data_GLL
#
_chem_comp.id GLL
_chem_comp.name GLYCOLURIL
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C4 H6 N4 O2"
_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 2011-06-04
_chem_comp.pdbx_ambiguous_flag N
_chem_comp.pdbx_release_status REL
_chem_comp.pdbx_replaced_by ?
_chem_comp.pdbx_replaces GUR
_chem_comp.formula_weight 142.116
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code GLL
_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 ?
_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
GLL C1 C1 C 0 1 N N N N N N 35.815 11.716 -4.377 -0.000 0.240 -1.815 C1 GLL 1
GLL O1 O1 O 0 1 N N N N N N 36.726 12.261 -3.788 -0.002 0.897 -2.838 O1 GLL 2
GLL N1 N1 N 0 1 N N N N N N 35.265 12.064 -5.499 1.122 -0.152 -1.201 N1 GLL 3
GLL N2 N2 N 0 1 N N N N N N 35.246 10.645 -3.928 -1.122 -0.152 -1.198 N2 GLL 4
GLL C2 C2 C 0 1 N N N N N N 34.159 11.152 -5.921 0.776 -0.924 -0.000 C2 GLL 5
GLL C3 C3 C 0 1 N N N N N N 34.145 10.134 -4.798 -0.773 -0.927 0.000 C3 GLL 6
GLL "N1'" "N1'" N 0 1 N N N N N N 32.743 11.643 -5.845 1.123 -0.151 1.200 "N1'" GLL 7
GLL "N2'" "N2'" N 0 1 N N N N N N 32.741 10.223 -4.266 -1.122 -0.155 1.201 "N2'" GLL 8
GLL "C1'" "C1'" C 0 1 N N N N N N 32.024 11.092 -4.920 -0.000 0.241 1.814 "C1'" GLL 9
GLL "O1'" "O1'" O 0 1 N N N N N N 30.865 11.344 -4.707 -0.001 0.898 2.837 "O1'" GLL 10
GLL HN1 HN1 H 0 1 N N N N N N 35.965 12.149 -6.235 2.023 0.042 -1.503 HN1 GLL 11
GLL HN2 HN2 H 0 1 N N N N N N 35.601 10.271 -3.047 -2.024 0.041 -1.498 HN2 GLL 12
GLL H2 H2 H 0 1 N N N N N N 34.369 10.888 -6.983 1.214 -1.922 0.000 H2 GLL 13
GLL H3 H3 H 0 1 N N N N N N 34.333 9.052 -4.994 -1.196 -1.931 0.006 H3 GLL 14
GLL "HN1'" "'HN1" H 0 0 N N N N N N 32.286 11.545 -6.751 2.024 0.044 1.501 "HN1'" GLL 15
GLL "HN2'" "'HN2" H 0 0 N N N N N N 32.296 9.718 -3.498 -2.024 0.036 1.502 "HN2'" GLL 16
#
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
GLL C1 O1 DOUB N N 1
GLL C1 N1 SING N N 2
GLL C1 N2 SING N N 3
GLL N1 C2 SING N N 4
GLL N1 HN1 SING N N 5
GLL N2 C3 SING N N 6
GLL N2 HN2 SING N N 7
GLL C2 C3 SING N N 8
GLL C2 "N1'" SING N N 9
GLL C2 H2 SING N N 10
GLL C3 "N2'" SING N N 11
GLL C3 H3 SING N N 12
GLL "N1'" "C1'" SING N N 13
GLL "N1'" "HN1'" SING N N 14
GLL "N2'" "C1'" SING N N 15
GLL "N2'" "HN2'" SING N N 16
GLL "C1'" "O1'" DOUB N N 17
#
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
GLL SMILES ACDLabs 10.04 O=C1NC2NC(=O)NC2N1
GLL SMILES_CANONICAL CACTVS 3.341 O=C1N[C@@H]2NC(=O)N[C@@H]2N1
GLL SMILES CACTVS 3.341 O=C1N[CH]2NC(=O)N[CH]2N1
GLL SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 C12C(NC(=O)N1)NC(=O)N2
GLL SMILES "OpenEye OEToolkits" 1.5.0 C12C(NC(=O)N1)NC(=O)N2
GLL InChI InChI 1.03 InChI=1S/C4H6N4O2/c9-3-5-1-2(7-3)8-4(10)6-1/h1-2H,(H2,5,7,9)(H2,6,8,10)/t1-,2+
GLL InChIKey InChI 1.03 VPVSTMAPERLKKM-XIXRPRMCSA-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
GLL "SYSTEMATIC NAME" ACDLabs 10.04 cis-tetrahydroimidazo[4,5-d]imidazole-2,5(1H,3H)-dione
GLL "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 1,3,3a,4,6,6a-hexahydroimidazo[4,5-d]imidazole-2,5-dione
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
GLL 'Create component' 1999-07-08 EBI
GLL 'Modify descriptor' 2011-06-04 RCSB
#
_pdbe_chem_comp_drugbank_details.comp_id GLL
_pdbe_chem_comp_drugbank_details.drugbank_id DB03533
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name Acetyleneurea
_pdbe_chem_comp_drugbank_details.description ?
_pdbe_chem_comp_drugbank_details.cas_number 496-46-8
_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
GLL cis-glycoluril DrugBank ?
GLL Glycoluril DrugBank ?
GLL Glyoxaldiureine DrugBank ?
GLL Glyoxaldiurene DrugBank ?
#
_pdbe_chem_comp_drugbank_classification.comp_id GLL
_pdbe_chem_comp_drugbank_classification.drugbank_id DB03533
_pdbe_chem_comp_drugbank_classification.parent Imidazolines
_pdbe_chem_comp_drugbank_classification.kingdom 'Organic compounds'
_pdbe_chem_comp_drugbank_classification.class Azolines
_pdbe_chem_comp_drugbank_classification.superclass 'Organoheterocyclic compounds'
_pdbe_chem_comp_drugbank_classification.description
'This compound belongs to the class of organic compounds known as imidazolines. These are organic compounds containing an imidazoline ring, which is an unsaturated ring (derived from imidazole) with two nitrogen atoms at positions 1 and 3 respectively, and containing only one CN double bond.'
#
_pdbe_chem_comp_drugbank_targets.comp_id GLL
_pdbe_chem_comp_drugbank_targets.drugbank_id DB03533
_pdbe_chem_comp_drugbank_targets.name Streptavidin
_pdbe_chem_comp_drugbank_targets.organism 'Streptomyces avidinii'
_pdbe_chem_comp_drugbank_targets.uniprot_id P22629
_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
GLL C1 C -2.308 0.002 1
GLL O1 O -3.808 0.003 2
GLL N1 N -1.427 -1.212 3
GLL N2 N -1.426 1.215 4
GLL C2 C -0.001 -0.750 5
GLL C3 C 0.001 0.750 6
GLL "N1'" N 1.426 -1.215 7
GLL "N2'" N 1.427 1.212 8
GLL "C1'" C 2.308 -0.002 9
GLL "O1'" O 3.808 -0.003 10
#
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
GLL C1 O1 DOUBLE NONE 1
GLL C1 N1 SINGLE NONE 2
GLL C1 N2 SINGLE NONE 3
GLL N1 C2 SINGLE NONE 4
GLL N2 C3 SINGLE NONE 5
GLL C2 C3 SINGLE NONE 6
GLL C2 "N1'" SINGLE NONE 7
GLL C3 "N2'" SINGLE NONE 8
GLL "N1'" "C1'" SINGLE NONE 9
GLL "N2'" "C1'" SINGLE NONE 10
GLL "C1'" "O1'" DOUBLE NONE 11
#
_pdbe_chem_comp_substructure.comp_id GLL
_pdbe_chem_comp_substructure.substructure_name MurckoScaffold
_pdbe_chem_comp_substructure.id S1
_pdbe_chem_comp_substructure.substructure_type scaffold
_pdbe_chem_comp_substructure.substructure_smiles 'O=C1N[C@H]2NC(=O)N[C@H]2N1'
_pdbe_chem_comp_substructure.substructure_inchis
InChI=1S/C4H6N4O2/c9-3-5-1-2(7-3)8-4(10)6-1/h1-2H,(H2,5,7,9)(H2,6,8,10)/t1-,2+
_pdbe_chem_comp_substructure.substructure_inchikeys VPVSTMAPERLKKM-XIXRPRMCSA-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
GLL C1 S1 1
GLL O1 S1 1
GLL N1 S1 1
GLL N2 S1 1
GLL C2 S1 1
GLL C3 S1 1
GLL "N1'" S1 1
GLL "N2'" S1 1
GLL "C1'" S1 1
GLL "O1'" S1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id GLL
_pdbe_chem_comp_rdkit_properties.exactmw 142.049
_pdbe_chem_comp_rdkit_properties.amw 142.118
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 6
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 4
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 0
_pdbe_chem_comp_rdkit_properties.NumHBD 4
_pdbe_chem_comp_rdkit_properties.NumHBA 2
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 10
_pdbe_chem_comp_rdkit_properties.NumAtoms 16
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 6
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 4
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.500
_pdbe_chem_comp_rdkit_properties.NumRings 2
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 0
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 2
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 2
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 2
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 2
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 2
_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 65.007
_pdbe_chem_comp_rdkit_properties.tpsa 82.260
_pdbe_chem_comp_rdkit_properties.CrippenClogP -1.736
_pdbe_chem_comp_rdkit_properties.CrippenMR 30.911
_pdbe_chem_comp_rdkit_properties.chi0v 4.605
_pdbe_chem_comp_rdkit_properties.chi1v 2.447
_pdbe_chem_comp_rdkit_properties.chi2v 1.006
_pdbe_chem_comp_rdkit_properties.chi3v 1.006
_pdbe_chem_comp_rdkit_properties.chi4v 0.662
_pdbe_chem_comp_rdkit_properties.chi0n 10.605
_pdbe_chem_comp_rdkit_properties.chi1n 5.236
_pdbe_chem_comp_rdkit_properties.chi2n 1.006
_pdbe_chem_comp_rdkit_properties.chi3n 1.006
_pdbe_chem_comp_rdkit_properties.chi4n 0.662
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.460
_pdbe_chem_comp_rdkit_properties.kappa1 2.010
_pdbe_chem_comp_rdkit_properties.kappa2 1.525
_pdbe_chem_comp_rdkit_properties.kappa3 0.584
_pdbe_chem_comp_rdkit_properties.Phi 0.307
#
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
GLL UniChem DrugBank DB03533
GLL UniChem PDBe GLL
GLL UniChem ChEBI 37083
GLL UniChem fdasrs U9H2W4OS13
GLL UniChem 'Probes And Drugs' PD059716
GLL UniChem Nikkaji J1.042.644H
GLL UniChem SureChEMBL SCHEMBL36250
#
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
GLL C1 1.768 0.667 0.338 ETKDGv3 1
GLL O1 2.755 1.242 0.868 ETKDGv3 2
GLL N1 0.896 1.301 -0.571 ETKDGv3 3
GLL N2 1.417 -0.674 0.598 ETKDGv3 4
GLL C2 -0.122 0.333 -0.960 ETKDGv3 5
GLL C3 0.225 -0.982 -0.181 ETKDGv3 6
GLL "N1'" -1.429 0.748 -0.468 ETKDGv3 7
GLL "N2'" -0.908 -1.226 0.702 ETKDGv3 8
GLL "C1'" -1.844 -0.191 0.499 ETKDGv3 9
GLL "O1'" -2.935 -0.111 1.122 ETKDGv3 10
GLL HN1 0.958 2.292 -0.892 ETKDGv3 11
GLL HN2 1.912 -1.323 1.249 ETKDGv3 12
GLL H2 -0.135 0.183 -2.060 ETKDGv3 13
GLL H3 0.400 -1.843 -0.860 ETKDGv3 14
GLL "HN1'" -1.956 1.600 -0.763 ETKDGv3 15
GLL "HN2'" -1.002 -2.016 1.379 ETKDGv3 16
#