data_5GL
#
_chem_comp.id 5GL
_chem_comp.name 4-propan-2-ylsulfanyl-1-propyl-6,7-dihydro-5~{H}-cyclopenta[d]pyrimidin-2-one
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C13 H20 N2 O S"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2015-09-24
_chem_comp.pdbx_modified_date 2016-09-23
_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 252.376
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code 5GL
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag Y
_chem_comp.pdbx_ideal_coordinates_details Corina
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code 5DR3
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site EBI
#
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
5GL C4 C1 C 0 1 N N N N N N -10.451 2.573 0.654 -0.009 -1.293 0.020 C4 5GL 1
5GL C5 C2 C 0 1 N N N N N N -10.827 3.938 0.799 -1.001 -0.289 0.079 C5 5GL 2
5GL C6 C3 C 0 1 N N N N N N -12.312 3.440 2.525 0.617 1.326 -0.246 C6 5GL 3
5GL N1 N1 N 0 1 N N N N N N -11.710 4.322 1.682 -0.655 0.985 -0.056 N1 5GL 4
5GL C10 C4 C 0 1 N N N N N N -9.493 1.895 -0.290 -0.120 -2.797 0.134 C10 5GL 5
5GL C11 C5 C 0 1 N N N N N N -9.762 0.406 -0.082 1.209 -3.341 -0.435 C11 5GL 6
5GL C12 C6 C 0 1 N N N N N N -10.567 0.252 1.202 2.168 -2.154 -0.196 C12 5GL 7
5GL O O1 O 0 1 N N N N N N -13.150 3.789 3.357 0.911 2.504 -0.367 O 5GL 8
5GL N N2 N 0 1 N N N N N N -11.951 2.086 2.420 1.584 0.393 -0.306 N 5GL 9
5GL C2 C7 C 0 1 N N N N N N -12.554 1.145 3.373 2.976 0.801 -0.516 C2 5GL 10
5GL C1 C8 C 0 1 N N N N N N -13.815 0.495 2.838 3.646 1.043 0.838 C1 5GL 11
5GL C C9 C 0 1 N N N N N N -14.306 -0.597 3.759 5.099 1.468 0.618 C 5GL 12
5GL S S1 S 0 1 N N N N N N -10.053 5.112 -0.237 -2.690 -0.727 0.329 S 5GL 13
5GL C3 C10 C 0 1 N N N N N N -11.027 1.653 1.477 1.279 -0.931 -0.172 C3 5GL 14
5GL H2 H2 H 0 1 N N N N N N -8.452 2.144 -0.036 -0.233 -3.091 1.178 H2 5GL 15
5GL H3 H3 H 0 1 N N N N N N -9.696 2.188 -1.331 -0.961 -3.161 -0.456 H3 5GL 16
5GL H4 H4 H 0 1 N N N N N N -10.334 0.007 -0.932 1.537 -4.223 0.115 H4 5GL 17
5GL H5 H5 H 0 1 N N N N N N -8.810 -0.137 0.006 1.117 -3.559 -1.499 H5 5GL 18
5GL H6 H6 H 0 1 N N N N N N -11.422 -0.424 1.055 2.685 -2.270 0.757 H6 5GL 19
5GL H7 H7 H 0 1 N N N N N N -9.938 -0.126 2.021 2.888 -2.079 -1.011 H7 5GL 20
5GL H8 H8 H 0 1 N N N N N N -11.821 0.357 3.600 3.508 0.013 -1.050 H8 5GL 21
5GL H9 H9 H 0 1 N N N N N N -12.804 1.690 4.295 3.001 1.719 -1.104 H9 5GL 22
5GL H10 H10 H 0 1 N N N N N N -14.599 1.261 2.741 3.113 1.830 1.371 H10 5GL 23
5GL H11 H11 H 0 1 N N N N N N -13.602 0.061 1.850 3.621 0.125 1.425 H11 5GL 24
5GL H12 H12 H 0 1 N N N N N N -15.220 -1.046 3.342 5.577 1.641 1.583 H12 5GL 25
5GL H13 H13 H 0 1 N N N N N N -13.530 -1.370 3.857 5.632 0.681 0.085 H13 5GL 26
5GL H14 H14 H 0 1 N N N N N N -14.526 -0.170 4.749 5.124 2.386 0.031 H14 5GL 27
5GL C7 C11 C 0 1 N N N N N N ? ? ? -3.446 0.917 0.311 C7 5GL 28
5GL C8 C12 C 0 1 N N N N N N ? ? ? -3.279 1.541 -1.076 C8 5GL 29
5GL C9 C13 C 0 1 N N N N N N ? ? ? -4.935 0.797 0.640 C9 5GL 30
5GL H1 H1 H 0 1 N N N N N N ? ? ? -2.960 1.549 1.055 H1 5GL 31
5GL H15 H15 H 0 1 N N N N N N ? ? ? -3.734 2.531 -1.086 H15 5GL 32
5GL H16 H16 H 0 1 N N N N N N ? ? ? -2.218 1.627 -1.310 H16 5GL 33
5GL H17 H17 H 0 1 N N N N N N ? ? ? -3.765 0.909 -1.819 H17 5GL 34
5GL H18 H18 H 0 1 N N N N N N ? ? ? -5.054 0.353 1.628 H18 5GL 35
5GL H19 H19 H 0 1 N N N N N N ? ? ? -5.391 1.787 0.630 H19 5GL 36
5GL H20 H20 H 0 1 N N N N N N ? ? ? -5.422 0.166 -0.103 H20 5GL 37
#
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
5GL C10 C11 SING N N 1
5GL C10 C4 SING N N 2
5GL S C5 SING N N 3
5GL C11 C12 SING N N 4
5GL C4 C5 SING N N 5
5GL C4 C3 DOUB N N 6
5GL C5 N1 DOUB N N 7
5GL C12 C3 SING N N 8
5GL C3 N SING N N 9
5GL N1 C6 SING N N 10
5GL N C6 SING N N 11
5GL N C2 SING N N 12
5GL C6 O DOUB N N 13
5GL C1 C2 SING N N 14
5GL C1 C SING N N 15
5GL C10 H2 SING N N 16
5GL C10 H3 SING N N 17
5GL C11 H4 SING N N 18
5GL C11 H5 SING N N 19
5GL C12 H6 SING N N 20
5GL C12 H7 SING N N 21
5GL C2 H8 SING N N 22
5GL C2 H9 SING N N 23
5GL C1 H10 SING N N 24
5GL C1 H11 SING N N 25
5GL C H12 SING N N 26
5GL C H13 SING N N 27
5GL C H14 SING N N 28
5GL S C7 SING N N 29
5GL C7 C8 SING N N 30
5GL C7 C9 SING N N 31
5GL C7 H1 SING N N 32
5GL C8 H15 SING N N 33
5GL C8 H16 SING N N 34
5GL C8 H17 SING N N 35
5GL C9 H18 SING N N 36
5GL C9 H19 SING N N 37
5GL C9 H20 SING N N 38
#
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
5GL InChI InChI 1.03 InChI=1S/C13H20N2OS/c1-4-8-15-11-7-5-6-10(11)12(14-13(15)16)17-9(2)3/h9H,4-8H2,1-3H3
5GL InChIKey InChI 1.03 KUWKRQXLULNLGL-UHFFFAOYSA-N
5GL SMILES_CANONICAL CACTVS 3.385 CCCN1C(=O)N=C(SC(C)C)C2=C1CCC2
5GL SMILES CACTVS 3.385 CCCN1C(=O)N=C(SC(C)C)C2=C1CCC2
5GL SMILES_CANONICAL "OpenEye OEToolkits" 2.0.4 CCCN1C2=C(CCC2)C(=NC1=O)SC(C)C
5GL SMILES "OpenEye OEToolkits" 2.0.4 CCCN1C2=C(CCC2)C(=NC1=O)SC(C)C
#
_pdbx_chem_comp_identifier.comp_id 5GL
_pdbx_chem_comp_identifier.type "SYSTEMATIC NAME"
_pdbx_chem_comp_identifier.program "OpenEye OEToolkits"
_pdbx_chem_comp_identifier.program_version 2.0.4
_pdbx_chem_comp_identifier.identifier 4-propan-2-ylsulfanyl-1-propyl-6,7-dihydro-5~{H}-cyclopenta[d]pyrimidin-2-one
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
5GL 'Create component' 2015-09-24 EBI
5GL 'Modify value order' 2015-10-20 EBI
5GL 'Initial release' 2016-09-28 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
5GL C4 C 6.897 -0.750 1
5GL C5 C 5.598 -1.500 2
5GL C6 C 4.299 0.750 3
5GL N1 N 4.299 -0.750 4
5GL C10 C 8.316 -1.207 5
5GL C11 C 9.192 0.000 6
5GL C12 C 8.316 1.207 7
5GL O O 3.000 1.500 8
5GL N N 5.598 1.500 9
5GL C2 C 5.598 3.000 10
5GL C1 C 4.299 3.750 11
5GL C C 4.299 5.250 12
5GL S S 5.598 -3.000 13
5GL C3 C 6.897 0.750 14
5GL C7 C 4.299 -3.750 15
5GL C8 C 4.299 -5.250 16
5GL C9 C 3.000 -3.000 17
#
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
5GL C10 C11 SINGLE NONE 1
5GL C10 C4 SINGLE NONE 2
5GL S C5 SINGLE NONE 3
5GL C11 C12 SINGLE NONE 4
5GL C4 C5 SINGLE NONE 5
5GL C4 C3 DOUBLE NONE 6
5GL C5 N1 DOUBLE NONE 7
5GL C12 C3 SINGLE NONE 8
5GL C3 N SINGLE NONE 9
5GL N1 C6 SINGLE NONE 10
5GL N C6 SINGLE NONE 11
5GL N C2 SINGLE NONE 12
5GL C6 O DOUBLE NONE 13
5GL C1 C2 SINGLE NONE 14
5GL C1 C SINGLE NONE 15
5GL S C7 SINGLE NONE 16
5GL C7 C8 SINGLE NONE 17
5GL C7 C9 SINGLE NONE 18
#
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
5GL MurckoScaffold S1 scaffold 'O=c1ncc2c([nH]1)CCC2' InChI=1S/C7H8N2O/c10-7-8-4-5-2-1-3-6(5)9-7/h4H,1-3H2,(H,8,9,10) MKCJNRRFJUUASK-UHFFFAOYSA-N
5GL pyrimidine F1 fragment c1cncnc1 InChI=1S/C4H4N2/c1-2-5-4-6-3-1/h1-4H CZPWVGJYEJSRLH-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
5GL C4 S1 1
5GL C5 S1 1
5GL C6 S1 1
5GL N1 S1 1
5GL C10 S1 1
5GL C11 S1 1
5GL C12 S1 1
5GL O S1 1
5GL N S1 1
5GL C3 S1 1
5GL C4 F1 1
5GL C5 F1 1
5GL N1 F1 1
5GL C6 F1 1
5GL N F1 1
5GL C3 F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id 5GL
_pdbe_chem_comp_rdkit_properties.exactmw 252.130
_pdbe_chem_comp_rdkit_properties.amw 252.383
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 3
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 0
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 7
_pdbe_chem_comp_rdkit_properties.NumHBD 0
_pdbe_chem_comp_rdkit_properties.NumHBA 4
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 17
_pdbe_chem_comp_rdkit_properties.NumAtoms 37
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 4
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.692
_pdbe_chem_comp_rdkit_properties.NumRings 2
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 1
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 1
_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 134.743
_pdbe_chem_comp_rdkit_properties.tpsa 34.890
_pdbe_chem_comp_rdkit_properties.CrippenClogP 3.325
_pdbe_chem_comp_rdkit_properties.CrippenMR 71.952
_pdbe_chem_comp_rdkit_properties.chi0v 9.027
_pdbe_chem_comp_rdkit_properties.chi1v 5.047
_pdbe_chem_comp_rdkit_properties.chi2v 2.490
_pdbe_chem_comp_rdkit_properties.chi3v 2.490
_pdbe_chem_comp_rdkit_properties.chi4v 1.783
_pdbe_chem_comp_rdkit_properties.chi0n 28.211
_pdbe_chem_comp_rdkit_properties.chi1n 14.230
_pdbe_chem_comp_rdkit_properties.chi2n 1.798
_pdbe_chem_comp_rdkit_properties.chi3n 1.798
_pdbe_chem_comp_rdkit_properties.chi4n 1.216
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.770
_pdbe_chem_comp_rdkit_properties.kappa1 2.716
_pdbe_chem_comp_rdkit_properties.kappa2 5.253
_pdbe_chem_comp_rdkit_properties.kappa3 2.566
_pdbe_chem_comp_rdkit_properties.Phi 0.839
#
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
5GL UniChem PDBe 5GL
5GL UniChem ZINC ZINC000028288872
5GL UniChem PubChem 35574508
5GL UniChem Mcule MCULE-6893290615
5GL UniChem eMolecules 15306547
#
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
5GL C4 -0.445 0.561 0.644 ETKDGv3 1
5GL C5 -1.093 -0.748 0.863 ETKDGv3 2
5GL C6 0.839 -1.810 -0.054 ETKDGv3 3
5GL N1 -0.470 -1.842 0.535 ETKDGv3 4
5GL C10 -1.013 1.891 0.978 ETKDGv3 5
5GL C11 0.091 2.879 0.573 ETKDGv3 6
5GL C12 1.221 2.044 -0.046 ETKDGv3 7
5GL O 1.417 -2.891 -0.345 ETKDGv3 8
5GL N 1.475 -0.539 -0.303 ETKDGv3 9
5GL C2 2.844 -0.465 -0.829 ETKDGv3 10
5GL C1 3.856 -0.560 0.316 ETKDGv3 11
5GL C 5.288 -0.461 -0.203 ETKDGv3 12
5GL S -2.726 -0.848 1.601 ETKDGv3 13
5GL C3 0.752 0.642 0.099 ETKDGv3 14
5GL H2 -1.939 2.070 0.391 ETKDGv3 15
5GL H3 -1.227 1.956 2.066 ETKDGv3 16
5GL H4 -0.298 3.616 -0.163 ETKDGv3 17
5GL H5 0.463 3.425 1.467 ETKDGv3 18
5GL H6 1.350 2.294 -1.121 ETKDGv3 19
5GL H7 2.174 2.197 0.504 ETKDGv3 20
5GL H8 3.016 -1.290 -1.553 ETKDGv3 21
5GL H9 2.991 0.485 -1.387 ETKDGv3 22
5GL H10 3.729 -1.529 0.845 ETKDGv3 23
5GL H11 3.678 0.261 1.043 ETKDGv3 24
5GL H12 5.446 0.513 -0.712 ETKDGv3 25
5GL H13 5.997 -0.537 0.648 ETKDGv3 26
5GL H14 5.498 -1.287 -0.915 ETKDGv3 27
5GL C7 -3.633 -0.700 0.016 ETKDGv3 28
5GL C8 -5.019 -0.117 0.287 ETKDGv3 29
5GL C9 -3.747 -2.069 -0.657 ETKDGv3 30
5GL H1 -3.098 -0.005 -0.667 ETKDGv3 31
5GL H15 -4.922 0.882 0.761 ETKDGv3 32
5GL H16 -5.578 0.002 -0.666 ETKDGv3 33
5GL H17 -5.597 -0.781 0.965 ETKDGv3 34
5GL H18 -4.264 -2.790 0.012 ETKDGv3 35
5GL H19 -4.317 -1.983 -1.606 ETKDGv3 36
5GL H20 -2.738 -2.464 -0.898 ETKDGv3 37
#