data_RGT
#
_chem_comp.id RGT
_chem_comp.name
;2-amino-9-{5-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-ribofuranosyl}-9H-purin-6-yl
5-O-phosphono-beta-D-ribofuranoside
;
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C15 H25 N5 O21 P4"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms "(Ribose-5'-phosphate)-(guanosine-5'-triphosphate)"
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2008-07-31
_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 735.275
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code RGT
_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 3DZI
_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.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
RGT O2P O2P O 0 1 N N N 5.585 4.038 3.830 9.961 2.586 0.291 O2P RGT 1
RGT P P P 0 1 N N N 4.138 4.543 4.036 10.046 1.282 -0.649 P RGT 2
RGT O3P O3P O 0 1 N N N 3.737 5.811 3.250 9.624 1.636 -2.023 O3P RGT 3
RGT O1P O1P O 0 1 N N N 3.695 4.518 5.518 11.561 0.738 -0.677 O1P RGT 4
RGT O5R O5R O 0 1 N N N 3.213 3.394 3.336 9.075 0.137 -0.068 O5R RGT 5
RGT C5R C5R C 0 1 N N N 1.769 3.471 3.286 8.848 -1.105 -0.737 C5R RGT 6
RGT C4R C4R C 0 1 N N R 1.221 3.724 1.882 7.878 -1.957 0.084 C4R RGT 7
RGT O4R O4R O 0 1 N N N 1.734 2.711 1.008 6.581 -1.339 0.104 O4R RGT 8
RGT C3R C3R C 0 1 N N S -0.303 3.627 1.790 7.719 -3.345 -0.568 C3R RGT 9
RGT O3R O3R O 0 1 N N N -0.825 4.757 1.081 8.132 -4.372 0.334 O3R RGT 10
RGT C2R C2R C 0 1 N N R -0.625 2.408 0.949 6.202 -3.454 -0.860 C2R RGT 11
RGT O2R O2R O 0 1 N N N -1.414 2.874 -0.146 5.719 -4.765 -0.561 O2R RGT 12
RGT C1R C1R C 0 1 N N S 0.697 1.986 0.337 5.607 -2.405 0.119 C1R RGT 13
RGT O6 O6 O 0 1 N N N 1.778 0.586 1.099 4.341 -1.936 -0.350 O6 RGT 14
RGT C6 C6 C 0 1 Y N N 1.999 -0.214 2.014 3.701 -1.021 0.417 C6 RGT 15
RGT C5 C5 C 0 1 Y N N 3.292 -0.407 2.380 2.453 -0.508 0.030 C5 RGT 16
RGT C4 C4 C 0 1 Y N N 3.547 -1.300 3.416 1.834 0.438 0.864 C4 RGT 17
RGT N3 N3 N 0 1 Y N N 2.547 -1.985 4.073 2.444 0.814 1.982 N3 RGT 18
RGT C2 C2 C 0 1 Y N N 1.240 -1.797 3.699 3.621 0.305 2.309 C2 RGT 19
RGT N2 N2 N 0 1 N N N 0.233 -2.459 4.306 4.228 0.720 3.483 N2 RGT 20
RGT N1 N1 N 0 1 Y N N 0.990 -0.915 2.658 4.237 -0.596 1.553 N1 RGT 21
RGT N7 N7 N 0 1 Y N N 4.437 0.115 1.909 1.628 -0.709 -1.028 N7 RGT 22
RGT C8 C8 C 0 1 Y N N 5.463 -0.430 2.636 0.569 0.035 -0.898 C8 RGT 23
RGT N9 N9 N 0 1 Y N N 4.910 -1.301 3.570 0.648 0.762 0.254 N9 RGT 24
RGT "C1'" "C1'" C 0 1 N N R 5.556 -2.162 4.577 -0.350 1.714 0.748 "C1'" RGT 25
RGT "C2'" "C2'" C 0 1 N N R 7.069 -2.264 4.468 -0.028 3.139 0.247 "C2'" RGT 26
RGT "O2'" "O2'" O 0 1 N N N 7.494 -2.933 3.293 0.654 3.884 1.258 "O2'" RGT 27
RGT "C3'" "C3'" C 0 1 N N S 7.301 -3.044 5.737 -1.414 3.759 -0.040 "C3'" RGT 28
RGT "O3'" "O3'" O 0 1 N N N 6.860 -4.374 5.504 -1.631 4.904 0.786 "O3'" RGT 29
RGT "O4'" "O4'" O 0 1 N N N 5.311 -1.770 5.921 -1.649 1.413 0.194 "O4'" RGT 30
RGT "C4'" "C4'" C 0 1 N N R 6.321 -2.394 6.717 -2.409 2.634 0.322 "C4'" RGT 31
RGT "C5'" "C5'" C 0 1 N N N 6.993 -1.407 7.681 -3.589 2.632 -0.653 "C5'" RGT 32
RGT "O5'" "O5'" O 0 1 N N N 7.563 -0.335 6.959 -4.552 1.664 -0.233 "O5'" RGT 33
RGT PA PA P 0 1 N N R 7.862 1.097 7.645 -5.925 1.392 -1.029 PA RGT 34
RGT O1A O1A O 0 1 N N N 7.064 1.286 8.927 -5.592 0.791 -2.485 O1A RGT 35
RGT O2A O2A O 0 1 N N N 7.621 2.195 6.629 -6.669 2.662 -1.178 O2A RGT 36
RGT O3A O3A O 0 1 N N N 9.419 1.039 8.054 -6.822 0.338 -0.206 O3A RGT 37
RGT PB PB P 0 1 N N R 10.575 0.884 6.939 -8.367 -0.110 -0.275 PB RGT 38
RGT O1B O1B O 0 1 N N N 10.532 2.054 5.963 -8.757 -0.320 -1.687 O1B RGT 39
RGT O2B O2B O 0 1 N N N 10.460 -0.453 6.213 -9.289 1.041 0.371 O2B RGT 40
RGT O3B O3B O 0 1 N N N 11.909 0.972 7.865 -8.566 -1.480 0.546 O3B RGT 41
RGT PG PG P 0 1 N N N 13.399 0.712 7.279 -9.689 -2.634 0.542 PG RGT 42
RGT O1G O1G O 0 1 N N N 14.216 1.945 7.616 -9.613 -3.462 1.920 O1G RGT 43
RGT O3G O3G O 0 1 N N N 13.344 0.499 5.779 -11.028 -2.018 0.410 O3G RGT 44
RGT O2G O2G O 0 1 N N N 14.016 -0.514 7.936 -9.432 -3.629 -0.697 O2G RGT 45
RGT HO2P HO2P H 0 0 N N N 5.756 3.934 2.901 10.522 3.318 0.000 HO2P RGT 46
RGT HO1P HO1P H 0 0 N N N 4.462 4.513 6.078 11.904 0.486 0.192 HO1P RGT 47
RGT H5R H5R H 0 1 N N N 1.362 2.514 3.646 8.421 -0.915 -1.722 H5R RGT 48
RGT H5RA H5RA H 0 0 N N N 1.466 4.323 3.913 9.794 -1.636 -0.848 H5RA RGT 49
RGT H4R H4R H 0 1 N N N 1.526 4.745 1.611 8.252 -2.067 1.102 H4R RGT 50
RGT H3R H3R H 0 1 N N N -0.732 3.578 2.802 8.290 -3.399 -1.495 H3R RGT 51
RGT HO3R HO3R H 0 0 N N N -0.941 5.483 1.683 8.053 -5.267 -0.025 HO3R RGT 52
RGT H2R H2R H 0 1 N N N -1.121 1.612 1.524 5.985 -3.188 -1.895 H2R RGT 53
RGT HO2R HO2R H 0 0 N N N -2.316 2.977 0.134 4.773 -4.883 -0.728 HO2R RGT 54
RGT H1R H1R H 0 1 N N N 0.356 1.939 -0.708 5.514 -2.826 1.120 H1R RGT 55
RGT HN2 HN2 H 0 1 N N N 0.471 -2.623 5.263 3.789 1.374 4.050 HN2 RGT 56
RGT HN2A HN2A H 0 0 N N N -0.602 -1.911 4.259 5.090 0.358 3.738 HN2A RGT 57
RGT H8 H8 H 0 1 N N N 6.515 -0.221 2.507 -0.252 0.072 -1.599 H8 RGT 58
RGT "H1'" "H1'" H 0 1 N N N 5.087 -3.129 4.344 -0.387 1.692 1.837 "H1'" RGT 59
RGT "H2'" "H2'" H 0 1 N N N 7.624 -1.318 4.381 0.568 3.098 -0.665 "H2'" RGT 60
RGT "HO2'" "HO2'" H 0 0 N N N 7.589 -2.304 2.587 0.881 4.787 0.996 "HO2'" RGT 61
RGT "H3'" "H3'" H 0 1 N N N 8.345 -3.049 6.083 -1.504 4.023 -1.094 "H3'" RGT 62
RGT "HO3'" "HO3'" H 0 0 N N N 6.762 -4.516 4.570 -0.995 5.619 0.642 "HO3'" RGT 63
RGT "H4'" "H4'" H 0 1 N N N 5.888 -3.157 7.380 -2.763 2.756 1.346 "H4'" RGT 64
RGT "H5'" "H5'" H 0 1 N N N 6.241 -1.014 8.381 -4.049 3.620 -0.669 "H5'" RGT 65
RGT "H5'A" "H5'A" H 0 0 N N N 7.786 -1.929 8.237 -3.233 2.381 -1.652 "H5'A" RGT 66
RGT HO1A HO1A H 0 0 N N N 7.658 1.325 9.667 -5.104 -0.043 -2.463 HO1A RGT 67
RGT HO2B HO2B H 0 0 N N N 10.436 -0.304 5.275 -9.089 1.232 1.297 HO2B RGT 68
RGT HO1G HO1G H 0 0 N N N 14.387 1.967 8.550 -10.263 -4.175 1.987 HO1G RGT 69
RGT HO2G HO2G H 0 0 N N N 14.145 -1.192 7.284 -8.571 -4.069 -0.676 HO2G RGT 70
# #
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
RGT O2P P SING N N 1
RGT O2P HO2P SING N N 2
RGT O3P P DOUB N N 3
RGT O5R P SING N N 4
RGT P O1P SING N N 5
RGT O1P HO1P SING N N 6
RGT C5R O5R SING N N 7
RGT C4R C5R SING N N 8
RGT C5R H5R SING N N 9
RGT C5R H5RA SING N N 10
RGT O4R C4R SING N N 11
RGT C3R C4R SING N N 12
RGT C4R H4R SING N N 13
RGT C1R O4R SING N N 14
RGT C2R C3R SING N N 15
RGT O3R C3R SING N N 16
RGT C3R H3R SING N N 17
RGT O3R HO3R SING N N 18
RGT O2R C2R SING N N 19
RGT C1R C2R SING N N 20
RGT C2R H2R SING N N 21
RGT O2R HO2R SING N N 22
RGT C1R O6 SING N N 23
RGT C1R H1R SING N N 24
RGT O6 C6 SING N N 25
RGT C6 C5 DOUB Y N 26
RGT C6 N1 SING Y N 27
RGT N7 C5 SING Y N 28
RGT C5 C4 SING Y N 29
RGT C4 N9 SING Y N 30
RGT C4 N3 DOUB Y N 31
RGT C2 N3 SING Y N 32
RGT N1 C2 DOUB Y N 33
RGT C2 N2 SING N N 34
RGT N2 HN2 SING N N 35
RGT N2 HN2A SING N N 36
RGT N7 C8 DOUB Y N 37
RGT C8 N9 SING Y N 38
RGT C8 H8 SING N N 39
RGT N9 "C1'" SING N N 40
RGT "C2'" "C1'" SING N N 41
RGT "C1'" "O4'" SING N N 42
RGT "C1'" "H1'" SING N N 43
RGT "O2'" "C2'" SING N N 44
RGT "C2'" "C3'" SING N N 45
RGT "C2'" "H2'" SING N N 46
RGT "O2'" "HO2'" SING N N 47
RGT "O3'" "C3'" SING N N 48
RGT "C3'" "C4'" SING N N 49
RGT "C3'" "H3'" SING N N 50
RGT "O3'" "HO3'" SING N N 51
RGT "O4'" "C4'" SING N N 52
RGT "C4'" "C5'" SING N N 53
RGT "C4'" "H4'" SING N N 54
RGT "O5'" "C5'" SING N N 55
RGT "C5'" "H5'" SING N N 56
RGT "C5'" "H5'A" SING N N 57
RGT "O5'" PA SING N N 58
RGT O2A PA DOUB N N 59
RGT PA O3A SING N N 60
RGT PA O1A SING N N 61
RGT O1A HO1A SING N N 62
RGT PB O3A SING N N 63
RGT O1B PB DOUB N N 64
RGT O2B PB SING N N 65
RGT PB O3B SING N N 66
RGT O2B HO2B SING N N 67
RGT PG O3B SING N N 68
RGT O3G PG DOUB N N 69
RGT PG O1G SING N N 70
RGT PG O2G SING N N 71
RGT O1G HO1G SING N N 72
RGT O2G HO2G SING N N 73
# #
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
RGT SMILES ACDLabs 10.04 "O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC4OC(n2cnc1c(nc(nc12)N)OC3OC(C(O)C3O)COP(=O)(O)O)C(O)C4O"
RGT SMILES_CANONICAL CACTVS 3.341 "Nc1nc(O[C@@H]2O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]2O)c3ncn([C@@H]4O[C@H](CO[P@](O)(=O)O[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]4O)c3n1"
RGT SMILES CACTVS 3.341 "Nc1nc(O[CH]2O[CH](CO[P](O)(O)=O)[CH](O)[CH]2O)c3ncn([CH]4O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]4O)c3n1"
RGT SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(O)O[P@](=O)(O)OP(=O)(O)O)O)O)nc(nc2O[C@H]4[C@@H]([C@@H]([C@H](O4)COP(=O)(O)O)O)O)N"
RGT SMILES "OpenEye OEToolkits" 1.5.0 "c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)nc(nc2OC4C(C(C(O4)COP(=O)(O)O)O)O)N"
RGT InChI InChI 1.03 "InChI=1S/C15H25N5O21P4/c16-15-18-11-6(12(19-15)39-14-10(24)8(22)5(38-14)1-35-42(25,26)27)17-3-20(11)13-9(23)7(21)4(37-13)2-36-44(31,32)41-45(33,34)40-43(28,29)30/h3-5,7-10,13-14,21-24H,1-2H2,(H,31,32)(H,33,34)(H2,16,18,19)(H2,25,26,27)(H2,28,29,30)/t4-,5-,7-,8-,9-,10-,13-,14+/m1/s1"
RGT InChIKey InChI 1.03 CZRRKFZDNKXXKR-MHJQXXNXSA-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
RGT "SYSTEMATIC NAME" ACDLabs 10.04 "2-amino-9-{5-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-ribofuranosyl}-9H-purin-6-yl 5-O-phosphono-beta-D-ribofuranoside"
RGT "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,4R,5R)-5-[2-amino-6-[(2S,3R,4S,5R)-3,4-dihydroxy-5-(phosphonooxymethyl)oxolan-2-yl]oxy-purin-9-yl]-3,4-dihydroxy-oxolan-2-yl]methyl (hydroxy-phosphonooxy-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
RGT "Create component" 2008-07-31 RCSB
RGT "Modify aromatic_flag" 2011-06-04 RCSB
RGT "Modify descriptor" 2011-06-04 RCSB
RGT "Modify synonyms" 2020-06-05 PDBE
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id RGT
_pdbx_chem_comp_synonyms.name "(Ribose-5'-phosphate)-(guanosine-5'-triphosphate)"
_pdbx_chem_comp_synonyms.provenance ?
_pdbx_chem_comp_synonyms.type ?
##