data_GPL
#
_chem_comp.id GPL
_chem_comp.name
;LYSINE GUANOSINE-5'-MONOPHOSPHATE
;
_chem_comp.type "L-PEPTIDE LINKING"
_chem_comp.pdbx_type ATOMP
_chem_comp.formula "C16 H26 N7 O9 P"
_chem_comp.mon_nstd_parent_comp_id LYS
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 1999-07-08
_chem_comp.pdbx_modified_date 2024-09-27
_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 491.393
_chem_comp.one_letter_code K
_chem_comp.three_letter_code GPL
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag Y
_chem_comp.pdbx_ideal_coordinates_details ?
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code 1CKN
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site RCSB
_chem_comp.pdbx_pcm N
#
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.pdbx_backbone_atom_flag
_chem_comp_atom.pdbx_n_terminal_atom_flag
_chem_comp_atom.pdbx_c_terminal_atom_flag
_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
GPL P P P 0 1 N N S N N N 26.889 27.319 49.016 -2.195 2.799 -0.642 P GPL 1
GPL O1P O1P O 0 1 N N N N N N 26.415 27.319 47.586 -2.864 1.977 -1.712 O1P GPL 2
GPL O2P O2P O 0 1 N N N N N N 27.341 28.619 49.548 -3.288 3.538 0.307 O2P GPL 3
GPL "O5'" O5* O 0 1 N N N N N N 25.716 26.715 49.959 -1.405 1.865 0.430 "O5'" GPL 4
GPL "C5'" C5* C 0 1 N N N N N N 24.915 25.537 49.665 -0.881 2.428 1.621 "C5'" GPL 5
GPL "C4'" C4* C 0 1 N N R N N N 25.300 24.682 48.485 -0.199 1.333 2.429 "C4'" GPL 6
GPL "O4'" O4* O 0 1 N N N N N N 26.631 24.140 48.410 0.895 0.803 1.646 "O4'" GPL 7
GPL "C3'" C3* C 0 1 N N S N N N 24.421 23.514 48.302 0.409 1.846 3.730 "C3'" GPL 8
GPL "O3'" O3* O 0 1 N N N N N N 23.122 23.892 47.913 0.470 0.769 4.665 "O3'" GPL 9
GPL "C2'" C2* C 0 1 N N R N N N 25.094 22.792 47.204 1.814 2.225 3.303 "C2'" GPL 10
GPL "O2'" O2* O 0 1 N N N N N N 24.766 23.442 45.977 2.731 2.249 4.377 "O2'" GPL 11
GPL "C1'" C1* C 0 1 N N R N N N 26.569 23.045 47.470 2.135 1.120 2.308 "C1'" GPL 12
GPL N9 N9 N 0 1 Y N N N N N 27.294 21.851 47.858 3.143 1.487 1.316 N9 GPL 13
GPL C8 C8 C 0 1 Y N N N N N 28.518 21.447 47.468 3.085 2.565 0.464 C8 GPL 14
GPL N7 N7 N 0 1 Y N N N N N 28.940 20.336 47.988 4.141 2.642 -0.322 N7 GPL 15
GPL C5 C5 C 0 1 Y N N N N N 27.862 19.973 48.816 4.902 1.571 0.044 C5 GPL 16
GPL C6 C6 C 0 1 N N N N N N 27.686 18.815 49.631 6.173 1.152 -0.478 C6 GPL 17
GPL O6 O6 O 0 1 N N N N N N 28.476 17.905 49.815 6.769 1.739 -1.372 O6 GPL 18
GPL N1 N1 N 0 1 N N N N N N 26.457 18.835 50.312 6.621 -0.005 0.173 N1 GPL 19
GPL C2 C2 C 0 1 N N N N N N 25.493 19.829 50.171 5.930 -0.682 1.206 C2 GPL 20
GPL N2 N2 N 0 1 N N N N N N 24.345 19.716 50.871 6.557 -1.796 1.700 N2 GPL 21
GPL N3 N3 N 0 1 N N N N N N 25.682 20.900 49.384 4.766 -0.275 1.665 N3 GPL 22
GPL C4 C4 C 0 1 Y N N N N N 26.883 20.894 48.720 4.316 0.841 1.050 C4 GPL 23
GPL N N N 0 1 N N N N N N 33.321 22.027 48.725 3.498 4.366 -6.005 N GPL 24
GPL CA CA C 0 1 N N S N N N 31.990 22.514 48.399 3.817 5.285 -4.943 CA GPL 25
GPL CB CB C 0 1 N N N N N N 31.703 23.786 49.195 2.599 5.630 -4.083 CB GPL 26
GPL CG CG C 0 1 N N N N N N 30.290 24.327 49.066 1.904 4.420 -3.445 CG GPL 27
GPL CD CD C 0 1 N N N N N N 30.179 25.484 50.045 0.659 4.796 -2.635 CD GPL 28
GPL CE CE C 0 1 N N N N N N 28.742 25.983 50.129 0.004 3.593 -1.953 CE GPL 29
GPL NZ NZ N 0 1 N N N N N N 28.310 26.527 48.868 -1.155 3.981 -1.159 NZ GPL 30
GPL C C C 0 1 N N N N N N 31.967 22.794 46.900 4.881 4.614 -4.097 C GPL 31
GPL O O O 0 1 N N N N N N 32.467 23.833 46.449 5.283 3.467 -4.246 O GPL 32
GPL OXT OXT O 0 1 N Y N N N N ? ? ? 5.319 5.424 -3.097 OXT GPL 33
GPL HOP2 2HOP H 0 0 N N N N N N 27.639 28.619 50.449 -4.238 3.324 0.184 HOP2 GPL 34
GPL "H5'1" 1H5* H 0 0 N N N N N N 24.865 24.896 50.576 -0.165 3.211 1.355 "H5'1" GPL 35
GPL "H5'2" 2H5* H 0 0 N N N N N N 23.847 25.841 49.558 -1.702 2.873 2.192 "H5'2" GPL 36
GPL "H4'" H4* H 0 1 N N N N N N 25.205 25.464 47.696 -0.908 0.517 2.602 "H4'" GPL 37
GPL "H3'" H3* H 0 1 N N N N N N 24.286 22.918 49.234 -0.145 2.663 4.199 "H3'" GPL 38
GPL "HO3'" *HO3 H 0 0 N N N N N N 22.555 23.138 47.795 -0.447 0.539 4.878 "HO3'" GPL 39
GPL "H2'" H2* H 0 1 N N N N N N 24.817 21.713 47.147 1.812 3.206 2.815 "H2'" GPL 40
GPL "HO2'" *HO2 H 0 0 N N N N N N 25.199 22.977 45.270 2.967 1.326 4.577 "HO2'" GPL 41
GPL "H1'" H1* H 0 1 N N N N N N 27.105 23.336 46.536 2.521 0.216 2.791 "H1'" GPL 42
GPL H8 H8 H 0 1 N N N N N N 29.148 22.002 46.753 2.250 3.253 0.465 H8 GPL 43
GPL HN1 HN1 H 0 1 N N N N N N 26.249 18.071 50.956 7.515 -0.390 -0.120 HN1 GPL 44
GPL HN21 1HN2 H 0 0 N N N N N N 23.638 20.444 50.767 6.493 -2.641 1.181 HN21 GPL 45
GPL HN22 2HN2 H 0 0 N N N N N N 24.569 19.609 51.860 7.051 -1.717 2.558 HN22 GPL 46
GPL H 1HN H 0 1 N N N N N N 33.512 21.177 48.193 4.166 4.222 -6.744 H GPL 47
GPL H2 2HN H 0 1 N Y N N N N 33.446 21.890 49.728 2.551 4.041 -6.103 H2 GPL 48
GPL HA HA H 0 1 N N N N N N 31.206 21.764 48.660 4.248 6.169 -5.423 HA GPL 49
GPL HB2 1HB H 0 1 N N N N N N 31.957 23.630 50.269 2.903 6.312 -3.278 HB2 GPL 50
GPL HB3 2HB H 0 1 N N N N N N 32.442 24.578 48.930 1.869 6.183 -4.687 HB3 GPL 51
GPL HG2 1HG H 0 1 N N N N N N 30.017 24.605 48.021 2.626 3.928 -2.780 HG2 GPL 52
GPL HG3 2HG H 0 1 N N N N N N 29.504 23.549 49.211 1.647 3.690 -4.221 HG3 GPL 53
GPL HD2 1HD H 0 1 N N N N N N 30.582 25.215 51.049 -0.078 5.289 -3.281 HD2 GPL 54
GPL HD3 2HD H 0 1 N N N N N N 30.888 26.307 49.794 0.937 5.522 -1.862 HD3 GPL 55
GPL HE2 1HE H 0 1 N N N N N N 28.050 25.186 50.491 -0.303 2.857 -2.704 HE2 GPL 56
GPL HE3 2HE H 0 1 N N N N N N 28.608 26.714 50.959 0.738 3.107 -1.299 HE3 GPL 57
GPL HZ HNZ H 0 1 N N N N N N 29.027 27.120 48.451 -0.845 4.638 -0.444 HZ GPL 58
GPL HXT HXT H 0 1 N Y N N N N -0.014 0.174 -0.933 5.985 5.025 -2.497 HXT GPL 59
#
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
GPL P O1P DOUB N N 1
GPL P O2P SING N N 2
GPL P "O5'" SING N N 3
GPL P NZ SING N N 4
GPL O2P HOP2 SING N N 5
GPL "O5'" "C5'" SING N N 6
GPL "C5'" "C4'" SING N N 7
GPL "C5'" "H5'1" SING N N 8
GPL "C5'" "H5'2" SING N N 9
GPL "C4'" "O4'" SING N N 10
GPL "C4'" "C3'" SING N N 11
GPL "C4'" "H4'" SING N N 12
GPL "O4'" "C1'" SING N N 13
GPL "C3'" "O3'" SING N N 14
GPL "C3'" "C2'" SING N N 15
GPL "C3'" "H3'" SING N N 16
GPL "O3'" "HO3'" SING N N 17
GPL "C2'" "O2'" SING N N 18
GPL "C2'" "C1'" SING N N 19
GPL "C2'" "H2'" SING N N 20
GPL "O2'" "HO2'" SING N N 21
GPL "C1'" N9 SING N N 22
GPL "C1'" "H1'" SING N N 23
GPL N9 C8 SING Y N 24
GPL N9 C4 SING Y N 25
GPL C8 N7 DOUB Y N 26
GPL C8 H8 SING N N 27
GPL N7 C5 SING Y N 28
GPL C5 C6 SING N N 29
GPL C5 C4 DOUB Y N 30
GPL C6 O6 DOUB N N 31
GPL C6 N1 SING N N 32
GPL N1 C2 SING N N 33
GPL N1 HN1 SING N N 34
GPL C2 N2 SING N N 35
GPL C2 N3 DOUB N N 36
GPL N2 HN21 SING N N 37
GPL N2 HN22 SING N N 38
GPL N3 C4 SING N N 39
GPL N CA SING N N 40
GPL N H SING N N 41
GPL N H2 SING N N 42
GPL CA CB SING N N 43
GPL CA C SING N N 44
GPL CA HA SING N N 45
GPL CB CG SING N N 46
GPL CB HB2 SING N N 47
GPL CB HB3 SING N N 48
GPL CG CD SING N N 49
GPL CG HG2 SING N N 50
GPL CG HG3 SING N N 51
GPL CD CE SING N N 52
GPL CD HD2 SING N N 53
GPL CD HD3 SING N N 54
GPL CE NZ SING N N 55
GPL CE HE2 SING N N 56
GPL CE HE3 SING N N 57
GPL NZ HZ SING N N 58
GPL C O DOUB N N 59
GPL C OXT SING N N 60
GPL OXT HXT SING N N 61
#
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
GPL SMILES ACDLabs 10.04 "O=C(O)C(N)CCCCNP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O"
GPL SMILES_CANONICAL CACTVS 3.341 "N[C@@H](CCCCN[P@@](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3C(=O)NC(=Nc23)N)C(O)=O"
GPL SMILES CACTVS 3.341 "N[CH](CCCCN[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3C(=O)NC(=Nc23)N)C(O)=O"
GPL SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(NCCCC[C@@H](C(=O)O)N)O)O)O)N=C(NC2=O)N"
GPL SMILES "OpenEye OEToolkits" 1.5.0 "c1nc2c(n1C3C(C(C(O3)COP(=O)(NCCCCC(C(=O)O)N)O)O)O)N=C(NC2=O)N"
GPL InChI InChI 1.03 "InChI=1S/C16H26N7O9P/c17-7(15(27)28)3-1-2-4-20-33(29,30)31-5-8-10(24)11(25)14(32-8)23-6-19-9-12(23)21-16(18)22-13(9)26/h6-8,10-11,14,24-25H,1-5,17H2,(H,27,28)(H2,20,29,30)(H3,18,21,22,26)/t7-,8+,10+,11+,14+/m0/s1"
GPL InChIKey InChI 1.03 FYWIJTNESKGCIU-TWBCTODHSA-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
GPL "SYSTEMATIC NAME" ACDLabs 10.04 "(2S)-2-amino-6-{[(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]amino}hexanoic acid (non-preferred name)"
GPL "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "(2S)-2-amino-6-[[[(2R,3S,4R,5R)-5-(2-amino-6-oxo-1H-purin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl]amino]hexanoic 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
GPL "Create component" 1999-07-08 RCSB
GPL "Modify descriptor" 2011-06-04 RCSB
GPL "Modify PCM" 2024-09-27 PDBE
#