data_G4P
#
_chem_comp.id G4P
_chem_comp.name "GUANOSINE-5',3'-TETRAPHOSPHATE"
_chem_comp.type "RNA LINKING"
_chem_comp.pdbx_type ATOMN
_chem_comp.formula "C10 H17 N5 O17 P4"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms "guanosine tetraphosphate;ppGpp"
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2002-05-16
_chem_comp.pdbx_modified_date 2020-06-24
_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 603.160
_chem_comp.one_letter_code N
_chem_comp.three_letter_code G4P
_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 1LNZ
_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.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
G4P PB PB P 0 1 N N N N N N 9.060 68.309 71.663 4.684 -4.187 -0.023 PB G4P 1
G4P O1B O1B O 0 1 N N N N N N 8.231 69.237 72.448 4.172 -4.147 1.365 O1B G4P 2
G4P O2B O2B O 0 1 N N N N N N 8.949 68.266 70.190 4.940 -5.716 -0.457 O2B G4P 3
G4P O3B O3B O 0 1 N N N N N N 10.582 68.480 71.740 6.067 -3.367 -0.109 O3B G4P 4
G4P O3A O3A O 0 1 N N N N N N 8.518 66.775 72.067 3.603 -3.522 -1.014 O3A G4P 5
G4P PA PA P 0 1 N N S N N N 8.407 66.284 73.590 3.099 -2.165 -0.308 PA G4P 6
G4P O1A O1A O 0 1 N N N N N N 9.338 65.150 73.418 2.938 -2.395 1.145 O1A G4P 7
G4P O2A O2A O 0 1 N N N N N N 8.707 67.255 74.678 4.183 -0.999 -0.551 O2A G4P 8
G4P "O5'" O5* O 0 1 N N N N N N 6.958 65.650 73.573 1.686 -1.724 -0.942 "O5'" G4P 9
G4P "C5'" C5* C 0 1 N N N N N N 5.728 66.309 73.723 1.237 -0.589 -0.199 "C5'" G4P 10
G4P "C4'" C4* C 0 1 N N R N N N 4.762 65.419 74.549 -0.109 -0.117 -0.753 "C4'" G4P 11
G4P "O4'" O4* O 0 1 N N N N N N 4.119 64.328 73.814 -1.129 -1.110 -0.510 "O4'" G4P 12
G4P "C3'" C3* C 0 1 N N S N N N 5.379 64.616 75.794 -0.594 1.140 0.004 "C3'" G4P 13
G4P "O3'" O3* O 0 1 N N N N N N 4.626 65.017 76.965 -0.281 2.322 -0.736 "O3'" G4P 14
G4P "C2'" C2* C 0 1 N N R N N N 5.183 63.104 75.525 -2.126 0.951 0.104 "C2'" G4P 15
G4P "O2'" O2* O 0 1 N N N N N N 4.584 62.437 76.653 -2.806 2.013 -0.569 "O2'" G4P 16
G4P "C1'" C1* C 0 1 N N R N N N 4.287 63.043 74.351 -2.382 -0.399 -0.602 "C1'" G4P 17
G4P N9 N9 N 0 1 Y N N N N N 4.783 62.114 73.268 -3.442 -1.141 0.086 N9 G4P 18
G4P C8 C8 C 0 1 Y N N N N N 5.920 62.060 72.496 -3.267 -2.078 1.063 C8 G4P 19
G4P N7 N7 N 0 1 Y N N N N N 5.942 61.057 71.661 -4.423 -2.533 1.449 N7 G4P 20
G4P C5 C5 C 0 1 Y N N N N N 4.765 60.395 71.858 -5.405 -1.919 0.745 C5 G4P 21
G4P C6 C6 C 0 1 N N N N N N 4.188 59.210 71.264 -6.816 -2.010 0.738 C6 G4P 22
G4P O6 O6 O 0 1 N N N N N N 4.657 58.509 70.396 -7.397 -2.778 1.486 O6 G4P 23
G4P N1 N1 N 0 1 N N N N N N 2.907 58.854 71.769 -7.506 -1.221 -0.115 N1 G4P 24
G4P C2 C2 C 0 1 N N N N N N 2.233 59.550 72.767 -6.847 -0.370 -0.952 C2 G4P 25
G4P N2 N2 N 0 1 N N N N N N 1.056 59.075 73.134 -7.573 0.415 -1.812 N2 G4P 26
G4P N3 N3 N 0 1 N N N N N N 2.769 60.689 73.368 -5.536 -0.276 -0.954 N3 G4P 27
G4P C4 C4 C 0 1 Y N N N N N 4.007 61.025 72.851 -4.787 -1.022 -0.133 C4 G4P 28
G4P PC PC P 0 1 N N S N N N 4.380 65.085 78.309 0.677 3.216 0.200 PC G4P 29
G4P O1C O1C O 0 1 N N N N N N 4.591 63.855 79.137 1.848 2.413 0.617 O1C G4P 30
G4P O2C O2C O 0 1 N N N N N N 3.045 65.740 78.340 -0.139 3.693 1.503 O2C G4P 31
G4P O3C O3C O 0 1 N N N N N N 5.774 65.917 78.744 1.176 4.507 -0.623 O3C G4P 32
G4P PD PD P 0 1 N N N N N N 5.792 67.631 78.985 2.495 5.052 0.123 PD G4P 33
G4P O1D O1D O 0 1 N N N N N N 5.095 68.226 77.816 2.307 4.960 1.588 O1D G4P 34
G4P O2D O2D O 0 1 N N N N N N 7.276 67.884 79.107 3.764 4.163 -0.312 O2D G4P 35
G4P O3D O3D O 0 1 N N N N N N 5.369 68.126 80.417 2.749 6.588 -0.290 O3D G4P 36
G4P HOB2 2HOB H 0 0 N N N N N N 8.032 68.257 69.941 5.591 -6.077 0.159 HOB2 G4P 37
G4P HOB3 3HOB H 0 0 N N N N N N 10.942 68.515 70.862 6.365 -3.417 -1.027 HOB3 G4P 38
G4P HOA2 2HOA H 0 0 N N N N N N 8.771 66.794 75.506 4.258 -0.882 -1.508 HOA2 G4P 39
G4P "H5'" 1H5* H 0 1 N N N N N N 5.292 66.502 72.732 1.968 0.215 -0.286 "H5'" G4P 40
G4P "H5''" 2H5* H 0 0 N N N N N N 5.885 67.264 74.246 1.122 -0.863 0.850 "H5''" G4P 41
G4P "H4'" H4* H 0 1 N N N N N N 4.081 66.225 74.859 -0.028 0.091 -1.820 "H4'" G4P 42
G4P "H3'" H3* H 0 1 N N N N N N 6.449 64.823 75.941 -0.148 1.183 0.998 "H3'" G4P 43
G4P "H2'" H2* H 0 1 N N N N N N 6.144 62.597 75.351 -2.437 0.901 1.147 "H2'" G4P 44
G4P "HO2'" *HO2 H 0 0 N N N N N N 4.452 61.519 76.445 -3.753 1.843 -0.474 "HO2'" G4P 45
G4P "H1'" H1* H 0 1 N N N N N N 3.329 62.640 74.710 -2.651 -0.236 -1.646 "H1'" G4P 46
G4P H8 H8 H 0 1 N N N N N N 6.721 62.781 72.574 -2.312 -2.394 1.457 H8 G4P 47
G4P HN1 HN1 H 0 1 N N N N N N 2.460 58.048 71.380 -8.475 -1.266 -0.138 HN1 G4P 48
G4P HN21 1HN2 H 0 0 N N N N N N 0.617 58.261 72.753 -7.119 1.028 -2.410 HN21 G4P 49
G4P HN22 2HN2 H 0 0 N N N N N N 0.673 59.656 73.852 -8.541 0.353 -1.824 HN22 G4P 50
G4P H2C H2C H 0 1 N N N N N N 2.781 65.880 79.242 -0.892 4.211 1.188 H2C G4P 51
G4P H2D H2D H 0 1 N N N N N N 7.661 67.937 78.240 3.851 4.250 -1.271 H2D G4P 52
G4P H3D H3D H 0 1 N N N N N N 5.284 67.379 80.998 3.546 6.874 0.177 H3D G4P 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
G4P PB O1B DOUB N N 1
G4P PB O2B SING N N 2
G4P PB O3B SING N N 3
G4P PB O3A SING N N 4
G4P O2B HOB2 SING N N 5
G4P O3B HOB3 SING N N 6
G4P O3A PA SING N N 7
G4P PA O1A DOUB N N 8
G4P PA O2A SING N N 9
G4P PA "O5'" SING N N 10
G4P O2A HOA2 SING N N 11
G4P "O5'" "C5'" SING N N 12
G4P "C5'" "C4'" SING N N 13
G4P "C5'" "H5'" SING N N 14
G4P "C5'" "H5''" SING N N 15
G4P "C4'" "O4'" SING N N 16
G4P "C4'" "C3'" SING N N 17
G4P "C4'" "H4'" SING N N 18
G4P "O4'" "C1'" SING N N 19
G4P "C3'" "O3'" SING N N 20
G4P "C3'" "C2'" SING N N 21
G4P "C3'" "H3'" SING N N 22
G4P "O3'" PC SING N N 23
G4P "C2'" "O2'" SING N N 24
G4P "C2'" "C1'" SING N N 25
G4P "C2'" "H2'" SING N N 26
G4P "O2'" "HO2'" SING N N 27
G4P "C1'" N9 SING N N 28
G4P "C1'" "H1'" SING N N 29
G4P N9 C8 SING Y N 30
G4P N9 C4 SING Y N 31
G4P C8 N7 DOUB Y N 32
G4P C8 H8 SING N N 33
G4P N7 C5 SING Y N 34
G4P C5 C6 SING N N 35
G4P C5 C4 DOUB Y N 36
G4P C6 O6 DOUB N N 37
G4P C6 N1 SING N N 38
G4P N1 C2 SING N N 39
G4P N1 HN1 SING N N 40
G4P C2 N2 SING N N 41
G4P C2 N3 DOUB N N 42
G4P N2 HN21 SING N N 43
G4P N2 HN22 SING N N 44
G4P N3 C4 SING N N 45
G4P PC O1C DOUB N N 46
G4P PC O2C SING N N 47
G4P PC O3C SING N N 48
G4P O2C H2C SING N N 49
G4P O3C PD SING N N 50
G4P PD O1D DOUB N N 51
G4P PD O2D SING N N 52
G4P PD O3D SING N N 53
G4P O2D H2D SING N N 54
G4P O3D H3D 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
G4P SMILES ACDLabs 10.04 O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3OP(=O)(O)OP(=O)(O)O
G4P SMILES_CANONICAL CACTVS 3.341 NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O[P@@](O)(=O)O[P](O)(O)=O)[C@H]3O
G4P SMILES CACTVS 3.341 NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O[P](O)(=O)O[P](O)(O)=O)[CH]3O
G4P SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O[P@](=O)(O)OP(=O)(O)O)O)N=C(NC2=O)N
G4P SMILES "OpenEye OEToolkits" 1.5.0 c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)OP(=O)(O)OP(=O)(O)O)O)N=C(NC2=O)N
G4P InChI InChI 1.03 InChI=1S/C10H17N5O17P4/c11-10-13-7-4(8(17)14-10)12-2-15(7)9-5(16)6(30-36(26,27)32-34(21,22)23)3(29-9)1-28-35(24,25)31-33(18,19)20/h2-3,5-6,9,16H,1H2,(H,24,25)(H,26,27)(H2,18,19,20)(H2,21,22,23)(H3,11,13,14,17)/t3-,5-,6-,9-/m1/s1
G4P InChIKey InChI 1.03 BUFLLCUFNHESEH-UUOKFMHZSA-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
G4P "SYSTEMATIC NAME" ACDLabs 10.04 "guanosine 3',5'-bis(trihydrogen diphosphate)"
G4P "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,4R,5R)-5-(2-amino-6-oxo-1H-purin-9-yl)-4-hydroxy-3-(hydroxy-phosphonooxy-phosphoryl)oxy-oxolan-2-yl]methyl phosphono 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
G4P 'Create component' 2002-05-16 RCSB
G4P 'Modify descriptor' 2011-06-04 RCSB
G4P 'Modify synonyms' 2020-06-24 PDBE
#
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 G4P "guanosine tetraphosphate" ? ?
2 G4P ppGpp ? ?
#
_pdbe_chem_comp_drugbank_details.comp_id G4P
_pdbe_chem_comp_drugbank_details.drugbank_id DB04022
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name 'Guanosine tetraphosphate'
_pdbe_chem_comp_drugbank_details.description
"Guanosine tetraphosphate is a guanine nucleotide containing four phosphate groups. Two phosphate groups are esterified to the sugar moiety in the 5' position and the other two in the 2' or 3' position. This nucleotide serves as a messenger to turn off the synthesis of ribosomal RNA when amino acids are not available for protein synthesis."
_pdbe_chem_comp_drugbank_details.cas_number 33503-72-9
_pdbe_chem_comp_drugbank_details.mechanism_of_action ?
#
loop_
_pdbe_chem_comp_synonyms.comp_id
_pdbe_chem_comp_synonyms.name
_pdbe_chem_comp_synonyms.provenance
_pdbe_chem_comp_synonyms.type
G4P 'guanosine tetraphosphate' wwPDB ?
G4P ppGpp wwPDB ?
G4P "Guanosine-5',3'-tetraphosphate" DrugBank ?
#
_pdbe_chem_comp_drugbank_classification.comp_id G4P
_pdbe_chem_comp_drugbank_classification.drugbank_id DB04022
_pdbe_chem_comp_drugbank_classification.parent 'Purine ribonucleoside diphosphates'
_pdbe_chem_comp_drugbank_classification.kingdom 'Organic compounds'
_pdbe_chem_comp_drugbank_classification.class 'Purine nucleotides'
_pdbe_chem_comp_drugbank_classification.superclass 'Nucleosides, nucleotides, and analogues'
_pdbe_chem_comp_drugbank_classification.description
'This compound belongs to the class of organic compounds known as purine ribonucleoside diphosphates. These are purine ribobucleotides with diphosphate group linked to the ribose moiety.'
#
loop_
_pdbe_chem_comp_drugbank_targets.comp_id
_pdbe_chem_comp_drugbank_targets.drugbank_id
_pdbe_chem_comp_drugbank_targets.name
_pdbe_chem_comp_drugbank_targets.organism
_pdbe_chem_comp_drugbank_targets.uniprot_id
_pdbe_chem_comp_drugbank_targets.pharmacologically_active
_pdbe_chem_comp_drugbank_targets.ordinal
G4P DB04022 'Hypoxanthine-guanine-xanthine phosphoribosyltransferase' 'Plasmodium falciparum (isolate FCR-3 / Gambia)' P20035 yes 1
G4P DB04022 'Xanthine phosphoribosyltransferase' 'Bacillus subtilis (strain 168)' P42085 unknown 2
G4P DB04022 'GTPase Obg' 'Bacillus subtilis (strain 168)' P20964 unknown 3
#
loop_
_software.name
_software.version
_software.description
rdkit 2023.09.6 'Core functionality.'
pdbeccdutils 0.8.6 'Wrapper to provide 2D templates and molecular fragments.'
#
loop_
_pdbe_chem_comp_atom_depiction.comp_id
_pdbe_chem_comp_atom_depiction.atom_id
_pdbe_chem_comp_atom_depiction.element
_pdbe_chem_comp_atom_depiction.model_Cartn_x
_pdbe_chem_comp_atom_depiction.model_Cartn_y
_pdbe_chem_comp_atom_depiction.pdbx_ordinal
G4P PB P 17.401 1.379 1
G4P O1B O 18.771 0.766 2
G4P O2B O 18.014 2.748 3
G4P O3B O 16.789 0.009 4
G4P O3A O 16.032 1.991 5
G4P PA P 14.817 1.111 6
G4P O1A O 15.697 -0.103 7
G4P O2A O 13.938 2.327 8
G4P "O5'" O 13.602 0.232 9
G4P "C5'" C 12.233 0.845 10
G4P "C4'" C 11.018 -0.035 11
G4P "O4'" O 11.015 -1.535 12
G4P "C3'" C 9.592 0.431 13
G4P "O3'" O 9.131 1.858 14
G4P "C2'" C 8.708 -0.781 15
G4P "O2'" O 7.208 -0.778 16
G4P "C1'" C 9.588 -1.996 17
G4P N9 N 9.122 -3.422 18
G4P C8 C 9.997 -4.629 19
G4P N7 N 9.122 -5.836 20
G4P C5 C 7.702 -5.379 21
G4P C6 C 6.404 -6.129 22
G4P O6 O 6.404 -7.629 23
G4P N1 N 5.104 -5.379 24
G4P C2 C 5.104 -3.879 25
G4P N2 N 3.805 -3.129 26
G4P N3 N 6.404 -3.129 27
G4P C4 C 7.702 -3.879 28
G4P PC P 10.136 2.971 29
G4P O1C O 9.024 3.977 30
G4P O2C O 11.249 1.966 31
G4P O3C O 11.142 4.084 32
G4P PD P 10.681 5.512 33
G4P O1D O 10.220 6.939 34
G4P O2D O 12.109 5.973 35
G4P O3D O 9.254 5.051 36
#
loop_
_pdbe_chem_comp_bond_depiction.comp_id
_pdbe_chem_comp_bond_depiction.atom_id_1
_pdbe_chem_comp_bond_depiction.atom_id_2
_pdbe_chem_comp_bond_depiction.value_order
_pdbe_chem_comp_bond_depiction.bond_dir
_pdbe_chem_comp_bond_depiction.pdbx_ordinal
G4P PB O1B DOUBLE NONE 1
G4P PB O2B SINGLE NONE 2
G4P PB O3B SINGLE NONE 3
G4P PB O3A SINGLE NONE 4
G4P O3A PA SINGLE NONE 5
G4P PA O1A DOUBLE NONE 6
G4P PA O2A SINGLE BEGINWEDGE 7
G4P PA "O5'" SINGLE NONE 8
G4P "O5'" "C5'" SINGLE NONE 9
G4P "C4'" "C5'" SINGLE BEGINWEDGE 10
G4P "C4'" "O4'" SINGLE NONE 11
G4P "C4'" "C3'" SINGLE NONE 12
G4P "O4'" "C1'" SINGLE NONE 13
G4P "C3'" "O3'" SINGLE BEGINDASH 14
G4P "C3'" "C2'" SINGLE NONE 15
G4P "O3'" PC SINGLE NONE 16
G4P "C2'" "O2'" SINGLE BEGINDASH 17
G4P "C2'" "C1'" SINGLE NONE 18
G4P "C1'" N9 SINGLE BEGINWEDGE 19
G4P N9 C8 SINGLE NONE 20
G4P N9 C4 SINGLE NONE 21
G4P C8 N7 DOUBLE NONE 22
G4P N7 C5 SINGLE NONE 23
G4P C5 C6 SINGLE NONE 24
G4P C5 C4 DOUBLE NONE 25
G4P C6 O6 DOUBLE NONE 26
G4P C6 N1 SINGLE NONE 27
G4P N1 C2 SINGLE NONE 28
G4P C2 N2 SINGLE NONE 29
G4P C2 N3 DOUBLE NONE 30
G4P N3 C4 SINGLE NONE 31
G4P PC O1C DOUBLE NONE 32
G4P PC O2C SINGLE BEGINDASH 33
G4P PC O3C SINGLE NONE 34
G4P O3C PD SINGLE NONE 35
G4P PD O1D DOUBLE NONE 36
G4P PD O2D SINGLE NONE 37
G4P PD O3D SINGLE NONE 38
#
loop_
_pdbe_chem_comp_substructure.comp_id
_pdbe_chem_comp_substructure.substructure_name
_pdbe_chem_comp_substructure.id
_pdbe_chem_comp_substructure.substructure_type
_pdbe_chem_comp_substructure.substructure_smiles
_pdbe_chem_comp_substructure.substructure_inchis
_pdbe_chem_comp_substructure.substructure_inchikeys
G4P MurckoScaffold S1 scaffold 'O=c1[nH]cnc2c1ncn2[C@H]1CCCO1' InChI=1S/C9H10N4O2/c14-9-7-8(10-4-11-9)13(5-12-7)6-2-1-3-15-6/h4-6H,1-3H2,(H,10,11,14)/t6-/m1/s1 JBXHFRZBULGPSC-ZCFIWIBFSA-N
G4P imidazole F1 fragment 'c1c[nH]cn1' InChI=1S/C3H4N2/c1-2-5-3-4-1/h1-3H,(H,4,5) RAXXELZNTBOGNW-UHFFFAOYSA-N
G4P phosphate F2 fragment O=P(O)(O)O InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4) NBIIXXVUZAFLBC-UHFFFAOYSA-N
G4P purine F3 fragment 'c1ncc2[nH]cnc2n1' InChI=1S/C5H4N4/c1-4-5(8-2-6-1)9-3-7-4/h1-3H,(H,6,7,8,9) KDCGOANMDULRCW-UHFFFAOYSA-N
G4P pyrimidine F4 fragment c1cncnc1 InChI=1S/C4H4N2/c1-2-5-4-6-3-1/h1-4H CZPWVGJYEJSRLH-UHFFFAOYSA-N
G4P ribose F5 fragment OCC1OCC(O)C1O InChI=1S/C5H10O4/c6-1-4-5(8)3(7)2-9-4/h3-8H,1-2H2 KZVAAIRBJJYZOW-UHFFFAOYSA-N
#
loop_
_pdbe_chem_comp_substructure_mapping.comp_id
_pdbe_chem_comp_substructure_mapping.atom_id
_pdbe_chem_comp_substructure_mapping.substructure_id
_pdbe_chem_comp_substructure_mapping.substructure_ordinal
G4P "C4'" S1 1
G4P "O4'" S1 1
G4P "C3'" S1 1
G4P "C2'" S1 1
G4P "C1'" S1 1
G4P N9 S1 1
G4P C8 S1 1
G4P N7 S1 1
G4P C5 S1 1
G4P C6 S1 1
G4P O6 S1 1
G4P N1 S1 1
G4P C2 S1 1
G4P N3 S1 1
G4P C4 S1 1
G4P C5 F1 1
G4P C4 F1 1
G4P N9 F1 1
G4P C8 F1 1
G4P N7 F1 1
G4P O2B F2 1
G4P PB F2 1
G4P O1B F2 1
G4P O3B F2 1
G4P O3A F2 1
G4P O3A F2 2
G4P PA F2 2
G4P O1A F2 2
G4P O2A F2 2
G4P "O5'" F2 2
G4P "O3'" F2 3
G4P PC F2 3
G4P O1C F2 3
G4P O2C F2 3
G4P O3C F2 3
G4P O3C F2 4
G4P PD F2 4
G4P O1D F2 4
G4P O2D F2 4
G4P O3D F2 4
G4P N7 F3 1
G4P C8 F3 1
G4P N9 F3 1
G4P C4 F3 1
G4P C5 F3 1
G4P C6 F3 1
G4P N1 F3 1
G4P C2 F3 1
G4P N3 F3 1
G4P C5 F4 1
G4P C6 F4 1
G4P N1 F4 1
G4P C2 F4 1
G4P N3 F4 1
G4P C4 F4 1
G4P "C2'" F5 1
G4P "C3'" F5 1
G4P "C4'" F5 1
G4P "O4'" F5 1
G4P "C1'" F5 1
G4P "C5'" F5 1
G4P "O5'" F5 1
G4P "O3'" F5 1
G4P "O2'" F5 1
#
_pdbe_chem_comp_rdkit_properties.comp_id G4P
_pdbe_chem_comp_rdkit_properties.exactmw 602.957
_pdbe_chem_comp_rdkit_properties.amw 603.160
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 22
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 10
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 18
_pdbe_chem_comp_rdkit_properties.NumHBD 9
_pdbe_chem_comp_rdkit_properties.NumHBA 21
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 36
_pdbe_chem_comp_rdkit_properties.NumAtoms 53
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 26
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.500
_pdbe_chem_comp_rdkit_properties.NumRings 3
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 2
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 1
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 1
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 3
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 2
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumSpiroAtoms 0
_pdbe_chem_comp_rdkit_properties.NumBridgeheadAtoms 0
_pdbe_chem_comp_rdkit_properties.NumAtomStereoCenters 6
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 221.503
_pdbe_chem_comp_rdkit_properties.tpsa 345.630
_pdbe_chem_comp_rdkit_properties.CrippenClogP -2.128
_pdbe_chem_comp_rdkit_properties.CrippenMR 106.290
_pdbe_chem_comp_rdkit_properties.chi0v 19.543
_pdbe_chem_comp_rdkit_properties.chi1v 13.724
_pdbe_chem_comp_rdkit_properties.chi2v 7.078
_pdbe_chem_comp_rdkit_properties.chi3v 7.078
_pdbe_chem_comp_rdkit_properties.chi4v 4.940
_pdbe_chem_comp_rdkit_properties.chi0n 32.965
_pdbe_chem_comp_rdkit_properties.chi1n 15.581
_pdbe_chem_comp_rdkit_properties.chi2n 3.157
_pdbe_chem_comp_rdkit_properties.chi3n 3.157
_pdbe_chem_comp_rdkit_properties.chi4n 2.129
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.410
_pdbe_chem_comp_rdkit_properties.kappa1 13.589
_pdbe_chem_comp_rdkit_properties.kappa2 10.047
_pdbe_chem_comp_rdkit_properties.kappa3 7.334
_pdbe_chem_comp_rdkit_properties.Phi 3.793
#
loop_
_pdbe_chem_comp_external_mappings.comp_id
_pdbe_chem_comp_external_mappings.source
_pdbe_chem_comp_external_mappings.resource
_pdbe_chem_comp_external_mappings.resource_id
G4P UniChem DrugBank DB04022
G4P UniChem 'KEGG LIGAND' C01228
G4P UniChem ChEBI 17633
G4P UniChem ZINC ZINC000008217069
G4P UniChem SureChEMBL SCHEMBL234673
G4P UniChem HMDB HMDB0059638
G4P UniChem PubChem 135398637
G4P UniChem NMRShiftDB 60022131
G4P UniChem ACTor 33503-72-9
G4P UniChem Nikkaji J40.058K
G4P UniChem MetaboLights MTBLC17633
G4P UniChem BRENDA 133443
G4P UniChem BRENDA 152273
G4P UniChem BRENDA 177678
G4P UniChem BRENDA 214111
G4P UniChem BRENDA 3703
G4P UniChem BRENDA 44202
G4P UniChem BRENDA 46041
G4P UniChem BRENDA 51688
G4P UniChem BRENDA 93575
G4P UniChem 'Probes And Drugs' PD059517
G4P UniChem PubChem 439450
#
loop_
_pdbe_chem_comp_rdkit_conformer.comp_id
_pdbe_chem_comp_rdkit_conformer.atom_id
_pdbe_chem_comp_rdkit_conformer.Cartn_x_rdkit
_pdbe_chem_comp_rdkit_conformer.Cartn_y_rdkit
_pdbe_chem_comp_rdkit_conformer.Cartn_z_rdkit
_pdbe_chem_comp_rdkit_conformer.rdkit_method
_pdbe_chem_comp_rdkit_conformer.rdkit_ordinal
G4P PB 4.653 -0.543 1.025 ETKDGv3 1
G4P O1B 5.138 -1.797 0.334 ETKDGv3 2
G4P O2B 5.814 0.679 0.866 ETKDGv3 3
G4P O3B 4.439 -0.879 2.670 ETKDGv3 4
G4P O3A 3.156 -0.051 0.380 ETKDGv3 5
G4P PA 3.411 0.447 -1.230 ETKDGv3 6
G4P O1A 4.264 1.695 -1.253 ETKDGv3 7
G4P O2A 4.174 -0.763 -2.140 ETKDGv3 8
G4P "O5'" 1.901 0.826 -1.924 ETKDGv3 9
G4P "C5'" 1.141 -0.356 -2.042 ETKDGv3 10
G4P "C4'" -0.343 0.005 -2.149 ETKDGv3 11
G4P "O4'" -1.110 -1.165 -2.322 ETKDGv3 12
G4P "C3'" -0.846 0.719 -0.899 ETKDGv3 13
G4P "O3'" -0.629 2.112 -1.015 ETKDGv3 14
G4P "C2'" -2.318 0.361 -0.902 ETKDGv3 15
G4P "O2'" -3.114 1.367 -1.485 ETKDGv3 16
G4P "C1'" -2.368 -0.939 -1.721 ETKDGv3 17
G4P N9 -2.715 -2.076 -0.869 ETKDGv3 18
G4P C8 -4.030 -2.370 -0.373 ETKDGv3 19
G4P N7 -4.035 -3.067 0.726 ETKDGv3 20
G4P C5 -2.657 -3.259 1.021 ETKDGv3 21
G4P C6 -2.052 -3.865 2.200 ETKDGv3 22
G4P O6 -2.747 -4.411 3.096 ETKDGv3 23
G4P N1 -0.620 -3.807 2.298 ETKDGv3 24
G4P C2 0.138 -3.148 1.256 ETKDGv3 25
G4P N2 1.561 -3.082 1.344 ETKDGv3 26
G4P N3 -0.474 -2.612 0.232 ETKDGv3 27
G4P C4 -1.904 -2.681 0.124 ETKDGv3 28
G4P PC -0.425 2.792 0.539 ETKDGv3 29
G4P O1C 0.938 2.403 1.066 ETKDGv3 30
G4P O2C -1.609 2.216 1.605 ETKDGv3 31
G4P O3C -0.504 4.489 0.455 ETKDGv3 32
G4P PD -1.966 4.902 -0.315 ETKDGv3 33
G4P O1D -3.145 4.278 0.399 ETKDGv3 34
G4P O2D -2.141 6.584 -0.274 ETKDGv3 35
G4P O3D -1.950 4.397 -1.930 ETKDGv3 36
G4P HOB2 5.463 1.431 1.406 ETKDGv3 37
G4P HOB3 5.346 -1.093 3.005 ETKDGv3 38
G4P HOA2 3.677 -1.595 -1.934 ETKDGv3 39
G4P "H5'" 1.444 -0.895 -2.966 ETKDGv3 40
G4P "H5''" 1.267 -1.043 -1.174 ETKDGv3 41
G4P "H4'" -0.488 0.653 -3.043 ETKDGv3 42
G4P "H3'" -0.357 0.258 -0.005 ETKDGv3 43
G4P "H2'" -2.670 0.202 0.141 ETKDGv3 44
G4P "HO2'" -2.799 1.510 -2.417 ETKDGv3 45
G4P "H1'" -3.131 -0.861 -2.527 ETKDGv3 46
G4P H8 -4.937 -2.021 -0.847 ETKDGv3 47
G4P HN1 -0.133 -4.231 3.119 ETKDGv3 48
G4P HN21 2.119 -2.640 0.581 ETKDGv3 49
G4P HN22 2.060 -3.489 2.165 ETKDGv3 50
G4P H2C -1.447 2.705 2.450 ETKDGv3 51
G4P H2D -1.326 6.932 -0.716 ETKDGv3 52
G4P H3D -1.115 4.775 -2.304 ETKDGv3 53
#