data_G0F
#
_chem_comp.id G0F
_chem_comp.name "[6-methyl-4-[(3-methylsulfanylpropylamino)methyl]-5-oxidanyl-pyridin-3-yl]methyl dihydrogen phosphate"
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C12 H21 N2 O5 P S"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2020-07-14
_chem_comp.pdbx_modified_date 2021-01-22
_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 336.344
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code G0F
_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 7CIM
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site PDBJ
#
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
G0F C4 C1 C 0 1 Y N N N N N 27.854 -12.885 -4.332 0.770 -1.758 -0.489 C4 G0F 1
G0F C5 C2 C 0 1 Y N N N N N 28.657 -11.887 -3.750 1.789 -0.902 -0.103 C5 G0F 2
G0F C6 C3 C 0 1 Y N N N N N 29.766 -12.285 -2.995 2.898 -1.419 0.540 C6 G0F 3
G0F N1 N1 N 0 1 Y N N N N N 30.061 -13.579 -2.801 2.995 -2.711 0.788 N1 G0F 4
G0F C3 C4 C 0 1 Y N N N N N 28.212 -14.223 -4.116 0.905 -3.115 -0.212 C3 G0F 5
G0F OP1 O1 O 0 1 N N N N N N 26.133 -9.101 -5.025 2.970 3.226 -1.434 OP1 G0F 6
G0F P P1 P 0 1 N N N N N N 26.280 -8.826 -3.549 3.091 2.821 -0.016 P G0F 7
G0F OP2 O2 O 0 1 N N N N N N 25.270 -9.240 -2.585 4.561 3.193 0.524 OP2 G0F 8
G0F OP3 O3 O 0 1 N N N N N N 27.154 -7.680 -3.237 1.985 3.597 0.860 OP3 G0F 9
G0F OP4 O4 O 0 1 N N N N N N 27.250 -10.080 -3.186 2.859 1.233 0.111 OP4 G0F 10
G0F C5A C5 C 0 1 N N N N N N 28.403 -10.374 -3.922 1.689 0.576 -0.382 C5A G0F 11
G0F C2 C6 C 0 1 Y N N N N N 29.316 -14.596 -3.363 2.049 -3.559 0.437 C2 G0F 12
G0F C2A C7 C 0 1 N N N N N N 29.687 -16.035 -3.106 2.209 -5.025 0.745 C2A G0F 13
G0F O3 O5 O 0 1 N N N N N N 27.441 -15.180 -4.667 -0.069 -3.992 -0.570 O3 G0F 14
G0F C4A C8 C 0 1 N N N N N N 26.691 -12.637 -5.076 -0.458 -1.232 -1.187 C4A G0F 15
G0F N N2 N 0 1 N N N N N N 26.613 -13.072 -6.486 -1.472 -0.872 -0.187 N G0F 16
G0F CA C9 C 0 1 N N N N N N 25.440 -12.939 -7.356 -2.686 -0.353 -0.832 CA G0F 17
G0F CB C10 C 0 1 N N N N N N 24.900 -11.538 -7.212 -3.717 0.010 0.238 CB G0F 18
G0F CG C11 C 0 1 N N N N N N 23.563 -11.393 -7.918 -4.981 0.550 -0.434 CG G0F 19
G0F SD S1 S 0 1 N N N N N N 22.196 -12.530 -7.405 -6.204 0.982 0.835 SD G0F 20
G0F CE C12 C 0 1 N N N N N N 21.673 -11.829 -5.848 -7.607 1.591 -0.140 CE G0F 21
G0F H1 H1 H 0 1 N N N N N N 30.402 -11.530 -2.557 3.695 -0.757 0.843 H1 G0F 22
G0F H2 H2 H 0 1 N N N N N N 24.561 -9.681 -3.038 4.771 4.136 0.478 H2 G0F 23
G0F H3 H3 H 0 1 N N N N N N 27.483 -7.303 -4.045 2.007 3.380 1.802 H3 G0F 24
G0F H4 H4 H 0 1 N N N N N N 29.257 -9.799 -3.536 1.607 0.738 -1.456 H4 G0F 25
G0F H5 H5 H 0 1 N N N N N N 28.248 -10.133 -4.984 0.808 0.981 0.116 H5 G0F 26
G0F H6 H6 H 0 1 N N N N N N 30.572 -16.075 -2.453 2.709 -5.518 -0.089 H6 G0F 27
G0F H7 H7 H 0 1 N N N N N N 28.846 -16.548 -2.616 2.808 -5.143 1.648 H7 G0F 28
G0F H8 H8 H 0 1 N N N N N N 29.913 -16.531 -4.061 1.228 -5.474 0.897 H8 G0F 29
G0F H9 H9 H 0 1 N N N N N N 27.791 -16.035 -4.446 0.046 -4.366 -1.455 H9 G0F 30
G0F H10 H10 H 0 1 N N N N N N 26.535 -11.548 -5.070 -0.194 -0.350 -1.771 H10 G0F 31
G0F H11 H11 H 0 1 N N N N N N 24.671 -13.667 -7.057 -2.438 0.534 -1.414 H11 G0F 32
G0F H12 H12 H 0 1 N N N N N N 25.730 -13.120 -8.402 -3.101 -1.116 -1.492 H12 G0F 33
G0F H13 H13 H 0 1 N N N N N N 25.617 -10.829 -7.652 -3.966 -0.877 0.820 H13 G0F 34
G0F H14 H14 H 0 1 N N N N N N 24.769 -11.311 -6.144 -3.303 0.773 0.898 H14 G0F 35
G0F H15 H15 H 0 1 N N N N N N 23.739 -11.553 -8.992 -4.733 1.438 -1.016 H15 G0F 36
G0F H16 H16 H 0 1 N N N N N N 23.214 -10.363 -7.753 -5.396 -0.212 -1.094 H16 G0F 37
G0F H17 H17 H 0 1 N N N N N N 20.848 -12.428 -5.434 -7.292 2.453 -0.729 H17 G0F 38
G0F H18 H18 H 0 1 N N N N N N 22.517 -11.831 -5.143 -7.955 0.803 -0.807 H18 G0F 39
G0F H19 H19 H 0 1 N N N N N N 21.331 -10.796 -6.008 -8.415 1.884 0.530 H19 G0F 40
G0F H20 H20 H 0 1 N N N N N N 25.863 -13.129 -4.545 -0.857 -2.000 -1.849 H20 G0F 41
G0F H21 H21 H 0 1 N N N N N N 26.822 -14.050 -6.473 -1.105 -0.208 0.478 H21 G0F 42
#
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
G0F CG SD SING N N 1
G0F CG CB SING N N 2
G0F SD CE SING N N 3
G0F CA CB SING N N 4
G0F CA N SING N N 5
G0F N C4A SING N N 6
G0F C4A C4 SING N N 7
G0F OP1 P DOUB N N 8
G0F O3 C3 SING N N 9
G0F C4 C3 DOUB Y N 10
G0F C4 C5 SING Y N 11
G0F C3 C2 SING Y N 12
G0F C5A C5 SING N N 13
G0F C5A OP4 SING N N 14
G0F C5 C6 DOUB Y N 15
G0F P OP3 SING N N 16
G0F P OP4 SING N N 17
G0F P OP2 SING N N 18
G0F C2 C2A SING N N 19
G0F C2 N1 DOUB Y N 20
G0F C6 N1 SING Y N 21
G0F C6 H1 SING N N 22
G0F OP2 H2 SING N N 23
G0F OP3 H3 SING N N 24
G0F C5A H4 SING N N 25
G0F C5A H5 SING N N 26
G0F C2A H6 SING N N 27
G0F C2A H7 SING N N 28
G0F C2A H8 SING N N 29
G0F O3 H9 SING N N 30
G0F C4A H10 SING N N 31
G0F CA H11 SING N N 32
G0F CA H12 SING N N 33
G0F CB H13 SING N N 34
G0F CB H14 SING N N 35
G0F CG H15 SING N N 36
G0F CG H16 SING N N 37
G0F CE H17 SING N N 38
G0F CE H18 SING N N 39
G0F CE H19 SING N N 40
G0F C4A H20 SING N N 41
G0F N H21 SING N N 42
#
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
G0F InChI InChI 1.03 InChI=1S/C12H21N2O5PS/c1-9-12(15)11(7-13-4-3-5-21-2)10(6-14-9)8-19-20(16,17)18/h6,13,15H,3-5,7-8H2,1-2H3,(H2,16,17,18)
G0F InChIKey InChI 1.03 AGFAHJKGUOFCGH-UHFFFAOYSA-N
G0F SMILES_CANONICAL CACTVS 3.385 CSCCCNCc1c(O)c(C)ncc1CO[P](O)(O)=O
G0F SMILES CACTVS 3.385 CSCCCNCc1c(O)c(C)ncc1CO[P](O)(O)=O
G0F SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 Cc1c(c(c(cn1)COP(=O)(O)O)CNCCCSC)O
G0F SMILES "OpenEye OEToolkits" 2.0.7 Cc1c(c(c(cn1)COP(=O)(O)O)CNCCCSC)O
#
_pdbx_chem_comp_identifier.comp_id G0F
_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
"[6-methyl-4-[(3-methylsulfanylpropylamino)methyl]-5-oxidanyl-pyridin-3-yl]methyl dihydrogen 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
G0F 'Create component' 2020-07-14 PDBJ
G0F 'Initial release' 2021-01-27 RCSB
#
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
G0F C4 C 6.404 -2.625 1
G0F C5 C 7.702 -3.375 2
G0F C6 C 7.702 -4.875 3
G0F N1 N 6.404 -5.625 4
G0F C3 C 5.104 -3.375 5
G0F OP1 O 12.899 -1.875 6
G0F P P 11.600 -2.625 7
G0F OP2 O 10.850 -1.326 8
G0F OP3 O 12.350 -3.924 9
G0F OP4 O 10.301 -3.375 10
G0F C5A C 9.002 -2.625 11
G0F C2 C 5.104 -4.875 12
G0F C2A C 3.805 -5.625 13
G0F O3 O 3.805 -2.625 14
G0F C4A C 6.404 -1.125 15
G0F N N 7.702 -0.375 16
G0F CA C 7.702 1.125 17
G0F CB C 6.404 1.875 18
G0F CG C 6.404 3.375 19
G0F SD S 5.104 4.125 20
G0F CE C 5.104 5.625 21
#
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
G0F CG SD SINGLE NONE 1
G0F CG CB SINGLE NONE 2
G0F SD CE SINGLE NONE 3
G0F CA CB SINGLE NONE 4
G0F CA N SINGLE NONE 5
G0F N C4A SINGLE NONE 6
G0F C4A C4 SINGLE NONE 7
G0F OP1 P DOUBLE NONE 8
G0F O3 C3 SINGLE NONE 9
G0F C4 C3 DOUBLE NONE 10
G0F C4 C5 SINGLE NONE 11
G0F C3 C2 SINGLE NONE 12
G0F C5A C5 SINGLE NONE 13
G0F C5A OP4 SINGLE NONE 14
G0F C5 C6 DOUBLE NONE 15
G0F P OP3 SINGLE NONE 16
G0F P OP4 SINGLE NONE 17
G0F P OP2 SINGLE NONE 18
G0F C2 C2A SINGLE NONE 19
G0F C2 N1 DOUBLE NONE 20
G0F C6 N1 SINGLE NONE 21
#
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
G0F MurckoScaffold S1 scaffold c1ccncc1 InChI=1S/C5H5N/c1-2-4-6-5-3-1/h1-5H JUJWROOIHBZHMG-UHFFFAOYSA-N
G0F phosphate F1 fragment O=P(O)(O)O InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4) NBIIXXVUZAFLBC-UHFFFAOYSA-N
G0F pyridine F2 fragment c1ccncc1 InChI=1S/C5H5N/c1-2-4-6-5-3-1/h1-5H JUJWROOIHBZHMG-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
G0F C4 S1 1
G0F C5 S1 1
G0F C6 S1 1
G0F N1 S1 1
G0F C3 S1 1
G0F C2 S1 1
G0F OP2 F1 1
G0F P F1 1
G0F OP1 F1 1
G0F OP3 F1 1
G0F OP4 F1 1
G0F C6 F2 1
G0F C5 F2 1
G0F C4 F2 1
G0F C3 F2 1
G0F C2 F2 1
G0F N1 F2 1
#
_pdbe_chem_comp_rdkit_properties.comp_id G0F
_pdbe_chem_comp_rdkit_properties.exactmw 336.091
_pdbe_chem_comp_rdkit_properties.amw 336.350
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 7
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 4
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 14
_pdbe_chem_comp_rdkit_properties.NumHBD 4
_pdbe_chem_comp_rdkit_properties.NumHBA 8
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 21
_pdbe_chem_comp_rdkit_properties.NumAtoms 42
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 9
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.583
_pdbe_chem_comp_rdkit_properties.NumRings 1
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 1
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 0
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumSpiroAtoms 0
_pdbe_chem_comp_rdkit_properties.NumBridgeheadAtoms 0
_pdbe_chem_comp_rdkit_properties.NumAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 157.747
_pdbe_chem_comp_rdkit_properties.tpsa 111.910
_pdbe_chem_comp_rdkit_properties.CrippenClogP 0.921
_pdbe_chem_comp_rdkit_properties.CrippenMR 80.770
_pdbe_chem_comp_rdkit_properties.chi0v 11.502
_pdbe_chem_comp_rdkit_properties.chi1v 6.968
_pdbe_chem_comp_rdkit_properties.chi2v 2.132
_pdbe_chem_comp_rdkit_properties.chi3v 2.132
_pdbe_chem_comp_rdkit_properties.chi4v 1.192
_pdbe_chem_comp_rdkit_properties.chi0n 30.791
_pdbe_chem_comp_rdkit_properties.chi1n 14.863
_pdbe_chem_comp_rdkit_properties.chi2n 1.613
_pdbe_chem_comp_rdkit_properties.chi3n 1.613
_pdbe_chem_comp_rdkit_properties.chi4n 0.893
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.630
_pdbe_chem_comp_rdkit_properties.kappa1 4.466
_pdbe_chem_comp_rdkit_properties.kappa2 8.726
_pdbe_chem_comp_rdkit_properties.kappa3 6.775
_pdbe_chem_comp_rdkit_properties.Phi 1.855
#
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
G0F UniChem PDBe G0F
G0F UniChem PubChem 155387735
#
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
G0F C4 -1.351 -0.698 -0.815 ETKDGv3 1
G0F C5 -2.092 -0.826 0.485 ETKDGv3 2
G0F C6 -3.022 -1.789 0.607 ETKDGv3 3
G0F N1 -3.291 -2.687 -0.477 ETKDGv3 4
G0F C3 -1.655 -1.540 -1.829 ETKDGv3 5
G0F OP1 -2.846 2.049 3.792 ETKDGv3 6
G0F P -2.170 2.502 2.517 ETKDGv3 7
G0F OP2 -0.504 2.653 2.779 ETKDGv3 8
G0F OP3 -2.798 4.007 2.066 ETKDGv3 9
G0F OP4 -2.473 1.382 1.267 ETKDGv3 10
G0F C5A -1.892 0.149 1.620 ETKDGv3 11
G0F C2 -2.678 -2.601 -1.619 ETKDGv3 12
G0F C2A -3.021 -3.576 -2.703 ETKDGv3 13
G0F O3 -1.016 -1.405 -3.064 ETKDGv3 14
G0F C4A -0.280 0.367 -1.016 ETKDGv3 15
G0F N 1.081 -0.196 -1.070 ETKDGv3 16
G0F CA 1.569 -0.677 0.232 ETKDGv3 17
G0F CB 2.172 0.466 1.065 ETKDGv3 18
G0F CG 3.357 1.154 0.377 ETKDGv3 19
G0F SD 4.803 0.041 0.283 ETKDGv3 20
G0F CE 5.863 1.247 -0.575 ETKDGv3 21
G0F H1 -3.595 -1.896 1.519 ETKDGv3 22
G0F H2 -0.419 3.371 3.455 ETKDGv3 23
G0F H3 -2.319 4.237 1.230 ETKDGv3 24
G0F H4 -0.804 0.252 1.816 ETKDGv3 25
G0F H5 -2.357 -0.245 2.553 ETKDGv3 26
G0F H6 -3.434 -3.033 -3.579 ETKDGv3 27
G0F H7 -3.780 -4.307 -2.352 ETKDGv3 28
G0F H8 -2.111 -4.135 -3.007 ETKDGv3 29
G0F H9 -1.214 -2.008 -3.852 ETKDGv3 30
G0F H10 -0.335 1.167 -0.253 ETKDGv3 31
G0F H11 2.353 -1.447 0.066 ETKDGv3 32
G0F H12 0.765 -1.182 0.806 ETKDGv3 33
G0F H13 1.394 1.228 1.275 ETKDGv3 34
G0F H14 2.503 0.063 2.046 ETKDGv3 35
G0F H15 3.638 2.050 0.971 ETKDGv3 36
G0F H16 3.067 1.492 -0.641 ETKDGv3 37
G0F H17 5.414 1.524 -1.551 ETKDGv3 38
G0F H18 6.858 0.791 -0.754 ETKDGv3 39
G0F H19 5.992 2.155 0.051 ETKDGv3 40
G0F H20 -0.478 0.891 -1.976 ETKDGv3 41
G0F H21 1.105 -0.992 -1.749 ETKDGv3 42
#