TDX PB "O1'" SINGLE NONE 26
TDX "C1'" "O1'" SINGLE BEGINDASH 27
TDX "C1'" "O5'" SINGLE NONE 28
TDX "C1'" "C2'" SINGLE NONE 29
TDX "O5'" "C5'" SINGLE NONE 30
TDX "C5'" "C4'" SINGLE NONE 31
TDX "C2'" "O2'" SINGLE BEGINDASH 32
TDX "C2'" "C3'" SINGLE NONE 33
TDX "C3'" "O3'" SINGLE BEGINWEDGE 34
TDX "C3'" "C4'" SINGLE NONE 35
TDX "C4'" "O4'" SINGLE BEGINDASH 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
TDX 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
TDX 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
TDX 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
TDX pyranose F3 fragment OC1CCCCO1 InChI=1S/C5H10O2/c6-5-3-1-2-4-7-5/h5-6H,1-4H2 CELWCAITJAEQNL-UHFFFAOYSA-N
TDX 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
TDX O4 S1 1
TDX C4 S1 1
TDX N3 S1 1
TDX C2 S1 1
TDX O2 S1 1
TDX C5 S1 1
TDX C6 S1 1
TDX N1 S1 1
TDX C1B S1 1
TDX C2B S1 1
TDX C3B S1 1
TDX O4B S1 1
TDX C4B S1 1
TDX C5B S1 1
TDX O5B S1 1
TDX PA S1 1
TDX O1A S1 1
TDX O3A S1 1
TDX PB S1 1
TDX O1B S1 1
TDX "O1'" S1 1
TDX "C1'" S1 1
TDX "O5'" S1 1
TDX "C5'" S1 1
TDX "C2'" S1 1
TDX "C3'" S1 1
TDX "C4'" S1 1
TDX C1B F1 1
TDX C2B F1 1
TDX C3B F1 1
TDX O3B F1 1
TDX C4B F1 1
TDX O4B F1 1
TDX C5B F1 1
TDX O5B F1 1
TDX O5B F2 1
TDX PA F2 1
TDX O1A F2 1
TDX O2A F2 1
TDX O3A F2 1
TDX O3A F2 2
TDX PB F2 2
TDX O1B F2 2
TDX O2B F2 2
TDX "O1'" F2 2
TDX "C4'" F3 1
TDX "C5'" F3 1
TDX "O5'" F3 1
TDX "C1'" F3 1
TDX "C2'" F3 1
TDX "C3'" F3 1
TDX "O1'" F3 1
TDX C5 F4 1
TDX C4 F4 1
TDX N3 F4 1
TDX C2 F4 1
TDX N1 F4 1
TDX C6 F4 1
#
_pdbe_chem_comp_rdkit_properties.comp_id TDX
_pdbe_chem_comp_rdkit_properties.exactmw 534.065
_pdbe_chem_comp_rdkit_properties.amw 534.304
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 17
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 7
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 15
_pdbe_chem_comp_rdkit_properties.NumHBD 7
_pdbe_chem_comp_rdkit_properties.NumHBA 16
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 34
_pdbe_chem_comp_rdkit_properties.NumAtoms 58
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 19
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.733
_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 9
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 224.136
_pdbe_chem_comp_rdkit_properties.tpsa 256.530
_pdbe_chem_comp_rdkit_properties.CrippenClogP -1.072
_pdbe_chem_comp_rdkit_properties.CrippenMR 106.077
_pdbe_chem_comp_rdkit_properties.chi0v 17.201
_pdbe_chem_comp_rdkit_properties.chi1v 10.699
_pdbe_chem_comp_rdkit_properties.chi2v 5.438
_pdbe_chem_comp_rdkit_properties.chi3v 5.438
_pdbe_chem_comp_rdkit_properties.chi4v 3.589
_pdbe_chem_comp_rdkit_properties.chi0n 39.413
_pdbe_chem_comp_rdkit_properties.chi1n 19.175
_pdbe_chem_comp_rdkit_properties.chi2n 3.134
_pdbe_chem_comp_rdkit_properties.chi3n 3.134
_pdbe_chem_comp_rdkit_properties.chi4n 1.825
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.300
_pdbe_chem_comp_rdkit_properties.kappa1 9.537
_pdbe_chem_comp_rdkit_properties.kappa2 10.361
_pdbe_chem_comp_rdkit_properties.kappa3 6.469
_pdbe_chem_comp_rdkit_properties.Phi 2.906
#
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
TDX UniChem DrugBank DB03161
TDX UniChem PDBe TDX
TDX UniChem ZINC ZINC000015634247
TDX UniChem SureChEMBL SCHEMBL1764158
TDX UniChem Nikkaji J1.895.113D
TDX UniChem 'Probes And Drugs' PD059839
TDX UniChem PubChem 447462
#
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
TDX O4 6.432 0.416 3.489 ETKDGv3 1
TDX C4 5.874 -0.119 2.494 ETKDGv3 2
TDX N3 6.412 -1.322 1.944 ETKDGv3 3
TDX C2 5.796 -1.909 0.798 ETKDGv3 4
TDX O2 6.245 -2.992 0.337 ETKDGv3 5
TDX C5 4.666 0.486 1.893 ETKDGv3 6
TDX C5M 4.089 1.753 2.463 ETKDGv3 7
TDX C6 4.125 -0.062 0.792 ETKDGv3 8
TDX N1 4.668 -1.255 0.185 ETKDGv3 9
TDX C1B 3.997 -1.862 -0.976 ETKDGv3 10
TDX C2B 2.868 -2.774 -0.531 ETKDGv3 11
TDX C3B 1.897 -2.677 -1.671 ETKDGv3 12
TDX O3B 2.181 -3.676 -2.617 ETKDGv3 13
TDX O4B 3.472 -0.867 -1.828 ETKDGv3 14
TDX C4B 2.192 -1.290 -2.253 ETKDGv3 15
TDX C5B 1.145 -0.262 -1.808 ETKDGv3 16
TDX O5B 1.485 1.002 -2.328 ETKDGv3 17
TDX PA 0.453 2.175 -1.643 ETKDGv3 18
TDX O1A 0.385 3.351 -2.592 ETKDGv3 19
TDX O2A 1.115 2.695 -0.173 ETKDGv3 20
TDX O3A -1.111 1.529 -1.429 ETKDGv3 21
TDX PB -2.017 2.627 -0.490 ETKDGv3 22
TDX O1B -1.934 4.020 -1.074 ETKDGv3 23
TDX O2B -1.443 2.662 1.104 ETKDGv3 24
TDX "O1'" -3.656 2.147 -0.505 ETKDGv3 25
TDX "C1'" -3.789 0.875 0.101 ETKDGv3 26
TDX "O5'" -3.735 0.996 1.520 ETKDGv3 27
TDX "C5'" -4.979 1.409 2.046 ETKDGv3 28
TDX "C2'" -5.086 0.171 -0.407 ETKDGv3 29
TDX "O2'" -6.000 1.124 -0.894 ETKDGv3 30
TDX "C3'" -5.736 -0.640 0.728 ETKDGv3 31
TDX "O3'" -4.874 -1.690 1.089 ETKDGv3 32
TDX "C4'" -6.013 0.266 1.953 ETKDGv3 33
TDX "O4'" -7.307 0.804 1.854 ETKDGv3 34
TDX H3 7.248 -1.771 2.380 ETKDGv3 35
TDX H5M1 2.998 1.822 2.262 ETKDGv3 36
TDX H5M2 4.597 2.628 2.006 ETKDGv3 37
TDX H5M3 4.230 1.785 3.564 ETKDGv3 38
TDX H6 3.256 0.406 0.349 ETKDGv3 39
TDX H1B 4.727 -2.454 -1.573 ETKDGv3 40
TDX "H2'1" 2.392 -2.384 0.397 ETKDGv3 41
TDX "H2'2" 3.221 -3.814 -0.357 ETKDGv3 42
TDX H3B 0.850 -2.788 -1.299 ETKDGv3 43
TDX "HO3'" 1.409 -3.700 -3.241 ETKDGv3 44
TDX H4B 2.182 -1.331 -3.365 ETKDGv3 45
TDX "H5'1" 0.153 -0.579 -2.203 ETKDGv3 46
TDX "H5'2" 1.113 -0.250 -0.694 ETKDGv3 47
TDX H2A 1.182 1.879 0.383 ETKDGv3 48
TDX H2B -1.170 1.730 1.299 ETKDGv3 49
TDX "H1'" -2.955 0.198 -0.198 ETKDGv3 50
TDX H5B -4.840 1.684 3.113 ETKDGv3 51
TDX H5D -5.344 2.325 1.527 ETKDGv3 52
TDX "H2'" -4.811 -0.522 -1.238 ETKDGv3 53
TDX "HO2'" -6.662 0.633 -1.447 ETKDGv3 54
TDX "H3'" -6.695 -1.071 0.353 ETKDGv3 55
TDX HO3A -5.421 -2.357 1.581 ETKDGv3 56
TDX "H4'" -5.948 -0.357 2.876 ETKDGv3 57
TDX "HO4'" -7.531 1.175 2.748 ETKDGv3 58
#