data_THD
#
_chem_comp.id THD
_chem_comp.name
;2-[3-[(4-AMINO-2-METHYL-5-PYRIMIDINYL)METHYL]-2-(1,2-DIHYDROXYETHYL)-4-METHYL-1,3-THIAZOL-3-IUM-5-YL]ETHYL TRIHYDROGEN
DIPHOSPHATE
;
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C14 H22 N4 O9 P2 S"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms "({ALPHA,BETA}-DIHYDROXYETHYL)-THIAMIN DIPHOSPHATE"
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2001-11-09
_chem_comp.pdbx_modified_date 2020-06-17
_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 484.358
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code THD
_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 1GPU
_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.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
THD "N1'" "N1'" N 0 1 Y N N -3.041 61.454 19.848 1.428 1.481 5.541 "N1'" THD 1
THD "C2'" "C2'" C 0 1 Y N N -2.184 60.470 20.188 2.050 0.833 6.505 "C2'" THD 2
THD CM2 CM2 C 0 1 N N N -0.873 60.838 20.682 2.653 1.615 7.643 CM2 THD 3
THD "N3'" "N3'" N 0 1 Y N N -2.532 59.196 20.071 2.164 -0.479 6.498 "N3'" THD 4
THD "C4'" "C4'" C 0 1 Y N N -3.803 58.840 19.598 1.639 -1.201 5.512 "C4'" THD 5
THD "N4'" "N4'" N 0 1 N N N -4.019 57.528 19.535 1.757 -2.581 5.511 "N4'" THD 6
THD "C5'" "C5'" C 0 1 Y N N -4.775 59.864 19.219 0.974 -0.545 4.475 "C5'" THD 7
THD "C6'" "C6'" C 0 1 Y N N -4.314 61.147 19.373 0.884 0.832 4.522 "C6'" THD 8
THD "C7'" "C7'" C 0 1 N N N -6.195 59.594 18.689 0.369 -1.320 3.333 "C7'" THD 9
THD N3 N3 N 0 1 N N N -6.112 58.680 17.427 -0.262 -0.391 2.393 N3 THD 10
THD C2 C2 C 0 1 N N N -6.228 57.285 17.358 -1.577 0.052 2.586 C2 THD 11
THD S1 S1 S 0 1 N N N -5.973 56.722 15.756 -1.793 1.127 1.176 S1 THD 12
THD C5 C5 C 0 1 N N N -5.752 58.299 15.189 -0.178 0.909 0.448 C5 THD 13
THD C4 C4 C 0 1 N N N -5.856 59.211 16.208 0.409 0.067 1.292 C4 THD 14
THD CM4 CM4 C 0 1 N N N -5.708 60.684 16.020 1.823 -0.385 1.035 CM4 THD 15
THD C6 C6 C 0 1 N N N -5.468 58.595 13.730 0.379 1.526 -0.809 C6 THD 16
THD C7 C7 C 0 1 N N N -5.621 57.464 12.801 0.070 0.619 -2.002 C7 THD 17
THD O7 O7 O 0 1 N N N -4.798 57.778 11.677 0.598 1.203 -3.194 O7 THD 18
THD PA PA P 0 1 N N R -3.699 56.763 11.303 0.239 0.202 -4.402 PA THD 19
THD O1A O1A O 0 1 N N N -2.538 56.617 12.250 -1.358 0.038 -4.506 O1A THD 20
THD O2A O2A O 0 1 N N N -3.433 57.289 9.996 0.855 -1.119 -4.147 O2A THD 21
THD O3A O3A O 0 1 N N N -4.402 55.393 10.820 0.808 0.801 -5.783 O3A THD 22
THD PB PB P 0 1 N N N -5.639 54.735 10.025 0.415 -0.244 -6.942 PB THD 23
THD O1B O1B O 0 1 N N N -4.978 54.712 8.730 -1.056 -0.388 -6.998 O1B THD 24
THD O2B O2B O 0 1 N N N -5.798 53.395 10.573 0.957 0.294 -8.359 O2B THD 25
THD O3B O3B O 0 1 N N N -6.849 55.575 10.209 1.082 -1.674 -6.622 O3B THD 26
THD C8 C8 C 0 1 N N N -6.621 56.702 18.419 -2.436 -0.242 3.566 C8 THD 27
THD O9 O9 O 0 1 N N N -6.947 57.126 19.553 -2.030 -1.006 4.622 O9 THD 28
THD C9 C9 C 0 1 N N N -6.659 55.276 18.152 -3.852 0.268 3.505 C9 THD 29
THD O10 O10 O 0 1 N N N -5.679 54.612 18.927 -4.757 -0.837 3.499 O10 THD 30
THD HM21 1HM2 H 0 0 N N N -0.164 60.024 20.963 1.915 1.728 8.438 HM21 THD 31
THD HM22 2HM2 H 0 0 N N N -0.993 61.530 21.548 3.523 1.083 8.029 HM22 THD 32
THD HM23 3HM2 H 0 0 N N N -0.380 61.508 19.939 2.957 2.599 7.287 HM23 THD 33
THD "H4'1" "1H4'" H 0 0 N N N -5.019 57.248 19.163 2.221 -3.029 6.236 "H4'1" THD 34
THD "H4'2" "2H4'" H 0 0 N N N -3.286 56.755 19.821 1.375 -3.100 4.786 "H4'2" THD 35
THD "H6'" "H6'" H 0 1 N N N -4.987 61.979 19.107 0.376 1.373 3.737 "H6'" THD 36
THD "H7'1" "1H7'" H 0 0 N N N -6.758 60.536 18.491 1.150 -1.881 2.821 "H7'1" THD 37
THD "H7'2" "2H7'" H 0 0 N N N -6.865 59.170 19.473 -0.379 -2.011 3.720 "H7'2" THD 38
THD HM41 1HM4 H 0 0 N N N -5.497 61.121 15.016 2.193 0.079 0.121 HM41 THD 39
THD HM42 2HM4 H 0 0 N N N -4.922 61.044 16.724 2.456 -0.092 1.873 HM42 THD 40
THD HM43 3HM4 H 0 0 N N N -6.623 61.176 16.425 1.844 -1.469 0.926 HM43 THD 41
THD H6C1 1H6C H 0 0 N N N -4.450 59.036 13.625 -0.077 2.503 -0.967 H6C1 THD 42
THD H6C2 2H6C H 0 0 N N N -6.094 59.452 13.389 1.458 1.640 -0.709 H6C2 THD 43
THD H7C1 1H7C H 0 0 N N N -6.681 57.245 12.533 0.526 -0.357 -1.843 H7C1 THD 44
THD H7C2 2H7C H 0 0 N N N -5.394 56.473 13.260 -1.009 0.504 -2.101 H7C2 THD 45
THD HO1A HO1A H 0 0 N N N -1.861 55.992 12.020 -1.719 0.919 -4.672 HO1A THD 46
THD HO2B HO2B H 0 0 N N N -6.527 53.007 10.104 0.701 -0.359 -9.023 HO2B THD 47
THD HO3B HO3B H 0 0 N N N -7.578 55.187 9.740 2.039 -1.537 -6.594 HO3B THD 48
THD H9 H9 H 0 1 N N N -7.240 56.691 20.345 -2.075 -0.443 5.407 H9 THD 49
THD H9C1 1H9C H 0 0 N N N -6.555 55.051 17.065 -4.050 0.894 4.375 H9C1 THD 50
THD H9C2 2H9C H 0 0 N N N -7.677 54.848 18.310 -3.989 0.854 2.596 H9C2 THD 51
THD H10 H10 H 0 1 N N N -5.704 53.679 18.752 -5.650 -0.468 3.460 H10 THD 52
# #
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
THD "N1'" "C2'" DOUB Y N 1
THD "N1'" "C6'" SING Y N 2
THD "C2'" CM2 SING N N 3
THD "C2'" "N3'" SING Y N 4
THD CM2 HM21 SING N N 5
THD CM2 HM22 SING N N 6
THD CM2 HM23 SING N N 7
THD "N3'" "C4'" DOUB Y N 8
THD "C4'" "N4'" SING N N 9
THD "C4'" "C5'" SING Y N 10
THD "N4'" "H4'1" SING N N 11
THD "N4'" "H4'2" SING N N 12
THD "C5'" "C6'" DOUB Y N 13
THD "C5'" "C7'" SING N N 14
THD "C6'" "H6'" SING N N 15
THD "C7'" N3 SING N N 16
THD "C7'" "H7'1" SING N N 17
THD "C7'" "H7'2" SING N N 18
THD N3 C2 SING N N 19
THD N3 C4 SING N N 20
THD C2 S1 SING N N 21
THD C2 C8 DOUB N E 22
THD S1 C5 SING N N 23
THD C5 C4 DOUB N N 24
THD C5 C6 SING N N 25
THD C4 CM4 SING N N 26
THD CM4 HM41 SING N N 27
THD CM4 HM42 SING N N 28
THD CM4 HM43 SING N N 29
THD C6 C7 SING N N 30
THD C6 H6C1 SING N N 31
THD C6 H6C2 SING N N 32
THD C7 O7 SING N N 33
THD C7 H7C1 SING N N 34
THD C7 H7C2 SING N N 35
THD O7 PA SING N N 36
THD PA O1A SING N N 37
THD PA O2A DOUB N N 38
THD PA O3A SING N N 39
THD O1A HO1A SING N N 40
THD O3A PB SING N N 41
THD PB O1B DOUB N N 42
THD PB O2B SING N N 43
THD PB O3B SING N N 44
THD O2B HO2B SING N N 45
THD O3B HO3B SING N N 46
THD C8 O9 SING N N 47
THD C8 C9 SING N N 48
THD O9 H9 SING N N 49
THD C9 O10 SING N N 50
THD C9 H9C1 SING N N 51
THD C9 H9C2 SING N N 52
THD O10 H10 SING N N 53
# #
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
THD SMILES ACDLabs 10.04 "O=P(O)(O)OP(=O)(O)OCCC=1S\C(=C(\O)CO)N(C=1C)Cc2cnc(nc2N)C"
THD SMILES_CANONICAL CACTVS 3.341 "Cc1ncc(CN\2C(=C(CCO[P@](O)(=O)O[P](O)(O)=O)SC\2=C(/O)CO)C)c(N)n1"
THD SMILES CACTVS 3.341 "Cc1ncc(CN2C(=C(CCO[P](O)(=O)O[P](O)(O)=O)SC2=C(O)CO)C)c(N)n1"
THD SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "Cc1ncc(c(n1)N)CN\2C(=C(S/C2=C(\CO)/O)CCO[P@@](=O)(O)OP(=O)(O)O)C"
THD SMILES "OpenEye OEToolkits" 1.5.0 "Cc1ncc(c(n1)N)CN2C(=C(SC2=C(CO)O)CCOP(=O)(O)OP(=O)(O)O)C"
THD InChI InChI 1.03 "InChI=1S/C14H22N4O9P2S/c1-8-12(3-4-26-29(24,25)27-28(21,22)23)30-14(11(20)7-19)18(8)6-10-5-16-9(2)17-13(10)15/h5,19-20H,3-4,6-7H2,1-2H3,(H,24,25)(H2,15,16,17)(H2,21,22,23)/b14-11+"
THD InChIKey InChI 1.03 LXZUEFPJZTWGEL-SDNWHVSQSA-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
THD "SYSTEMATIC NAME" ACDLabs 10.04 "2-[(2E)-3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-2-(1,2-dihydroxyethylidene)-4-methyl-2,3-dihydro-1,3-thiazol-5-yl]ethyl trihydrogen diphosphate"
THD "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "2-[(2E)-3-[(4-amino-2-methyl-pyrimidin-5-yl)methyl]-2-(1,2-dihydroxyethylidene)-4-methyl-1,3-thiazol-5-yl]ethyl phosphono 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
THD "Create component" 2001-11-09 EBI
THD "Modify descriptor" 2011-06-04 RCSB
THD "Modify synonyms" 2020-06-05 PDBE
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id THD
_pdbx_chem_comp_synonyms.name "({ALPHA,BETA}-DIHYDROXYETHYL)-THIAMIN DIPHOSPHATE"
_pdbx_chem_comp_synonyms.provenance ?
_pdbx_chem_comp_synonyms.type ?
##