data_GCP
#
_chem_comp.id GCP
_chem_comp.name 'PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER'
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula 'C11 H18 N5 O13 P3'
_chem_comp.mon_nstd_parent_comp_id ?
_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 GTO
_chem_comp.formula_weight 521.208
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code GCP
_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 1HOP
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site RCSB
_chem_comp.pdbx_pcm Y
#
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
GCP PG PG P 0 1 N N N N N N 8.611 24.356 -18.319 -1.285 -0.306 7.434 PG GCP 1
GCP O1G O1G O 0 1 N N N N N N 9.946 24.604 -17.696 -1.812 1.072 7.323 O1G GCP 2
GCP O2G O2G O 0 1 N N N N N N 8.464 22.985 -18.867 -2.228 -1.163 8.418 O2G GCP 3
GCP O3G O3G O 0 1 N N N N N N 8.152 25.445 -19.223 0.210 -0.261 8.029 O3G GCP 4
GCP C3B C3B C 0 1 N N N N N N 7.382 24.457 -17.000 -1.260 -1.083 5.786 C3B GCP 5
GCP PB PB P 0 1 N N R N N N 6.838 23.478 -15.600 -0.192 -0.111 4.672 PB GCP 6
GCP O1B O1B O 0 1 N N N N N N 8.013 22.870 -14.923 -0.719 1.266 4.560 O1B GCP 7
GCP O2B O2B O 0 1 N N N N N N 6.078 24.506 -14.877 1.303 -0.067 5.267 O2B GCP 8
GCP O3A O3A O 0 1 N N N N N N 5.744 22.325 -15.930 -0.170 -0.798 3.216 O3A GCP 9
GCP PA PA P 0 1 N N S N N N 4.424 21.795 -15.117 0.786 0.106 2.290 PA GCP 10
GCP O1A O1A O 0 1 N N N N N N 4.095 22.670 -13.959 0.244 1.481 2.215 O1A GCP 11
GCP O2A O2A O 0 1 N N N N N N 3.404 21.555 -16.176 2.265 0.147 2.925 O2A GCP 12
GCP "O5'" O5* O 0 1 N N N N N N 4.586 20.385 -14.335 0.855 -0.525 0.810 "O5'" GCP 13
GCP "C5'" C5* C 0 1 N N N N N N 5.327 19.200 -14.753 1.714 0.318 0.041 "C5'" GCP 14
GCP "C4'" C4* C 0 1 N N R N N N 4.674 17.905 -14.320 1.823 -0.229 -1.383 "C4'" GCP 15
GCP "O4'" O4* O 0 1 N N N N N N 4.837 17.700 -12.940 0.526 -0.237 -2.019 "O4'" GCP 16
GCP "C3'" C3* C 0 1 N N S N N N 3.189 18.015 -14.467 2.685 0.708 -2.258 "C3'" GCP 17
GCP "O3'" O3* O 0 1 N N N N N N 2.827 17.409 -15.728 4.023 0.216 -2.350 "O3'" GCP 18
GCP "C2'" C2* C 0 1 N N R N N N 2.686 17.409 -13.181 1.995 0.670 -3.642 "C2'" GCP 19
GCP "O2'" O2* O 0 1 N N N N N N 1.740 16.472 -13.696 2.888 0.156 -4.632 "O2'" GCP 20
GCP "C1'" C1* C 0 1 N N R N N N 3.903 16.763 -12.448 0.797 -0.282 -3.437 "C1'" GCP 21
GCP N9 N9 N 0 1 Y N N N N N 4.139 16.877 -11.086 -0.364 0.189 -4.194 N9 GCP 22
GCP C8 C8 C 0 1 Y N N N N N 4.410 18.049 -10.451 -1.313 1.065 -3.753 C8 GCP 23
GCP N7 N7 N 0 1 Y N N N N N 4.900 18.009 -9.232 -2.200 1.260 -4.685 N7 GCP 24
GCP C5 C5 C 0 1 Y N N N N N 4.971 16.623 -9.015 -1.875 0.523 -5.775 C5 GCP 25
GCP C6 C6 C 0 1 Y N N N N N 5.424 15.933 -7.861 -2.458 0.342 -7.051 C6 GCP 26
GCP O6 O6 O 0 1 N N N N N N 5.895 16.426 -6.838 -3.483 0.926 -7.358 O6 GCP 27
GCP N1 N1 N 0 1 Y N N N N N 5.338 14.550 -7.983 -1.846 -0.488 -7.923 N1 GCP 28
GCP C2 C2 C 0 1 Y N N N N N 4.898 13.847 -9.094 -0.703 -1.140 -7.568 C2 GCP 29
GCP N2 N2 N 0 1 N N N N N N 4.889 12.511 -9.019 -0.107 -1.982 -8.472 N2 GCP 30
GCP N3 N3 N 0 1 Y N N N N N 4.477 14.525 -10.199 -0.152 -0.980 -6.385 N3 GCP 31
GCP C4 C4 C 0 1 Y N N N N N 4.518 15.910 -10.118 -0.697 -0.169 -5.472 C4 GCP 32
GCP HOG2 2HOG H 0 0 N N N N N N 7.615 22.827 -19.263 -2.214 -0.719 9.277 HOG2 GCP 33
GCP HOG3 3HOG H 0 0 N N N N N N 7.303 25.287 -19.619 0.515 -1.177 8.086 HOG3 GCP 34
GCP H3B1 1H3B H 0 0 N N N N N N 7.616 25.439 -16.528 -2.272 -1.113 5.383 H3B1 GCP 35
GCP H3B2 2H3B H 0 0 N N N N N N 6.434 24.611 -17.566 -0.871 -2.098 5.868 H3B2 GCP 36
GCP HOB2 2HOB H 0 0 N N N N N N 5.789 23.987 -14.135 1.609 -0.983 5.324 HOB2 GCP 37
GCP HOA2 2HOA H 0 0 N N N N N N 2.638 21.247 -15.704 2.581 -0.765 2.956 HOA2 GCP 38
GCP "H5'2" 2H5* H 0 0 N N N N N N 5.345 19.191 -15.840 1.302 1.327 0.012 "H5'2" GCP 39
GCP "H5'1" 1H5* H 0 0 N N N N N N 6.338 19.251 -14.345 2.703 0.342 0.497 "H5'1" GCP 40
GCP "H4'" H4* H 0 1 N N N N N N 5.071 17.062 -14.887 2.246 -1.233 -1.372 "H4'" GCP 41
GCP "H3'" H3* H 0 1 N N N N N N 2.870 19.059 -14.440 2.678 1.720 -1.854 "H3'" GCP 42
GCP "HO3'" *HO3 H 0 0 N N N N N N 3.454 16.705 -15.927 4.512 0.838 -2.905 "HO3'" GCP 43
GCP "H2'" H2* H 0 1 N N N N N N 2.231 18.193 -12.573 1.647 1.664 -3.922 "H2'" GCP 44
GCP "HO2'" *HO2 H 0 0 N N N N N N 0.940 16.955 -13.924 3.642 0.761 -4.670 "HO2'" GCP 45
GCP "H1'" H1* H 0 1 N N N N N N 4.110 15.755 -12.813 1.062 -1.295 -3.741 "H1'" GCP 46
GCP H8 H8 H 0 1 N N N N N N 4.242 19.009 -10.940 -1.325 1.528 -2.777 H8 GCP 47
GCP HN1 HN1 H 0 1 N N N N N N 5.616 13.961 -7.209 -2.227 -0.628 -8.804 HN1 GCP 48
GCP HN21 1HN2 H 0 0 N N N N N N 5.407 11.980 -9.664 0.708 -2.450 -8.235 HN21 GCP 49
GCP HN22 2HN2 H 0 0 N N N N N N 4.318 12.041 -8.375 -0.505 -2.113 -9.348 HN22 GCP 50
#
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
GCP PG O1G DOUB N N 1
GCP PG O2G SING N N 2
GCP PG O3G SING N N 3
GCP PG C3B SING N N 4
GCP O2G HOG2 SING N N 5
GCP O3G HOG3 SING N N 6
GCP C3B PB SING N N 7
GCP C3B H3B1 SING N N 8
GCP C3B H3B2 SING N N 9
GCP PB O1B DOUB N N 10
GCP PB O2B SING N N 11
GCP PB O3A SING N N 12
GCP O2B HOB2 SING N N 13
GCP O3A PA SING N N 14
GCP PA O1A DOUB N N 15
GCP PA O2A SING N N 16
GCP PA "O5'" SING N N 17
GCP O2A HOA2 SING N N 18
GCP "O5'" "C5'" SING N N 19
GCP "C5'" "C4'" SING N N 20
GCP "C5'" "H5'2" SING N N 21
GCP "C5'" "H5'1" SING N N 22
GCP "C4'" "O4'" SING N N 23
GCP "C4'" "C3'" SING N N 24
GCP "C4'" "H4'" SING N N 25
GCP "O4'" "C1'" SING N N 26
GCP "C3'" "O3'" SING N N 27
GCP "C3'" "C2'" SING N N 28
GCP "C3'" "H3'" SING N N 29
GCP "O3'" "HO3'" SING N N 30
GCP "C2'" "O2'" SING N N 31
GCP "C2'" "C1'" SING N N 32
GCP "C2'" "H2'" SING N N 33
GCP "O2'" "HO2'" SING N N 34
GCP "C1'" N9 SING N N 35
GCP "C1'" "H1'" SING N N 36
GCP N9 C8 SING Y N 37
GCP N9 C4 SING Y N 38
GCP C8 N7 DOUB Y N 39
GCP C8 H8 SING N N 40
GCP N7 C5 SING Y N 41
GCP C5 C6 SING Y N 42
GCP C5 C4 DOUB Y N 43
GCP C6 O6 DOUB N N 44
GCP C6 N1 SING Y N 45
GCP N1 C2 SING Y N 46
GCP N1 HN1 SING N N 47
GCP C2 N2 SING N N 48
GCP C2 N3 DOUB Y N 49
GCP N2 HN21 SING N N 50
GCP N2 HN22 SING N N 51
GCP N3 C4 SING Y 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
GCP SMILES ACDLabs 10.04 'O=P(O)(O)CP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O'
GCP SMILES_CANONICAL CACTVS 3.341 'NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P@@](O)(=O)C[P](O)(O)=O)[C@@H](O)[C@H]3O'
GCP SMILES CACTVS 3.341 'NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)C[P](O)(O)=O)[CH](O)[CH]3O'
GCP SMILES_CANONICAL 'OpenEye OEToolkits' 1.5.0 'c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(CP(=O)(O)O)O)O)O)N=C(NC2=O)N'
GCP SMILES 'OpenEye OEToolkits' 1.5.0 'c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(CP(=O)(O)O)O)O)O)N=C(NC2=O)N'
GCP InChI InChI 1.03 'InChI=1S/C11H18N5O13P3/c12-11-14-8-5(9(19)15-11)13-2-16(8)10-7(18)6(17)4(28-10)1-27-32(25,26)29-31(23,24)3-30(20,21)22/h2,4,6-7,10,17-18H,1,3H2,(H,23,24)(H,25,26)(H2,20,21,22)(H3,12,14,15,19)/t4-,6-,7-,10-/m1/s1'
GCP InChIKey InChI 1.03 PHBDHXOBFUBCJD-KQYNXXCUSA-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
GCP 'SYSTEMATIC NAME' ACDLabs 10.04 "5'-O-[(S)-hydroxy{[(R)-hydroxy(phosphonomethyl)phosphoryl]oxy}phosphoryl]guanosine"
GCP 'SYSTEMATIC NAME' 'OpenEye OEToolkits' 1.5.0 '[[[(2R,3S,4R,5R)-5-(2-amino-6-oxo-1H-purin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl]oxy-hydroxy-phosphoryl]methylphosphonic 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
GCP 'Create component' 1999-07-08 RCSB
GCP 'Modify descriptor' 2011-06-04 RCSB
GCP 'Modify PCM' 2024-09-27 PDBE
#
loop_
_pdbx_chem_comp_pcm.pcm_id
_pdbx_chem_comp_pcm.comp_id
_pdbx_chem_comp_pcm.modified_residue_id
_pdbx_chem_comp_pcm.type
_pdbx_chem_comp_pcm.category
_pdbx_chem_comp_pcm.position
_pdbx_chem_comp_pcm.polypeptide_position
_pdbx_chem_comp_pcm.comp_id_linking_atom
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession
_pdbx_chem_comp_pcm.first_instance_model_db_code
1 GCP ILE None 'Covalent chemical modification' 'Amino-acid side chain' 'Any position' O1G CD1 ? ? 7L20
2 GCP LYS None 'Covalent chemical modification' 'Amino-acid side chain' 'Any position' O1B CB ? ? 7L20
#
_pdbe_chem_comp_drugbank_details.comp_id GCP
_pdbe_chem_comp_drugbank_details.drugbank_id DB03725
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name "5'-Guanylylmethylenebisphosphonate"
_pdbe_chem_comp_drugbank_details.description ?
_pdbe_chem_comp_drugbank_details.cas_number 13912-93-1
_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
GCP "5'-Guanosyl-methylene-triphosphate" DrugBank ?
GCP "5'-Guanylylmethylenediphosphonate" DrugBank ?
GCP GppCp DrugBank ?
GCP "guanosine 5'-[beta,gamma-methylene]triphosphate" DrugBank ?
#
_pdbe_chem_comp_drugbank_classification.comp_id GCP
_pdbe_chem_comp_drugbank_classification.drugbank_id DB03725
_pdbe_chem_comp_drugbank_classification.parent 'Purine ribonucleoside monophosphates'
_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 monophosphates. These are nucleotides consisting of a purine base linked to a ribose to which one monophosphate group is attached.'
#
_pdbe_chem_comp_drugbank_targets.comp_id GCP
_pdbe_chem_comp_drugbank_targets.drugbank_id DB03725
_pdbe_chem_comp_drugbank_targets.name 'Phosphoenolpyruvate carboxykinase, cytosolic [GTP]'
_pdbe_chem_comp_drugbank_targets.organism Humans
_pdbe_chem_comp_drugbank_targets.uniprot_id P35558
_pdbe_chem_comp_drugbank_targets.pharmacologically_active unknown
_pdbe_chem_comp_drugbank_targets.ordinal 1
#
loop_
_software.name
_software.version
_software.description
rdkit 2023.03.3 'Core functionality.'
pdbeccdutils 0.8.4 '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
GCP PG P 19.986 3.710 1
GCP O1G O 21.201 4.589 2
GCP O2G O 20.865 2.495 3
GCP O3G O 19.106 4.925 4
GCP C3B C 18.771 2.830 5
GCP PB P 17.401 3.442 6
GCP O1B O 18.014 4.812 7
GCP O2B O 16.789 2.073 8
GCP O3A O 16.032 4.055 9
GCP PA P 14.817 3.175 10
GCP O1A O 15.697 1.960 11
GCP O2A O 13.938 4.391 12
GCP "O5'" O 13.602 2.296 13
GCP "C5'" C 12.233 2.908 14
GCP "C4'" C 11.018 2.029 15
GCP "O4'" O 11.015 0.529 16
GCP "C3'" C 9.592 2.495 17
GCP "O3'" O 9.131 3.922 18
GCP "C2'" C 8.708 1.283 19
GCP "O2'" O 7.208 1.285 20
GCP "C1'" C 9.588 0.068 21
GCP N9 N 9.122 -1.358 22
GCP C8 C 9.997 -2.565 23
GCP N7 N 9.122 -3.772 24
GCP C5 C 7.702 -3.315 25
GCP C6 C 6.404 -4.065 26
GCP O6 O 6.404 -5.565 27
GCP N1 N 5.104 -3.315 28
GCP C2 C 5.104 -1.815 29
GCP N2 N 3.805 -1.065 30
GCP N3 N 6.404 -1.065 31
GCP C4 C 7.702 -1.815 32
#
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
GCP PG O1G DOUBLE NONE 1
GCP PG O2G SINGLE NONE 2
GCP PG O3G SINGLE NONE 3
GCP PG C3B SINGLE NONE 4
GCP C3B PB SINGLE NONE 5
GCP PB O1B DOUBLE NONE 6
GCP PB O2B SINGLE BEGINDASH 7
GCP PB O3A SINGLE NONE 8
GCP O3A PA SINGLE NONE 9
GCP PA O1A DOUBLE NONE 10
GCP PA O2A SINGLE BEGINWEDGE 11
GCP PA "O5'" SINGLE NONE 12
GCP "O5'" "C5'" SINGLE NONE 13
GCP "C4'" "C5'" SINGLE BEGINWEDGE 14
GCP "C4'" "O4'" SINGLE NONE 15
GCP "C4'" "C3'" SINGLE NONE 16
GCP "O4'" "C1'" SINGLE NONE 17
GCP "C3'" "O3'" SINGLE BEGINDASH 18
GCP "C3'" "C2'" SINGLE NONE 19
GCP "C2'" "O2'" SINGLE BEGINDASH 20
GCP "C2'" "C1'" SINGLE NONE 21
GCP "C1'" N9 SINGLE BEGINWEDGE 22
GCP N9 C8 SINGLE NONE 23
GCP N9 C4 SINGLE NONE 24
GCP C8 N7 DOUBLE NONE 25
GCP N7 C5 SINGLE NONE 26
GCP C5 C6 SINGLE NONE 27
GCP C5 C4 DOUBLE NONE 28
GCP C6 O6 DOUBLE NONE 29
GCP C6 N1 SINGLE NONE 30
GCP N1 C2 SINGLE NONE 31
GCP C2 N2 SINGLE NONE 32
GCP C2 N3 DOUBLE NONE 33
GCP N3 C4 SINGLE NONE 34
#
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
GCP 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
GCP imidazole F1 fragment 'c1c[nH]cn1' InChI=1S/C3H4N2/c1-2-5-3-4-1/h1-3H,(H,4,5) RAXXELZNTBOGNW-UHFFFAOYSA-N
GCP 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
GCP 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
GCP pyrimidine F4 fragment c1cncnc1 InChI=1S/C4H4N2/c1-2-5-4-6-3-1/h1-4H CZPWVGJYEJSRLH-UHFFFAOYSA-N
GCP 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
GCP "C4'" S1 1
GCP "O4'" S1 1
GCP "C3'" S1 1
GCP "C2'" S1 1
GCP "C1'" S1 1
GCP N9 S1 1
GCP C8 S1 1
GCP N7 S1 1
GCP C5 S1 1
GCP C6 S1 1
GCP O6 S1 1
GCP N1 S1 1
GCP C2 S1 1
GCP N3 S1 1
GCP C4 S1 1
GCP C5 F1 1
GCP C4 F1 1
GCP N9 F1 1
GCP C8 F1 1
GCP N7 F1 1
GCP O3A F2 1
GCP PA F2 1
GCP O1A F2 1
GCP O2A F2 1
GCP "O5'" F2 1
GCP N7 F3 1
GCP C8 F3 1
GCP N9 F3 1
GCP C4 F3 1
GCP C5 F3 1
GCP C6 F3 1
GCP N1 F3 1
GCP C2 F3 1
GCP N3 F3 1
GCP C5 F4 1
GCP C6 F4 1
GCP N1 F4 1
GCP C2 F4 1
GCP N3 F4 1
GCP C4 F4 1
GCP "C2'" F5 1
GCP "C3'" F5 1
GCP "C4'" F5 1
GCP "O4'" F5 1
GCP "C1'" F5 1
GCP "C5'" F5 1
GCP "O5'" F5 1
GCP "O3'" F5 1
GCP "O2'" F5 1
#
_pdbe_chem_comp_rdkit_properties.comp_id GCP
_pdbe_chem_comp_rdkit_properties.exactmw 521.011
_pdbe_chem_comp_rdkit_properties.amw 521.209
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 18
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 9
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 15
_pdbe_chem_comp_rdkit_properties.NumHBD 8
_pdbe_chem_comp_rdkit_properties.NumHBA 17
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 32
_pdbe_chem_comp_rdkit_properties.NumAtoms 50
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 21
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.545
_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 202.442
_pdbe_chem_comp_rdkit_properties.tpsa 289.870
_pdbe_chem_comp_rdkit_properties.CrippenClogP -2.134
_pdbe_chem_comp_rdkit_properties.CrippenMR 99.161
_pdbe_chem_comp_rdkit_properties.chi0v 17.068
_pdbe_chem_comp_rdkit_properties.chi1v 11.780
_pdbe_chem_comp_rdkit_properties.chi2v 6.941
_pdbe_chem_comp_rdkit_properties.chi3v 6.941
_pdbe_chem_comp_rdkit_properties.chi4v 5.029
_pdbe_chem_comp_rdkit_properties.chi0n 32.385
_pdbe_chem_comp_rdkit_properties.chi1n 15.525
_pdbe_chem_comp_rdkit_properties.chi2n 3.007
_pdbe_chem_comp_rdkit_properties.chi3n 3.007
_pdbe_chem_comp_rdkit_properties.chi4n 1.973
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.520
_pdbe_chem_comp_rdkit_properties.kappa1 10.395
_pdbe_chem_comp_rdkit_properties.kappa2 8.682
_pdbe_chem_comp_rdkit_properties.kappa3 5.690
_pdbe_chem_comp_rdkit_properties.Phi 2.820
#
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
GCP UniChem DrugBank DB03725
GCP UniChem PDBe GCP
GCP UniChem 'KEGG LIGAND' C06500
GCP UniChem ChEBI 1963
GCP UniChem ZINC ZINC000008220535
GCP UniChem fdasrs 4E15I11U9B
GCP UniChem SureChEMBL SCHEMBL196559
GCP UniChem 'PubChem TPHARMA' 85857164
GCP UniChem PubChem 135398731
GCP UniChem ACTor 13912-93-1
GCP UniChem ACTor 14997-54-7
GCP UniChem BRENDA 105555
GCP UniChem BRENDA 140146
GCP UniChem BRENDA 144597
GCP UniChem BRENDA 20888
GCP UniChem BRENDA 247887
GCP UniChem BRENDA 45575
GCP UniChem BRENDA 75673
GCP UniChem BRENDA 92711
GCP UniChem BRENDA 92757
GCP UniChem BRENDA 93578
GCP UniChem BRENDA 96582
GCP UniChem 'Probes And Drugs' PD059499
GCP UniChem Nikkaji J152.191H
#
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
GCP PG 7.410 -0.458 -0.339 ETKDGv3 1
GCP O1G 7.865 -1.858 -0.685 ETKDGv3 2
GCP O2G 6.801 0.302 -1.723 ETKDGv3 3
GCP O3G 8.725 0.427 0.255 ETKDGv3 4
GCP C3B 6.123 -0.525 0.944 ETKDGv3 5
GCP PB 4.633 -1.378 0.330 ETKDGv3 6
GCP O1B 4.086 -0.663 -0.889 ETKDGv3 7
GCP O2B 5.054 -2.959 -0.107 ETKDGv3 8
GCP O3A 3.481 -1.479 1.586 ETKDGv3 9
GCP PA 2.495 -0.090 1.547 ETKDGv3 10
GCP O1A 1.593 -0.128 2.761 ETKDGv3 11
GCP O2A 3.435 1.319 1.619 ETKDGv3 12
GCP "O5'" 1.540 -0.111 0.131 ETKDGv3 13
GCP "C5'" 0.702 1.021 0.137 ETKDGv3 14
GCP "C4'" -0.193 0.988 -1.109 ETKDGv3 15
GCP "O4'" -0.922 -0.223 -1.128 ETKDGv3 16
GCP "C3'" -1.176 2.164 -1.130 ETKDGv3 17
GCP "O3'" -1.349 2.662 -2.438 ETKDGv3 18
GCP "C2'" -2.442 1.546 -0.585 ETKDGv3 19
GCP "O2'" -3.598 2.106 -1.153 ETKDGv3 20
GCP "C1'" -2.292 0.081 -0.976 ETKDGv3 21
GCP N9 -2.886 -0.795 0.032 ETKDGv3 22
GCP C8 -2.325 -1.139 1.308 ETKDGv3 23
GCP N7 -3.211 -1.506 2.188 ETKDGv3 24
GCP C5 -4.451 -1.397 1.499 ETKDGv3 25
GCP C6 -5.803 -1.533 2.028 ETKDGv3 26
GCP O6 -6.017 -1.914 3.208 ETKDGv3 27
GCP N1 -6.883 -1.202 1.142 ETKDGv3 28
GCP C2 -6.589 -0.728 -0.194 ETKDGv3 29
GCP N2 -7.654 -0.372 -1.074 ETKDGv3 30
GCP N3 -5.350 -0.616 -0.598 ETKDGv3 31
GCP C4 -4.269 -0.975 0.276 ETKDGv3 32
GCP HOG2 7.551 0.294 -2.369 ETKDGv3 33
GCP HOG3 9.379 0.442 -0.490 ETKDGv3 34
GCP H3B1 6.516 -1.069 1.827 ETKDGv3 35
GCP H3B2 5.867 0.509 1.247 ETKDGv3 36
GCP HOB2 5.355 -2.898 -1.048 ETKDGv3 37
GCP HOA2 3.649 1.539 0.677 ETKDGv3 38
GCP "H5'2" 1.307 1.954 0.108 ETKDGv3 39
GCP "H5'1" 0.050 1.028 1.040 ETKDGv3 40
GCP "H4'" 0.465 1.026 -2.006 ETKDGv3 41
GCP "H3'" -0.845 3.004 -0.479 ETKDGv3 42
GCP "HO3'" -1.622 1.908 -3.025 ETKDGv3 43
GCP "H2'" -2.462 1.651 0.526 ETKDGv3 44
GCP "HO2'" -3.710 3.000 -0.737 ETKDGv3 45
GCP "H1'" -2.793 -0.105 -1.952 ETKDGv3 46
GCP H8 -1.269 -1.083 1.533 ETKDGv3 47
GCP HN1 -7.872 -1.288 1.467 ETKDGv3 48
GCP HN21 -8.647 -0.454 -0.762 ETKDGv3 49
GCP HN22 -7.452 -0.025 -2.038 ETKDGv3 50
#