data_GDX
#
_chem_comp.id GDX
_chem_comp.name
;GUANOSINE 5'-(TRIHYDROGEN DIPHOSPHATE), P'-D-MANNOPYRANOSYL ESTER
;
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C16 H23 N5 O17 P2"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2002-09-11
_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 619.325
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code GDX
_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 1MFZ
_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
GDX N2 N2 N 0 1 N N N 119.279 139.922 178.503 8.863 2.049 -1.990 N2 GDX 1
GDX C2 C2 C 0 1 N N N 119.454 139.911 179.862 7.917 2.077 -0.996 C2 GDX 2
GDX N1 N1 N 0 1 N N N 118.488 139.357 180.644 8.029 3.005 -0.003 N1 GDX 3
GDX N3 N3 N 0 1 N N N 120.573 140.448 180.386 6.928 1.213 -1.031 N3 GDX 4
GDX C4 C4 C 0 1 Y N N 120.786 140.447 181.702 5.983 1.204 -0.083 C4 GDX 5
GDX C5 C5 C 0 1 Y N N 119.786 139.868 182.605 6.045 2.128 0.967 C5 GDX 6
GDX C6 C6 C 0 1 N N N 118.580 139.298 181.989 7.112 3.056 0.989 C6 GDX 7
GDX O6 O6 O 0 1 N N N 117.691 138.794 182.719 7.203 3.882 1.881 O6 GDX 8
GDX N7 N7 N 0 1 Y N N 120.226 139.997 183.861 4.979 1.896 1.770 N7 GDX 9
GDX C8 C8 C 0 1 Y N N 121.431 140.616 183.829 4.283 0.908 1.288 C8 GDX 10
GDX N9 N9 N 0 1 Y N N 121.701 140.870 182.556 4.865 0.448 0.143 N9 GDX 11
GDX C1D "C1'A" C 0 1 N N R 122.933 141.296 182.215 4.381 -0.655 -0.692 C1D GDX 12
GDX C2D "C2'A" C 0 1 N N R 123.297 142.504 182.621 5.086 -1.980 -0.307 C2D GDX 13
GDX O2D "O2'A" O 0 1 N N N 122.674 143.342 181.957 6.323 -2.123 -1.008 O2D GDX 14
GDX C3D "C3'A" C 0 1 N N S 124.650 142.600 182.573 4.060 -3.041 -0.776 C3D GDX 15
GDX O3D "O3'A" O 0 1 N N N 125.130 143.182 181.325 4.420 -3.552 -2.060 O3D GDX 16
GDX C4D "C4'A" C 0 1 N N R 125.179 141.382 182.639 2.729 -2.268 -0.857 C4D GDX 17
GDX O4D "O4'A" O 0 1 N N N 124.094 140.460 182.387 2.989 -0.923 -0.423 O4D GDX 18
GDX C5D "C5'A" C 0 1 N N N 125.786 141.120 184.000 1.692 -2.920 0.060 C5D GDX 19
GDX O5D "O5'A" O 0 1 N N N 125.126 141.892 184.999 0.431 -2.269 -0.109 O5D GDX 20
GDX PA PA P 0 1 N N N 125.167 141.534 186.574 -0.892 -2.697 0.702 PA GDX 21
GDX O1A O1A O 0 1 N N N 125.777 140.162 186.789 -0.613 -2.662 2.155 O1A GDX 22
GDX O2A O2A O 0 1 N N N 123.790 141.868 187.106 -1.325 -4.188 0.275 O2A GDX 23
GDX O3A O3A O 0 1 N N N 126.172 142.624 187.160 -2.086 -1.673 0.360 O3A GDX 24
GDX PB PB P 0 1 N N N 127.708 142.262 187.364 -3.468 -1.283 1.089 PB GDX 25
GDX O2B O2B O 0 1 N N N 128.428 143.468 187.906 -3.170 -0.248 2.286 O2B GDX 26
GDX O3B O3B O 0 1 N N N 128.303 141.909 186.038 -4.098 -2.504 1.638 O3B GDX 27
GDX O1B O1B O 0 1 N N N 127.837 141.046 188.423 -4.462 -0.599 0.023 O1B GDX 28
GDX "C1'" "C1'" C 0 1 N N R 128.322 139.824 187.802 -5.808 -0.234 0.336 "C1'" GDX 29
GDX "O5'" "O5'" O 0 1 N N N 129.770 139.894 187.834 -5.836 1.106 0.831 "O5'" GDX 30
GDX "C5'" "C5'" C 0 1 N N S 130.245 139.732 189.204 -5.317 2.076 -0.082 "C5'" GDX 31
GDX "C6'" "C6'" C 0 1 N N N 131.574 139.544 189.169 -5.370 3.442 0.552 "C6'" GDX 32
GDX O6A O6A O 0 1 N N N 132.043 138.630 188.508 -5.889 3.586 1.633 O6A GDX 33
GDX O6B O6B O 0 1 N Y N 132.345 140.275 189.778 -4.839 4.498 -0.084 O6B GDX 34
GDX "C2'" "C2'" C 0 1 N N S 127.879 138.748 188.474 -6.670 -0.329 -0.926 "C2'" GDX 35
GDX "O2'" "O2'" O 0 1 N N N 128.216 137.705 187.910 -8.026 -0.017 -0.602 "O2'" GDX 36
GDX "C3'" "C3'" C 0 1 N N S 128.296 138.759 189.756 -6.149 0.666 -1.966 "C3'" GDX 37
GDX "O3'" "O3'" O 0 1 N N N 127.755 137.840 190.393 -6.992 0.637 -3.120 "O3'" GDX 38
GDX "C4'" "C4'" C 0 1 N N S 129.647 138.685 189.805 -6.159 2.073 -1.360 "C4'" GDX 39
GDX "O4'" "O4'" O 0 1 N N N 130.058 138.585 190.961 -5.607 3.000 -2.297 "O4'" GDX 40
GDX HN21 HN21 H 0 0 N N N 119.978 140.326 177.912 9.597 2.682 -1.980 HN21 GDX 41
GDX HN22 HN22 H 0 0 N N N 118.453 139.526 178.102 8.799 1.391 -2.701 HN22 GDX 42
GDX HN1 HN1 H 0 1 N N N 117.675 138.977 180.203 8.769 3.631 -0.009 HN1 GDX 43
GDX H8 H8 H 0 1 N N N 122.053 140.857 184.679 3.380 0.512 1.729 H8 GDX 44
GDX "H1'" "H1'" H 0 1 N N N 122.672 141.272 181.147 4.535 -0.431 -1.748 "H1'" GDX 45
GDX "H2'" "H2'" H 0 1 N N N 123.035 142.700 183.671 5.242 -2.039 0.770 "H2'" GDX 46
GDX HO2A HO2A H 0 0 N N N 122.923 144.216 182.235 6.801 -2.938 -0.800 HO2A GDX 47
GDX "H3'" "H3'" H 0 1 N N N 124.945 143.243 183.416 3.989 -3.851 -0.050 "H3'" GDX 48
GDX HO3A HO3A H 0 0 N N N 126.079 143.227 181.341 5.279 -3.998 -2.080 HO3A GDX 49
GDX "H4'" "H4'" H 0 1 N N N 125.990 141.268 181.905 2.366 -2.262 -1.885 "H4'" GDX 50
GDX "H5'2" "H5'2" H 0 0 N N N 125.680 140.052 184.242 1.594 -3.975 -0.195 "H5'2" GDX 51
GDX "H5'1" "H5'1" H 0 0 N N N 126.851 141.394 183.978 2.013 -2.824 1.097 "H5'1" GDX 52
GDX HOA2 HOA2 H 0 0 N N N 123.431 141.112 187.555 -1.524 -4.285 -0.667 HOA2 GDX 53
GDX HOB2 HOB2 H 0 0 N N N 129.099 143.740 187.291 -2.756 0.577 1.998 HOB2 GDX 54
GDX "HC1'" "HC1'" H 0 0 N N N 127.957 139.728 186.769 -6.200 -0.910 1.096 "HC1'" GDX 55
GDX "HC5'" "HC5'" H 0 0 N N N 129.999 140.633 189.784 -4.284 1.828 -0.326 "HC5'" GDX 56
GDX HO6B HO6B H 0 0 N Y N 133.239 139.991 189.625 -4.897 5.354 0.362 HO6B GDX 57
GDX "HC2'" "HC2'" H 0 0 N N N 126.780 138.793 188.482 -6.615 -1.341 -1.329 "HC2'" GDX 58
GDX "HO2'" "HO2'" H 0 0 N N N 127.892 136.960 188.402 -8.419 -0.606 0.056 "HO2'" GDX 59
GDX "HC3'" "HC3'" H 0 0 N N N 127.998 139.706 190.230 -5.132 0.398 -2.251 "HC3'" GDX 60
GDX "HO3'" "HO3'" H 0 0 N N N 128.056 137.858 191.294 -7.038 -0.227 -3.551 "HO3'" GDX 61
GDX "HC4'" "HC4'" H 0 0 N N N 129.914 137.773 189.250 -7.183 2.360 -1.123 "HC4'" GDX 62
GDX "HO4'" "HO4'" H 0 0 N N N 129.636 137.847 191.385 -5.577 3.912 -1.977 "HO4'" GDX 63
#
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
GDX N2 C2 SING N N 1
GDX N2 HN21 SING N N 2
GDX N2 HN22 SING N N 3
GDX C2 N1 SING N N 4
GDX C2 N3 DOUB N N 5
GDX N1 C6 SING N N 6
GDX N1 HN1 SING N N 7
GDX N3 C4 SING N N 8
GDX C4 C5 DOUB Y N 9
GDX C4 N9 SING Y N 10
GDX C5 C6 SING N N 11
GDX C5 N7 SING Y N 12
GDX C6 O6 DOUB N N 13
GDX N7 C8 DOUB Y N 14
GDX C8 N9 SING Y N 15
GDX C8 H8 SING N N 16
GDX N9 C1D SING N N 17
GDX C1D C2D SING N N 18
GDX C1D O4D SING N N 19
GDX C1D "H1'" SING N N 20
GDX C2D O2D SING N N 21
GDX C2D C3D SING N N 22
GDX C2D "H2'" SING N N 23
GDX O2D HO2A SING N N 24
GDX C3D O3D SING N N 25
GDX C3D C4D SING N N 26
GDX C3D "H3'" SING N N 27
GDX O3D HO3A SING N N 28
GDX C4D O4D SING N N 29
GDX C4D C5D SING N N 30
GDX C4D "H4'" SING N N 31
GDX C5D O5D SING N N 32
GDX C5D "H5'2" SING N N 33
GDX C5D "H5'1" SING N N 34
GDX O5D PA SING N N 35
GDX PA O1A DOUB N N 36
GDX PA O2A SING N N 37
GDX PA O3A SING N N 38
GDX O2A HOA2 SING N N 39
GDX O3A PB SING N N 40
GDX PB O2B SING N N 41
GDX PB O3B DOUB N N 42
GDX PB O1B SING N N 43
GDX O2B HOB2 SING N N 44
GDX O1B "C1'" SING N N 45
GDX "C1'" "O5'" SING N N 46
GDX "C1'" "C2'" SING N N 47
GDX "C1'" "HC1'" SING N N 48
GDX "O5'" "C5'" SING N N 49
GDX "C5'" "C6'" SING N N 50
GDX "C5'" "C4'" SING N N 51
GDX "C5'" "HC5'" SING N N 52
GDX "C6'" O6A DOUB N N 53
GDX "C6'" O6B SING N N 54
GDX O6B HO6B SING N N 55
GDX "C2'" "O2'" SING N N 56
GDX "C2'" "C3'" SING N N 57
GDX "C2'" "HC2'" SING N N 58
GDX "O2'" "HO2'" SING N N 59
GDX "C3'" "O3'" SING N N 60
GDX "C3'" "C4'" SING N N 61
GDX "C3'" "HC3'" SING N N 62
GDX "O3'" "HO3'" SING N N 63
GDX "C4'" "O4'" SING N N 64
GDX "C4'" "HC4'" SING N N 65
GDX "O4'" "HO4'" SING N N 66
#
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
GDX SMILES ACDLabs 12.01 "O=C4NC(=Nc1c4ncn1C2OC(C(O)C2O)COP(=O)(OP(=O)(OC3OC(C(=O)O)C(O)C(O)C3O)O)O)N"
GDX SMILES_CANONICAL CACTVS 3.370 "NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)O[C@H]4O[C@@H]([C@@H](O)[C@H](O)[C@@H]4O)C(O)=O)[C@@H](O)[C@H]3O"
GDX SMILES CACTVS 3.370 "NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[CH]4O[CH]([CH](O)[CH](O)[CH]4O)C(O)=O)[CH](O)[CH]3O"
GDX SMILES_CANONICAL "OpenEye OEToolkits" 1.7.0 "c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(O)O[C@@H]4[C@H]([C@H]([C@@H]([C@H](O4)C(=O)O)O)O)O)O)O)N=C(NC2=O)N"
GDX SMILES "OpenEye OEToolkits" 1.7.0 "c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OC4C(C(C(C(O4)C(=O)O)O)O)O)O)O)N=C(NC2=O)N"
GDX InChI InChI 1.03
"InChI=1S/C16H23N5O17P2/c17-16-19-11-4(12(27)20-16)18-2-21(11)13-8(25)5(22)3(35-13)1-34-39(30,31)38-40(32,33)37-15-9(26)6(23)7(24)10(36-15)14(28)29/h2-3,5-10,13,15,22-26H,1H2,(H,28,29)(H,30,31)(H,32,33)(H3,17,19,20,27)/t3-,5-,6+,7+,8-,9+,10+,13-,15-/m1/s1"
GDX InChIKey InChI 1.03 DNBSDUDYNPJVCN-ZXTXFPBHSA-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
GDX "SYSTEMATIC NAME" ACDLabs 12.01
;(2S,3S,4S,5S,6R)-6-{[(S)-{[(S)-{[(2R,3S,4R,5R)-5-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}-3,4,5-trihydroxytetrahydro-2H-pyran-2-carboxylic acid (non-preferred name)
;
GDX "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.0 "(2S,3S,4S,5S,6R)-6-[[[(2R,3S,4R,5R)-5-(2-azanyl-6-oxo-1H-purin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl]oxy-hydroxy-phosphoryl]oxy-3,4,5-trihydroxy-oxane-2-carboxylic acid"
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
GDX "Create component" 2002-09-11 RCSB
GDX "Modify leaving atom flag" 2011-01-07 RCSB
GDX "Modify descriptor" 2011-06-04 RCSB
#