data_C2G
#
_chem_comp.id C2G
_chem_comp.name "[CYTIDINE-5'-PHOSPHATE] GLYCERYLPHOSPHORIC ACID ESTER"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C12 H21 N3 O13 P2"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms "CYTIDINE 5'-DIPHOSPHOGLYCEROL"
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2002-10-29
_chem_comp.pdbx_modified_date 2021-03-01
_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 477.255
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code C2G
_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 1N1D
_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
C2G N1 N1 N 0 1 Y N N 21.014 61.175 27.797 0.747 0.546 -5.040 N1 C2G 1
C2G C2 C2 C 0 1 Y N N 20.007 61.830 28.489 1.298 -0.673 -4.906 C2 C2G 2
C2G N3 N3 N 0 1 Y N N 20.206 62.999 29.146 2.427 -0.990 -5.538 N3 C2G 3
C2G C4 C4 C 0 1 Y N N 21.434 63.566 29.137 3.038 -0.108 -6.318 C4 C2G 4
C2G C5 C5 C 0 1 Y N N 22.492 62.967 28.457 2.490 1.180 -6.474 C5 C2G 5
C2G C6 C6 C 0 1 Y N N 22.213 61.775 27.809 1.338 1.486 -5.830 C6 C2G 6
C2G O2 O2 O 0 1 N N N 18.848 61.384 28.549 0.756 -1.502 -4.195 O2 C2G 7
C2G N4 N4 N 0 1 N N N 21.587 64.706 29.798 4.204 -0.447 -6.965 N4 C2G 8
C2G "C1'" C1* C 0 1 N N R 20.782 59.853 27.150 -0.494 0.866 -4.332 "C1'" C2G 9
C2G "C2'" C2* C 0 1 N N R 20.825 59.936 25.666 -1.615 -0.114 -4.743 "C2'" C2G 10
C2G "O2'" O2* O 0 1 N N N 19.623 60.520 25.204 -2.459 0.468 -5.738 "O2'" C2G 11
C2G "C3'" C3* C 0 1 N N S 21.037 58.503 25.270 -2.404 -0.349 -3.433 "C3'" C2G 12
C2G "C4'" C4* C 0 1 N N R 21.801 57.909 26.461 -1.667 0.519 -2.390 "C4'" C2G 13
C2G "O4'" O4* O 0 1 N N N 21.863 58.988 27.405 -0.329 0.668 -2.911 "O4'" C2G 14
C2G "O3'" O3* O 0 1 N N N 19.854 57.734 25.132 -3.758 0.082 -3.579 "O3'" C2G 15
C2G "C5'" C5* C 0 1 N N N 23.117 57.600 25.781 -1.635 -0.186 -1.033 "C5'" C2G 16
C2G "O5'" O5* O 0 1 N N N 24.178 58.492 26.087 -0.888 0.601 -0.104 "O5'" C2G 17
C2G PA PA P 0 1 N N S 25.400 58.600 24.954 -0.895 -0.196 1.294 PA C2G 18
C2G O1A O1A O 0 1 N N N 26.688 58.248 25.767 -0.267 -1.523 1.107 O1A C2G 19
C2G O2A O2A O 0 1 N N N 25.465 60.070 24.426 -2.413 -0.386 1.796 O2A C2G 20
C2G O3A O3A O 0 1 N N N 25.223 57.448 23.798 -0.066 0.639 2.393 O3A C2G 21
C2G PB PB P 0 1 N N R 24.806 57.955 22.280 -0.114 -0.212 3.758 PB C2G 22
C2G O1B O1B O 0 1 N N N 26.077 58.574 21.600 0.500 -1.539 3.534 O1B C2G 23
C2G O2B O2B O 0 1 N N N 23.605 58.968 22.352 -1.645 -0.402 4.219 O2B C2G 24
C2G O3B O3B O 0 1 N N N 24.444 56.563 21.462 0.698 0.568 4.907 O3B C2G 25
C2G O1G O1G O 0 1 N N N 22.696 53.684 18.386 2.000 0.241 9.549 O1G C2G 26
C2G C1G C1G C 0 1 N N N 22.668 54.920 19.109 1.292 -0.402 8.487 C1G C2G 27
C2G C2G C2G C 0 1 N N S 24.108 55.221 19.372 1.377 0.456 7.224 C2G C2G 28
C2G O2G O2G O 0 1 N N N 24.721 54.194 20.176 0.793 1.735 7.477 O2G C2G 29
C2G C3G C3G C 0 1 N N N 24.328 56.560 20.041 0.619 -0.233 6.087 C3G C2G 30
C2G HC5 HC5 H 0 1 N N N 23.500 63.414 28.432 2.975 1.910 -7.106 HC5 C2G 31
C2G HC6 HC6 H 0 1 N N N 23.014 61.259 27.254 0.896 2.466 -5.938 HC6 C2G 32
C2G HN41 1HN4 H 0 0 N N N 22.513 65.133 29.791 4.581 -1.333 -6.852 HN41 C2G 33
C2G HN42 2HN4 H 0 0 N N N 21.280 64.580 30.762 4.646 0.198 -7.537 HN42 C2G 34
C2G HC1 HC1 H 0 1 N N N 19.796 59.513 27.545 -0.794 1.894 -4.539 HC1 C2G 35
C2G HC2 HC2 H 0 1 N N N 21.621 60.580 25.226 -1.188 -1.049 -5.105 HC2 C2G 36
C2G HO2 HO2 H 0 1 N N N 19.650 60.573 24.255 -3.170 -0.165 -5.907 HO2 C2G 37
C2G HC3 HC3 H 0 1 N N N 21.541 58.476 24.275 -2.368 -1.401 -3.148 HC3 C2G 38
C2G HC4 HC4 H 0 1 N N N 21.405 57.018 27.002 -2.149 1.493 -2.299 HC4 C2G 39
C2G HO3 HO3 H 0 1 N N N 19.988 56.827 24.881 -4.165 -0.493 -4.240 HO3 C2G 40
C2G HC51 1HC5 H 0 0 N N N 23.423 56.550 25.997 -2.653 -0.313 -0.665 HC51 C2G 41
C2G HC52 2HC5 H 0 0 N N N 22.973 57.538 24.677 -1.163 -1.162 -1.142 HC52 C2G 42
C2G H2A H2A H 0 1 N N N 26.160 60.131 23.781 -2.784 0.500 1.905 H2A C2G 43
C2G H2B H2B H 0 1 N N N 23.365 59.259 21.480 -2.008 0.484 4.354 H2B C2G 44
C2G H1G H1G H 0 1 N N N 21.780 53.492 18.218 1.922 -0.330 10.324 H1G C2G 45
C2G H1G1 1H1G H 0 0 N N N 22.115 55.739 18.592 0.247 -0.529 8.771 H1G1 C2G 46
C2G H1G2 2H1G H 0 0 N N N 22.030 54.901 20.023 1.737 -1.378 8.294 H1G2 C2G 47
C2G H2G H2G H 0 1 N N N 24.587 55.256 18.366 2.421 0.583 6.940 H2G C2G 48
C2G HOG HOG H 0 1 N N N 25.636 54.385 20.343 -0.127 1.578 7.725 HOG C2G 49
C2G H3G1 1H3G H 0 0 N N N 23.522 57.266 19.732 -0.424 -0.360 6.371 H3G1 C2G 50
C2G H3G2 2H3G H 0 0 N N N 25.220 57.056 19.594 1.064 -1.209 5.894 H3G2 C2G 51
# #
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
C2G N1 C2 SING Y N 1
C2G N1 C6 SING Y N 2
C2G N1 "C1'" SING N N 3
C2G C2 N3 SING Y N 4
C2G C2 O2 DOUB N N 5
C2G N3 C4 DOUB Y N 6
C2G C4 C5 SING Y N 7
C2G C4 N4 SING N N 8
C2G C5 C6 DOUB Y N 9
C2G C5 HC5 SING N N 10
C2G C6 HC6 SING N N 11
C2G N4 HN41 SING N N 12
C2G N4 HN42 SING N N 13
C2G "C1'" "C2'" SING N N 14
C2G "C1'" "O4'" SING N N 15
C2G "C1'" HC1 SING N N 16
C2G "C2'" "O2'" SING N N 17
C2G "C2'" "C3'" SING N N 18
C2G "C2'" HC2 SING N N 19
C2G "O2'" HO2 SING N N 20
C2G "C3'" "C4'" SING N N 21
C2G "C3'" "O3'" SING N N 22
C2G "C3'" HC3 SING N N 23
C2G "C4'" "O4'" SING N N 24
C2G "C4'" "C5'" SING N N 25
C2G "C4'" HC4 SING N N 26
C2G "O3'" HO3 SING N N 27
C2G "C5'" "O5'" SING N N 28
C2G "C5'" HC51 SING N N 29
C2G "C5'" HC52 SING N N 30
C2G "O5'" PA SING N N 31
C2G PA O1A DOUB N N 32
C2G PA O2A SING N N 33
C2G PA O3A SING N N 34
C2G O2A H2A SING N N 35
C2G O3A PB SING N N 36
C2G PB O1B DOUB N N 37
C2G PB O2B SING N N 38
C2G PB O3B SING N N 39
C2G O2B H2B SING N N 40
C2G O3B C3G SING N N 41
C2G O1G C1G SING N N 42
C2G O1G H1G SING N N 43
C2G C1G C2G SING N N 44
C2G C1G H1G1 SING N N 45
C2G C1G H1G2 SING N N 46
C2G C2G O2G SING N N 47
C2G C2G C3G SING N N 48
C2G C2G H2G SING N N 49
C2G O2G HOG SING N N 50
C2G C3G H3G1 SING N N 51
C2G C3G H3G2 SING N N 52
# #
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
C2G SMILES ACDLabs 10.04 "O=P(O)(OCC(O)CO)OP(=O)(O)OCC2OC(N1C(=O)N=C(N)C=C1)C(O)C2O"
C2G SMILES_CANONICAL CACTVS 3.341 "NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO[P@@](O)(=O)O[P@@](O)(=O)OC[C@@H](O)CO)[C@@H](O)[C@H]2O"
C2G SMILES CACTVS 3.341 "NC1=NC(=O)N(C=C1)[CH]2O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH](O)CO)[CH](O)[CH]2O"
C2G SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@](=O)(O)O[P@](=O)(O)OC[C@H](CO)O)O)O"
C2G SMILES "OpenEye OEToolkits" 1.5.0 "C1=CN(C(=O)N=C1N)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)OCC(CO)O)O)O"
C2G InChI InChI 1.03 "InChI=1S/C12H21N3O13P2/c13-8-1-2-15(12(20)14-8)11-10(19)9(18)7(27-11)5-26-30(23,24)28-29(21,22)25-4-6(17)3-16/h1-2,6-7,9-11,16-19H,3-5H2,(H,21,22)(H,23,24)(H2,13,14,20)/t6-,7+,9+,10+,11+/m0/s1"
C2G InChIKey InChI 1.03 HHPOUCCVONEPRK-CNYIRLTGSA-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
C2G "SYSTEMATIC NAME" ACDLabs 10.04 "5'-O-[(S)-{[(R)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]cytidine"
C2G "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,4R,5R)-5-(4-amino-2-oxo-pyrimidin-1-yl)-3,4-dihydroxy-oxolan-2-yl]methyl [[(2S)-2,3-dihydroxypropoxy]-hydroxy-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
C2G "Create component" 2002-10-29 RCSB
C2G "Modify descriptor" 2011-06-04 RCSB
C2G "Modify synonyms" 2021-03-01 PDBE
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id C2G
_pdbx_chem_comp_synonyms.name "CYTIDINE 5'-DIPHOSPHOGLYCEROL"
_pdbx_chem_comp_synonyms.provenance ?
_pdbx_chem_comp_synonyms.type ?
##