data_6WI
#
_chem_comp.id 6WI
_chem_comp.name "3-(guanosine-5'-diphospho)-D-glycerate"
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C13 H19 N5 O14 P2"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms "3GPPG; (2~{R})-3-[[[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-2-oxidanyl-propanoic acid"
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2021-08-04
_chem_comp.pdbx_modified_date 2022-01-28
_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 531.263
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code 6WI
_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 7P97
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site PDBE
# #
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
6WI C4 C4 C 0 1 Y N N -13.857 22.993 34.352 5.075 -1.180 0.059 C4 6WI 1
6WI C5 C5 C 0 1 Y N N -12.847 22.703 33.441 5.087 -2.219 -0.878 C5 6WI 2
6WI C6 C6 C 0 1 N N N -12.048 23.684 33.006 6.193 -3.102 -0.895 C6 6WI 3
6WI C8 C8 C 0 1 Y N N -13.896 20.860 33.884 3.246 -1.113 -1.170 C8 6WI 4
6WI N1 N1 N 0 1 N N N -12.272 24.950 33.539 7.189 -2.900 -0.004 N1 6WI 5
6WI N2 N2 N 0 1 N N N -13.462 26.456 34.834 8.145 -1.689 1.778 N2 6WI 6
6WI N3 N3 N 0 1 N N N -14.082 24.234 34.807 6.100 -1.039 0.907 N3 6WI 7
6WI OBF OBF O 0 1 N N N -13.792 13.144 40.675 -8.403 -3.403 1.299 OBF 6WI 8
6WI CBD CBD C 0 1 N N N -13.114 14.233 40.588 -7.438 -3.306 0.579 CBD 6WI 9
6WI OBG OBG O 0 1 N N N -11.855 14.384 40.732 -7.397 -3.978 -0.582 OBG 6WI 10
6WI CBC CBC C 0 1 N N R -13.875 15.492 40.255 -6.280 -2.431 0.984 CBC 6WI 11
6WI OBD OBD O 0 1 N N N -15.221 15.252 40.516 -6.507 -1.919 2.299 OBD 6WI 12
6WI CBE CBE C 0 1 N N N -13.774 15.807 38.751 -6.151 -1.266 0.000 CBE 6WI 13
6WI O3B OAT O 0 1 N N N -13.900 14.618 37.968 -4.985 -0.503 0.315 O3B 6WI 14
6WI PB PAQ P 0 1 N N N -14.958 14.492 36.826 -4.539 0.800 -0.518 PB 6WI 15
6WI O2B OAS O 0 1 N N N -16.255 14.049 37.557 -5.645 1.956 -0.340 O2B 6WI 16
6WI O1B OAR O 0 1 N N N -14.462 13.461 35.888 -4.416 0.451 -1.951 O1B 6WI 17
6WI O3A OAP O 0 1 N N N -14.963 15.952 36.236 -3.119 1.327 0.030 O3A 6WI 18
6WI PA PAM P 0 1 N N N -16.142 16.556 35.313 -2.012 2.349 -0.537 PA 6WI 19
6WI O2A OAO O 0 1 N N N -17.485 16.242 35.949 -2.478 3.862 -0.245 O2A 6WI 20
6WI O1A OAN O 0 1 N N N -16.040 16.358 33.873 -1.860 2.153 -1.996 O1A 6WI 21
6WI "O5'" "O5'" O 0 1 N N N -15.881 18.184 35.579 -0.603 2.072 0.192 "O5'" 6WI 22
6WI "C5'" "C5'" C 0 1 N N N -16.194 18.622 36.961 0.605 2.746 -0.167 "C5'" 6WI 23
6WI "C4'" "C4'" C 0 1 N N R -16.312 20.145 37.090 1.749 2.248 0.719 "C4'" 6WI 24
6WI "O4'" "O4'" O 0 1 N N N -15.146 20.880 36.633 2.028 0.869 0.427 "O4'" 6WI 25
6WI "C3'" "C3'" C 0 1 N N S -17.525 20.570 36.258 3.030 3.052 0.421 "C3'" 6WI 26
6WI "O3'" "O3'" O 0 1 N N N -18.325 21.603 36.965 3.480 3.728 1.596 "O3'" 6WI 27
6WI "C2'" "C2'" C 0 1 N N R -16.835 21.025 35.015 4.057 1.979 -0.014 "C2'" 6WI 28
6WI "O2'" "O2'" O 0 1 N N N -17.656 21.952 34.302 5.345 2.248 0.544 "O2'" 6WI 29
6WI "C1'" "C1'" C 0 1 N N R -15.596 21.724 35.579 3.451 0.683 0.592 "C1'" 6WI 30
6WI N9 N9 N 0 1 Y N N -14.494 21.838 34.627 3.907 -0.496 -0.148 N9 6WI 31
6WI C2 C2 C 0 1 N N N -13.284 25.209 34.433 7.119 -1.869 0.885 C2 6WI 32
6WI O6 O6 O 0 1 N N N -11.104 23.513 32.211 6.245 -4.021 -1.694 O6 6WI 33
6WI N7 N7 N 0 1 Y N N -12.876 21.357 33.172 3.945 -2.123 -1.601 N7 6WI 34
6WI H8 H8 H 0 1 N N N -14.204 19.825 33.872 2.290 -0.806 -1.567 H8 6WI 35
6WI HN1 H1 H 0 1 N N N -11.673 25.701 33.261 7.957 -3.492 0.003 HN1 6WI 36
6WI HN21 H22 H 0 0 N N N -14.223 26.682 35.442 8.905 -2.291 1.771 HN21 6WI 37
6WI HN22 H21 H 0 0 N N N -12.835 27.173 34.530 8.109 -0.960 2.417 HN22 6WI 38
6WI HBG H2 H 0 1 N N N -11.455 13.544 40.923 -8.163 -4.526 -0.800 HBG 6WI 39
6WI HBC HBC H 0 1 N N N -13.486 16.338 40.840 -5.361 -3.017 0.976 HBC 6WI 40
6WI HBD HBD H 0 1 N N N -15.348 14.330 40.707 -7.310 -1.387 2.381 HBD 6WI 41
6WI HBF HBF H 0 1 N N N -12.798 16.271 38.546 -6.067 -1.656 -1.014 HBF 6WI 42
6WI HBE HBE H 0 1 N N N -14.577 16.506 38.475 -7.033 -0.630 0.073 HBE 6WI 43
6WI HOB2 H3 H 0 0 N N N -16.502 13.179 37.265 -5.779 2.235 0.576 HOB2 6WI 44
6WI HOA2 H4 H 0 0 N N N -18.092 15.948 35.280 -2.598 4.063 0.693 HOA2 6WI 45
6WI "H5''" "H5'" H 0 0 N N N -17.149 18.169 37.265 0.839 2.541 -1.212 "H5''" 6WI 46
6WI "H5'" H5V H 0 1 N N N -15.393 18.274 37.630 0.477 3.819 -0.027 "H5'" 6WI 47
6WI "H4'" "H4'" H 0 1 N N N -16.510 20.390 38.144 1.479 2.358 1.769 "H4'" 6WI 48
6WI "H3'" "H3'" H 0 1 N N N -18.149 19.690 36.042 2.854 3.764 -0.385 "H3'" 6WI 49
6WI "HO3'" H8L H 0 0 N N N -18.723 21.221 37.738 4.284 4.250 1.465 "HO3'" 6WI 50
6WI "H2'" "H2'" H 0 1 N N N -16.542 20.168 34.390 4.112 1.911 -1.101 "H2'" 6WI 51
6WI "HO2'" H8M H 0 0 N N N -18.419 21.502 33.960 5.765 3.047 0.197 "HO2'" 6WI 52
6WI "H1'" "H1'" H 0 1 N N N -15.877 22.716 35.961 3.706 0.597 1.648 "H1'" 6WI 53
# #
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
6WI O6 C6 DOUB N N 1
6WI C6 C5 SING N N 2
6WI C6 N1 SING N N 3
6WI N7 C5 SING Y N 4
6WI N7 C8 DOUB Y N 5
6WI C5 C4 DOUB Y N 6
6WI N1 C2 SING N N 7
6WI O1A PA DOUB N N 8
6WI C8 N9 SING Y N 9
6WI "O2'" "C2'" SING N N 10
6WI C4 N9 SING Y N 11
6WI C4 N3 SING N N 12
6WI C2 N3 DOUB N N 13
6WI C2 N2 SING N N 14
6WI N9 "C1'" SING N N 15
6WI "C2'" "C1'" SING N N 16
6WI "C2'" "C3'" SING N N 17
6WI PA "O5'" SING N N 18
6WI PA O2A SING N N 19
6WI PA O3A SING N N 20
6WI "C1'" "O4'" SING N N 21
6WI "O5'" "C5'" SING N N 22
6WI O1B PB DOUB N N 23
6WI O3A PB SING N N 24
6WI "C3'" "O3'" SING N N 25
6WI "C3'" "C4'" SING N N 26
6WI "O4'" "C4'" SING N N 27
6WI PB O2B SING N N 28
6WI PB O3B SING N N 29
6WI "C5'" "C4'" SING N N 30
6WI O3B CBE SING N N 31
6WI CBE CBC SING N N 32
6WI CBC OBD SING N N 33
6WI CBC CBD SING N N 34
6WI CBD OBF DOUB N N 35
6WI CBD OBG SING N N 36
6WI C8 H8 SING N N 37
6WI N1 HN1 SING N N 38
6WI N2 HN21 SING N N 39
6WI N2 HN22 SING N N 40
6WI OBG HBG SING N N 41
6WI CBC HBC SING N N 42
6WI OBD HBD SING N N 43
6WI CBE HBF SING N N 44
6WI CBE HBE SING N N 45
6WI O2B HOB2 SING N N 46
6WI O2A HOA2 SING N N 47
6WI "C5'" "H5''" SING N N 48
6WI "C5'" "H5'" SING N N 49
6WI "C4'" "H4'" SING N N 50
6WI "C3'" "H3'" SING N N 51
6WI "O3'" "HO3'" SING N N 52
6WI "C2'" "H2'" SING N N 53
6WI "O2'" "HO2'" SING N N 54
6WI "C1'" "H1'" SING N N 55
# #
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
6WI InChI InChI 1.03 "InChI=1S/C13H19N5O14P2/c14-13-16-9-6(10(22)17-13)15-3-18(9)11-8(21)7(20)5(31-11)2-30-34(27,28)32-33(25,26)29-1-4(19)12(23)24/h3-5,7-8,11,19-21H,1-2H2,(H,23,24)(H,25,26)(H,27,28)(H3,14,16,17,22)/t4-,5-,7-,8-,11-/m1/s1"
6WI InChIKey InChI 1.03 UBONPDGCIQEDRL-QWEIRQIHSA-N
6WI SMILES_CANONICAL CACTVS 3.385 "NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)OC[C@@H](O)C(O)=O)[C@@H](O)[C@H]3O"
6WI SMILES CACTVS 3.385 "NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH](O)C(O)=O)[CH](O)[CH]3O"
6WI SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)OP(=O)(O)OC[C@H](C(=O)O)O)O)O)N=C(NC2=O)N"
6WI SMILES "OpenEye OEToolkits" 2.0.7 "c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC(C(=O)O)O)O)O)N=C(NC2=O)N"
#
_pdbx_chem_comp_identifier.comp_id 6WI
_pdbx_chem_comp_identifier.type "SYSTEMATIC NAME"
_pdbx_chem_comp_identifier.program "OpenEye OEToolkits"
_pdbx_chem_comp_identifier.program_version 2.0.7
_pdbx_chem_comp_identifier.identifier "(2~{R})-3-[[[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-2-oxidanyl-propanoic acid"
# #
loop_
_pdbx_chem_comp_synonyms.ordinal
_pdbx_chem_comp_synonyms.comp_id
_pdbx_chem_comp_synonyms.name
_pdbx_chem_comp_synonyms.provenance
_pdbx_chem_comp_synonyms.type
1 6WI 3GPPG AUTHOR ?
2 6WI "(2~{R})-3-[[[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-2-oxidanyl-propanoic acid" PDB ?
# #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
6WI "Create component" 2021-08-04 PDBE
6WI "Modify atom id" 2021-08-26 PDBE
6WI "Initial release" 2022-02-02 RCSB
##