data_GBM
#
_chem_comp.id GBM
_chem_comp.name 5-chloro-N-(2-{4-[(cyclohexylcarbamoyl)sulfamoyl]phenyl}ethyl)-2-methoxybenzamide
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C23 H28 Cl N3 O5 S"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms "Glibenclamide; Glyburide"
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2015-04-03
_chem_comp.pdbx_modified_date 2021-03-13
_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 494.004
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code GBM
_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 4YVP
_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
GBM O3 O1 O 0 1 N N N N N N -52.101 -6.447 42.294 4.821 0.201 -0.816 O3 GBM 1
GBM O4 O2 O 0 1 N N N N N N -49.747 -4.996 45.457 3.931 3.694 1.270 O4 GBM 2
GBM O5 O3 O 0 1 N N N N N N -48.017 -4.488 43.763 4.281 2.836 -1.051 O5 GBM 3
GBM O6 O4 O 0 1 N N N N N N -52.991 1.840 40.420 -4.766 1.761 -0.668 O6 GBM 4
GBM CL1 CL1 CL 0 0 N N N N N N -54.301 5.888 37.473 -7.474 -3.681 0.918 CL1 GBM 5
GBM S2 S1 S 0 1 N N N N N N -49.395 -4.554 44.143 4.002 2.633 0.327 S2 GBM 6
GBM O7 O5 O 0 1 N N N N N N -56.204 3.422 42.430 -7.236 1.838 -1.067 O7 GBM 7
GBM N8 N1 N 0 1 N N N N N N -52.096 -5.259 44.267 6.363 -0.400 0.666 N8 GBM 8
GBM N9 N2 N 0 1 N N N N N N -50.147 -5.538 43.065 5.155 1.585 0.889 N9 GBM 9
GBM N10 N3 N 0 1 N N N N N N -54.220 1.769 42.296 -3.694 -0.006 0.145 N10 GBM 10
GBM C11 C1 C 0 1 N N N N N N -53.508 -5.354 44.646 6.656 -1.630 -0.073 C11 GBM 11
GBM C12 C2 C 0 1 N N N N N N -54.138 -6.676 44.236 7.233 -2.675 0.885 C12 GBM 12
GBM C13 C3 C 0 1 N N N N N N -54.295 -4.183 44.092 7.674 -1.333 -1.176 C13 GBM 13
GBM C14 C4 C 0 1 N N N N N N -55.616 -6.502 43.892 7.539 -3.960 0.113 C14 GBM 14
GBM C15 C5 C 0 1 N N N N N N -55.698 -4.133 44.686 7.980 -2.618 -1.947 C15 GBM 15
GBM C16 C6 C 0 1 N N N N N N -56.287 -5.525 44.837 8.556 -3.663 -0.990 C16 GBM 16
GBM C17 C7 C 0 1 N N N N N N -51.507 -5.813 43.162 5.424 0.453 0.209 C17 GBM 17
GBM C18 C8 C 0 1 Y N N N N N -50.121 -2.971 43.884 2.454 1.796 0.404 C18 GBM 18
GBM C19 C9 C 0 1 Y N N N N N -51.460 -0.566 43.498 0.024 0.481 0.524 C19 GBM 19
GBM C20 C10 C 0 1 N N N N N N -52.200 0.736 43.286 -1.300 -0.235 0.589 C20 GBM 20
GBM C21 C11 C 0 1 Y N N N N N -50.510 -2.597 42.610 2.016 1.051 -0.676 C21 GBM 21
GBM C22 C12 C 0 1 Y N N N N N -50.377 -2.146 44.966 1.679 1.878 1.546 C22 GBM 22
GBM C23 C13 C 0 1 Y N N N N N -51.181 -1.401 42.429 0.802 0.394 -0.616 C23 GBM 23
GBM C24 C14 C 0 1 Y N N N N N -51.048 -0.952 44.764 0.464 1.221 1.606 C24 GBM 24
GBM C25 C15 C 0 1 N N N N N N -53.617 0.534 42.781 -2.407 0.691 0.081 C25 GBM 25
GBM C26 C16 C 0 1 N N N N N N -53.896 2.298 41.113 -4.819 0.619 -0.255 C26 GBM 26
GBM C27 C17 C 0 1 Y N N N N N -54.691 3.475 40.637 -6.115 -0.083 -0.190 C27 GBM 27
GBM C28 C18 C 0 1 Y N N N N N -55.814 4.025 41.266 -7.288 0.563 -0.605 C28 GBM 28
GBM C29 C19 C 0 1 Y N N N N N -54.245 4.056 39.449 -6.180 -1.397 0.279 C29 GBM 29
GBM C30 C20 C 0 1 Y N N N N N -56.469 5.118 40.721 -8.501 -0.106 -0.541 C30 GBM 30
GBM C31 C21 C 0 1 Y N N N N N -54.904 5.150 38.930 -7.394 -2.048 0.336 C31 GBM 31
GBM C32 C22 C 0 1 Y N N N N N -56.011 5.685 39.546 -8.552 -1.403 -0.071 C32 GBM 32
GBM C33 C23 C 0 1 N N N N N N -57.339 3.966 43.101 -8.471 2.432 -1.472 C33 GBM 33
GBM H1 H1 H 0 1 N N N N N N -51.502 -4.736 44.878 6.844 -0.199 1.484 H1 GBM 34
GBM H2 H2 H 0 1 N N N N N N -49.616 -5.948 42.323 5.636 1.786 1.707 H2 GBM 35
GBM H3 H3 H 0 1 N N N N N N -54.897 2.235 42.866 -3.736 -0.917 0.475 H3 GBM 36
GBM H4 H4 H 0 1 N N N N N N -53.566 -5.294 45.743 5.738 -2.014 -0.519 H4 GBM 37
GBM H5 H5 H 0 1 N N N N N N -54.045 -7.391 45.067 8.150 -2.292 1.331 H5 GBM 38
GBM H6 H6 H 0 1 N N N N N N -53.608 -7.068 43.355 6.507 -2.887 1.671 H6 GBM 39
GBM H7 H7 H 0 1 N N N N N N -53.768 -3.249 44.336 7.263 -0.589 -1.858 H7 GBM 40
GBM H8 H8 H 0 1 N N N N N N -54.371 -4.286 43.000 8.591 -0.949 -0.730 H8 GBM 41
GBM H9 H9 H 0 1 N N N N N N -55.703 -6.123 42.863 7.950 -4.704 0.796 H9 GBM 42
GBM H10 H10 H 0 1 N N N N N N -56.119 -7.477 43.967 6.621 -4.344 -0.333 H10 GBM 43
GBM H11 H11 H 0 1 N N N N N N -55.651 -3.655 45.676 7.062 -3.001 -2.393 H11 GBM 44
GBM H12 H12 H 0 1 N N N N N N -56.346 -3.540 44.024 8.705 -2.406 -2.733 H12 GBM 45
GBM H13 H13 H 0 1 N N N N N N -57.363 -5.487 44.611 9.474 -3.279 -0.544 H13 GBM 46
GBM H14 H14 H 0 1 N N N N N N -56.141 -5.867 45.872 8.775 -4.578 -1.539 H14 GBM 47
GBM H15 H15 H 0 1 N N N N N N -51.647 1.338 42.550 -1.260 -1.130 -0.033 H15 GBM 48
GBM H16 H16 H 0 1 N N N N N N -52.242 1.276 44.244 -1.508 -0.519 1.621 H16 GBM 49
GBM H17 H17 H 0 1 N N N N N N -50.292 -3.233 41.765 2.624 0.983 -1.566 H17 GBM 50
GBM H18 H18 H 0 1 N N N N N N -50.057 -2.431 45.957 2.022 2.456 2.391 H18 GBM 51
GBM H19 H19 H 0 1 N N N N N N -51.493 -1.113 41.436 0.460 -0.187 -1.459 H19 GBM 52
GBM H20 H20 H 0 1 N N N N N N -51.254 -0.310 45.608 -0.143 1.289 2.496 H20 GBM 53
GBM H21 H21 H 0 1 N N N N N N -54.232 0.141 43.604 -2.198 0.975 -0.950 H21 GBM 54
GBM H22 H22 H 0 1 N N N N N N -53.597 -0.195 41.958 -2.447 1.585 0.703 H22 GBM 55
GBM H23 H23 H 0 1 N N N N N N -53.385 3.649 38.937 -5.280 -1.903 0.596 H23 GBM 56
GBM H24 H24 H 0 1 N N N N N N -57.338 5.527 41.215 -9.407 0.389 -0.859 H24 GBM 57
GBM H25 H25 H 0 1 N N N N N N -56.516 6.538 39.117 -9.500 -1.919 -0.023 H25 GBM 58
GBM H26 H26 H 0 1 N N N N N N -57.538 3.387 44.015 -8.909 1.845 -2.279 H26 GBM 59
GBM H27 H27 H 0 1 N N N N N N -57.140 5.014 43.367 -9.158 2.454 -0.625 H27 GBM 60
GBM H28 H28 H 0 1 N N N N N N -58.215 3.916 42.438 -8.289 3.449 -1.819 H28 GBM 61
#
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
GBM CL1 C31 SING N N 1
GBM C31 C29 DOUB Y N 2
GBM C31 C32 SING Y N 3
GBM C29 C27 SING Y N 4
GBM C32 C30 DOUB Y N 5
GBM O6 C26 DOUB N N 6
GBM C27 C26 SING N N 7
GBM C27 C28 DOUB Y N 8
GBM C30 C28 SING Y N 9
GBM C26 N10 SING N N 10
GBM C28 O7 SING N N 11
GBM O3 C17 DOUB N N 12
GBM N10 C25 SING N N 13
GBM C23 C21 DOUB Y N 14
GBM C23 C19 SING Y N 15
GBM O7 C33 SING N N 16
GBM C21 C18 SING Y N 17
GBM C25 C20 SING N N 18
GBM N9 C17 SING N N 19
GBM N9 S2 SING N N 20
GBM C17 N8 SING N N 21
GBM C20 C19 SING N N 22
GBM C19 C24 DOUB Y N 23
GBM O5 S2 DOUB N N 24
GBM C18 S2 SING N N 25
GBM C18 C22 DOUB Y N 26
GBM C14 C12 SING N N 27
GBM C14 C16 SING N N 28
GBM C13 C11 SING N N 29
GBM C13 C15 SING N N 30
GBM S2 O4 DOUB N N 31
GBM C12 C11 SING N N 32
GBM N8 C11 SING N N 33
GBM C15 C16 SING N N 34
GBM C24 C22 SING Y N 35
GBM N8 H1 SING N N 36
GBM N9 H2 SING N N 37
GBM N10 H3 SING N N 38
GBM C11 H4 SING N N 39
GBM C12 H5 SING N N 40
GBM C12 H6 SING N N 41
GBM C13 H7 SING N N 42
GBM C13 H8 SING N N 43
GBM C14 H9 SING N N 44
GBM C14 H10 SING N N 45
GBM C15 H11 SING N N 46
GBM C15 H12 SING N N 47
GBM C16 H13 SING N N 48
GBM C16 H14 SING N N 49
GBM C20 H15 SING N N 50
GBM C20 H16 SING N N 51
GBM C21 H17 SING N N 52
GBM C22 H18 SING N N 53
GBM C23 H19 SING N N 54
GBM C24 H20 SING N N 55
GBM C25 H21 SING N N 56
GBM C25 H22 SING N N 57
GBM C29 H23 SING N N 58
GBM C30 H24 SING N N 59
GBM C32 H25 SING N N 60
GBM C33 H26 SING N N 61
GBM C33 H27 SING N N 62
GBM C33 H28 SING N N 63
#
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
GBM SMILES ACDLabs 12.01 O=C(NC1CCCCC1)NS(=O)(=O)c3ccc(CCNC(=O)c2c(OC)ccc(Cl)c2)cc3
GBM InChI InChI 1.03 InChI=1S/C23H28ClN3O5S/c1-32-21-12-9-17(24)15-20(21)22(28)25-14-13-16-7-10-19(11-8-16)33(30,31)27-23(29)26-18-5-3-2-4-6-18/h7-12,15,18H,2-6,13-14H2,1H3,(H,25,28)(H2,26,27,29)
GBM InChIKey InChI 1.03 ZNNLBTZKUZBEKO-UHFFFAOYSA-N
GBM SMILES_CANONICAL CACTVS 3.385 COc1ccc(Cl)cc1C(=O)NCCc2ccc(cc2)[S](=O)(=O)NC(=O)NC3CCCCC3
GBM SMILES CACTVS 3.385 COc1ccc(Cl)cc1C(=O)NCCc2ccc(cc2)[S](=O)(=O)NC(=O)NC3CCCCC3
GBM SMILES_CANONICAL "OpenEye OEToolkits" 1.9.2 COc1ccc(cc1C(=O)NCCc2ccc(cc2)S(=O)(=O)NC(=O)NC3CCCCC3)Cl
GBM SMILES "OpenEye OEToolkits" 1.9.2 COc1ccc(cc1C(=O)NCCc2ccc(cc2)S(=O)(=O)NC(=O)NC3CCCCC3)Cl
#
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
GBM "SYSTEMATIC NAME" ACDLabs 12.01 5-chloro-N-(2-{4-[(cyclohexylcarbamoyl)sulfamoyl]phenyl}ethyl)-2-methoxybenzamide
GBM "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.9.2 5-chloranyl-N-[2-[4-(cyclohexylcarbamoylsulfamoyl)phenyl]ethyl]-2-methoxy-benzamide
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
GBM 'Create component' 2015-04-03 PDBJ
GBM 'Initial release' 2015-11-25 RCSB
GBM 'Modify synonyms' 2016-03-28 RCSB
GBM 'Modify synonyms' 2021-03-13 RCSB
#
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 GBM Glibenclamide PDB ?
2 GBM Glyburide PDB ?
#
_pdbe_chem_comp_drugbank_details.comp_id GBM
_pdbe_chem_comp_drugbank_details.drugbank_id DB01016
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name Glyburide
_pdbe_chem_comp_drugbank_details.description
'Glyburide is a second generation sulfonylurea used to treat patients with diabetes mellitus type II.[L8123] It is typically given to patients who cannot be managed with the standard first line therapy, [metformin].[L8123] Glyburide stimulates insulin secretion through the closure of ATP-sensitive potassium channels on beta cells, raising intracellular potassium and calcium ion concentrations.[A183617]  Glyburide was granted FDA approval on 1 May 1984.[L8117] A formulation with metformin was granted FDA approval on on 31 July 2000.[L8120]'
_pdbe_chem_comp_drugbank_details.cas_number 10238-21-8
_pdbe_chem_comp_drugbank_details.mechanism_of_action
'Glyburide belongs to a class of drugs known as sulfonylureas.[A183617]  These drugs act by closing ATP-sensitive potassium channels on pancreatic beta cells.[A183617] The ATP-sensitive potassium channels on beta cells are known as sulfonylurea receptor 1 (SUR1).[A183617]  Under low glucose concentrations, SUR1 remains open, allowing for potassium ion efflux to create a -70mV membrane potential.[A183617]  Normally SUR1 closes in response to high glucose concentrations, the membrane potential of the cells becomes less negative, the cell depolarizes, voltage gated calcium channels open, calcium ions enter the cell, and the increased intracellular calcium concentration stimulates the release of insulin containing granules.[A183617]  Glyburide bypasses this process by forcing SUR1 closed and stimulating increased insulin secretion.[A183617]'
#
loop_
_pdbe_chem_comp_synonyms.comp_id
_pdbe_chem_comp_synonyms.name
_pdbe_chem_comp_synonyms.provenance
_pdbe_chem_comp_synonyms.type
GBM Glibenclamide wwPDB ?
GBM Glyburide wwPDB ?
GBM 1-((p-(2-(5-chloro-o-anisamido)ethyl)phenyl)sulfonyl)-3-cyclohexylurea DrugBank ?
GBM 1-(p-(2-(5-chloro-2-methoxybenzamido)ethyl)benzenesulfonyl)-3-cyclohexylurea DrugBank ?
GBM 5-chloro-N-(2-(4-((((cyclohexylamino)carbonyl)amino)sulfonyl)phenyl)ethyl)-2-methoxybenzamide DrugBank ?
GBM Glibenclamide DrugBank ?
GBM Glibenclamidum DrugBank ?
GBM Glyburide DrugBank ?
GBM Daonil DrugBank 'International brand'
GBM Delmide DrugBank 'International brand'
GBM Novo-Glyburide DrugBank 'International brand'
GBM Semi-Daonil DrugBank 'International brand'
#
_pdbe_chem_comp_drugbank_classification.comp_id GBM
_pdbe_chem_comp_drugbank_classification.drugbank_id DB01016
_pdbe_chem_comp_drugbank_classification.parent Benzenesulfonamides
_pdbe_chem_comp_drugbank_classification.kingdom 'Organic compounds'
_pdbe_chem_comp_drugbank_classification.class 'Benzene and substituted derivatives'
_pdbe_chem_comp_drugbank_classification.superclass Benzenoids
_pdbe_chem_comp_drugbank_classification.description
'This compound belongs to the class of organic compounds known as benzenesulfonamides. These are organic compounds containing a sulfonamide group that is S-linked to a benzene ring.'
#
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
GBM DB01016 'ATP-binding cassette sub-family C member 8' Humans Q09428 yes 1
GBM DB01016 'ATP-sensitive inward rectifier potassium channel 11' Humans Q14654 yes 2
GBM DB01016 'ATP-binding cassette sub-family C member 8' Humans Q09428 unknown 3
GBM DB01016 'ATP-binding cassette sub-family C member 9' Humans O60706 unknown 4
GBM DB01016 'Bile salt export pump' Humans O95342 unknown 5
GBM DB01016 'Phospholipid-transporting ATPase ABCA1' Humans O95477 unknown 6
GBM DB01016 'ATP-sensitive inward rectifier potassium channel 11' Humans Q14654 unknown 7
GBM DB01016 'ATP-sensitive inward rectifier potassium channel 8' Humans Q15842 unknown 8
GBM DB01016 'Carnitine O-palmitoyltransferase 1, liver isoform' Humans P50416 unknown 9
GBM DB01016 'Cystic fibrosis transmembrane conductance regulator' Humans P13569 unknown 10
GBM DB01016 'Transient receptor potential cation channel subfamily M member 4' Humans Q8TD43 unknown 11
#
loop_
_software.name
_software.version
_software.description
rdkit 2025.03.3 'Core functionality.'
pdbeccdutils 1.0.0 '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
GBM O3 O 12.093 4.875 1
GBM O4 O 7.995 3.375 2
GBM O5 O 10.995 3.375 3
GBM O6 O 5.598 -4.875 4
GBM CL1 Cl 9.495 -10.125 5
GBM S2 S 9.495 3.375 6
GBM O7 O 4.299 -7.125 7
GBM N8 N 10.794 7.125 8
GBM N9 N 9.495 4.875 9
GBM N10 N 8.196 -4.875 10
GBM C11 C 12.093 7.875 11
GBM C12 C 12.093 9.375 12
GBM C13 C 13.392 7.125 13
GBM C14 C 13.392 10.125 14
GBM C15 C 14.691 7.875 15
GBM C16 C 14.691 9.375 16
GBM C17 C 10.794 5.625 17
GBM C18 C 9.495 1.875 18
GBM C19 C 9.495 -1.125 19
GBM C20 C 9.495 -2.625 20
GBM C21 C 10.794 1.125 21
GBM C22 C 8.196 1.125 22
GBM C23 C 10.794 -0.375 23
GBM C24 C 8.196 -0.375 24
GBM C25 C 8.196 -3.375 25
GBM C26 C 6.897 -5.625 26
GBM C27 C 6.897 -7.125 27
GBM C28 C 5.598 -7.875 28
GBM C29 C 8.196 -7.875 29
GBM C30 C 5.598 -9.375 30
GBM C31 C 8.196 -9.375 31
GBM C32 C 6.897 -10.125 32
GBM C33 C 3.000 -7.875 33
#
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
GBM CL1 C31 SINGLE NONE 1
GBM C31 C29 DOUBLE NONE 2
GBM C31 C32 SINGLE NONE 3
GBM C29 C27 SINGLE NONE 4
GBM C32 C30 DOUBLE NONE 5
GBM O6 C26 DOUBLE NONE 6
GBM C27 C26 SINGLE NONE 7
GBM C27 C28 DOUBLE NONE 8
GBM C30 C28 SINGLE NONE 9
GBM C26 N10 SINGLE NONE 10
GBM C28 O7 SINGLE NONE 11
GBM O3 C17 DOUBLE NONE 12
GBM N10 C25 SINGLE NONE 13
GBM C23 C21 DOUBLE NONE 14
GBM C23 C19 SINGLE NONE 15
GBM O7 C33 SINGLE NONE 16
GBM C21 C18 SINGLE NONE 17
GBM C25 C20 SINGLE NONE 18
GBM N9 C17 SINGLE NONE 19
GBM N9 S2 SINGLE NONE 20
GBM C17 N8 SINGLE NONE 21
GBM C20 C19 SINGLE NONE 22
GBM C19 C24 DOUBLE NONE 23
GBM O5 S2 DOUBLE NONE 24
GBM C18 S2 SINGLE NONE 25
GBM C18 C22 DOUBLE NONE 26
GBM C14 C12 SINGLE NONE 27
GBM C14 C16 SINGLE NONE 28
GBM C13 C11 SINGLE NONE 29
GBM C13 C15 SINGLE NONE 30
GBM S2 O4 DOUBLE NONE 31
GBM C12 C11 SINGLE NONE 32
GBM N8 C11 SINGLE NONE 33
GBM C15 C16 SINGLE NONE 34
GBM C24 C22 SINGLE NONE 35
#
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
GBM MurckoScaffold S1 scaffold O=C(NC1CCCCC1)NS(=O)(=O)c1ccc(CCNC(=O)c2ccccc2)cc1 InChI=1S/C22H27N3O4S/c26-21(18-7-3-1-4-8-18)23-16-15-17-11-13-20(14-12-17)30(28,29)25-22(27)24-19-9-5-2-6-10-19/h1,3-4,7-8,11-14,19H,2,5-6,9-10,15-16H2,(H,23,26)(H2,24,25,27) WLLZOYXQWZDTCW-UHFFFAOYSA-N
GBM amide F1 fragment CC(N)=O InChI=1S/C2H5NO/c1-2(3)4/h1H3,(H2,3,4) DLFVBJFMPXGRIB-UHFFFAOYSA-N
GBM cyclohexane F2 fragment C1CCCCC1 InChI=1S/C6H12/c1-2-4-6-5-3-1/h1-6H2 XDTMQSROBMDMFD-UHFFFAOYSA-N
GBM phenyl F3 fragment c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-UHFFFAOYSA-N
GBM Z2856434770 F4 fragment CNCc1cccc(Cl)c1 InChI=1S/C8H10ClN/c1-10-6-7-3-2-4-8(9)5-7/h2-5,10H,6H2,1H3 ZPNLAQVYPIAHTO-UHFFFAOYSA-N
GBM Z30857828 F5 fragment CC(=O)NCCc1ccc(S(N)(=O)=O)cc1 InChI=1S/C10H14N2O3S/c1-8(13)12-7-6-9-2-4-10(5-3-9)16(11,14)15/h2-5H,6-7H2,1H3,(H,12,13)(H2,11,14,15) IIMGUEXQORZTID-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
GBM O3 S1 1
GBM O4 S1 1
GBM O5 S1 1
GBM O6 S1 1
GBM S2 S1 1
GBM N8 S1 1
GBM N9 S1 1
GBM N10 S1 1
GBM C11 S1 1
GBM C12 S1 1
GBM C13 S1 1
GBM C14 S1 1
GBM C15 S1 1
GBM C16 S1 1
GBM C17 S1 1
GBM C18 S1 1
GBM C19 S1 1
GBM C20 S1 1
GBM C21 S1 1
GBM C22 S1 1
GBM C23 S1 1
GBM C24 S1 1
GBM C25 S1 1
GBM C26 S1 1
GBM C27 S1 1
GBM C28 S1 1
GBM C29 S1 1
GBM C30 S1 1
GBM C31 S1 1
GBM C32 S1 1
GBM N10 F1 1
GBM C26 F1 1
GBM O6 F1 1
GBM C27 F1 1
GBM C11 F2 1
GBM C13 F2 1
GBM C15 F2 1
GBM C16 F2 1
GBM C14 F2 1
GBM C12 F2 1
GBM C18 F3 1
GBM C21 F3 1
GBM C23 F3 1
GBM C19 F3 1
GBM C24 F3 1
GBM C22 F3 1
GBM C27 F3 2
GBM C29 F3 2
GBM C31 F3 2
GBM C32 F3 2
GBM C30 F3 2
GBM C28 F3 2
GBM C25 F4 1
GBM N10 F4 1
GBM C26 F4 1
GBM C27 F4 1
GBM C28 F4 1
GBM C30 F4 1
GBM C32 F4 1
GBM C31 F4 1
GBM CL1 F4 1
GBM C29 F4 1
GBM C27 F5 1
GBM C26 F5 1
GBM O6 F5 1
GBM N10 F5 1
GBM C25 F5 1
GBM C20 F5 1
GBM C19 F5 1
GBM C23 F5 1
GBM C21 F5 1
GBM C18 F5 1
GBM C22 F5 1
GBM C24 F5 1
GBM S2 F5 1
GBM O5 F5 1
GBM O4 F5 1
GBM N9 F5 1
#
_pdbe_chem_comp_rdkit_properties.comp_id GBM
_pdbe_chem_comp_rdkit_properties.exactmw 493.144
_pdbe_chem_comp_rdkit_properties.amw 494.013
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 8
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 3
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 9
_pdbe_chem_comp_rdkit_properties.NumHBD 3
_pdbe_chem_comp_rdkit_properties.NumHBA 5
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 33
_pdbe_chem_comp_rdkit_properties.NumAtoms 61
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 10
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 3
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.391
_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 0
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 0
_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 238.161
_pdbe_chem_comp_rdkit_properties.tpsa 113.600
_pdbe_chem_comp_rdkit_properties.CrippenClogP 2.962
_pdbe_chem_comp_rdkit_properties.CrippenMR 125.637
_pdbe_chem_comp_rdkit_properties.chi0v 17.242
_pdbe_chem_comp_rdkit_properties.chi1v 9.912
_pdbe_chem_comp_rdkit_properties.chi2v 4.460
_pdbe_chem_comp_rdkit_properties.chi3v 4.460
_pdbe_chem_comp_rdkit_properties.chi4v 2.685
_pdbe_chem_comp_rdkit_properties.chi0n 43.669
_pdbe_chem_comp_rdkit_properties.chi1n 21.935
_pdbe_chem_comp_rdkit_properties.chi2n 3.154
_pdbe_chem_comp_rdkit_properties.chi3n 3.154
_pdbe_chem_comp_rdkit_properties.chi4n 1.846
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -2.780
_pdbe_chem_comp_rdkit_properties.kappa1 7.115
_pdbe_chem_comp_rdkit_properties.kappa2 11.380
_pdbe_chem_comp_rdkit_properties.kappa3 7.100
_pdbe_chem_comp_rdkit_properties.Phi 2.454
#
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
GBM UniChem DrugBank DB01016
GBM UniChem 'Guide to Pharmacology' 2414
GBM UniChem 'KEGG LIGAND' C07022
GBM UniChem ChEBI 5441
GBM UniChem NIH SAM002564212
GBM UniChem ZINC ZINC000000537805
GBM UniChem eMolecules 27520402
GBM UniChem atlas glibenclamide
GBM UniChem fdasrs SX6K58TVWC
GBM UniChem SureChEMBL SCHEMBL22009
GBM UniChem PharmGKB PA449782
GBM UniChem HMDB HMDB0015151
GBM UniChem Selleck Glyburide(Diabeta)
GBM UniChem PubChem 3488
GBM UniChem Nikkaji J3.430D
GBM UniChem BindingDb 50012957
GBM UniChem 'EPA CompTox Dashboard' DTXSID0037237
GBM UniChem DrugCentral 1314
GBM UniChem BRENDA 14374
GBM UniChem BRENDA 206663
GBM UniChem BRENDA 232858
GBM UniChem ChemicalBook CB1737679
GBM UniChem DailyMed GLYBURIDE
GBM UniChem ClinicalTrials CIRARA
GBM UniChem ClinicalTrials DIABETA
GBM UniChem ClinicalTrials GLIBENCLAMIDE
GBM UniChem ClinicalTrials GLYBURIDE
GBM UniChem ClinicalTrials GLYNASE
GBM UniChem ClinicalTrials 'HB 419'
GBM UniChem ClinicalTrials HB-419
GBM UniChem ClinicalTrials MICRONASE
GBM UniChem rxnorm GLYBURIDE
GBM UniChem rxnorm GLYNASE
GBM UniChem MedChemExpress HY-15206
GBM UniChem 'Probes And Drugs' PD000061
GBM UniChem CCDC DUNXAL
GBM UniChem ACTor 10238-21-8
GBM UniChem eMolecules 538570
GBM UniChem 'PubChem TPHARMA' 14835352
GBM UniChem Mcule MCULE-2351642942
GBM UniChem LINCS LSM-2811
#
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
GBM O3 4.073 -0.685 1.186 ETKDGv3 1
GBM O4 3.335 -2.702 3.455 ETKDGv3 2
GBM O5 2.158 -4.528 2.323 ETKDGv3 3
GBM O6 -4.285 0.704 -1.278 ETKDGv3 4
GBM CL1 -7.377 4.908 -2.714 ETKDGv3 5
GBM S2 2.615 -3.102 2.197 ETKDGv3 6
GBM O7 -7.525 0.104 0.863 ETKDGv3 7
GBM N8 5.176 -1.647 -0.638 ETKDGv3 8
GBM N9 3.705 -2.966 0.858 ETKDGv3 9
GBM N10 -4.700 0.403 1.002 ETKDGv3 10
GBM C11 5.833 -0.401 -1.047 ETKDGv3 11
GBM C12 6.321 -0.509 -2.504 ETKDGv3 12
GBM C13 7.017 -0.098 -0.108 ETKDGv3 13
GBM C14 7.054 0.768 -2.937 ETKDGv3 14
GBM C15 7.753 1.176 -0.542 ETKDGv3 15
GBM C16 8.227 1.072 -1.997 ETKDGv3 16
GBM C17 4.310 -1.718 0.503 ETKDGv3 17
GBM C18 1.213 -2.070 1.935 ETKDGv3 18
GBM C19 -1.036 -0.408 1.493 ETKDGv3 19
GBM C20 -2.254 0.441 1.248 ETKDGv3 20
GBM C21 0.726 -1.826 0.558 ETKDGv3 21
GBM C22 0.570 -1.514 2.974 ETKDGv3 22
GBM C23 -0.337 -1.041 0.349 ETKDGv3 23
GBM C24 -0.607 -0.651 2.744 ETKDGv3 24
GBM C25 -3.518 -0.424 1.231 ETKDGv3 25
GBM C26 -5.063 0.885 -0.302 ETKDGv3 26
GBM C27 -6.322 1.632 -0.516 ETKDGv3 27
GBM C28 -7.485 1.259 0.066 ETKDGv3 28
GBM C29 -6.301 2.806 -1.426 ETKDGv3 29
GBM C30 -8.713 2.068 -0.179 ETKDGv3 30
GBM C31 -7.413 3.516 -1.646 ETKDGv3 31
GBM C32 -8.675 3.132 -0.988 ETKDGv3 32
GBM C33 -8.693 -0.379 1.517 ETKDGv3 33
GBM H1 5.306 -2.511 -1.212 ETKDGv3 34
GBM H2 3.907 -3.819 0.291 ETKDGv3 35
GBM H3 -5.284 0.662 1.829 ETKDGv3 36
GBM H4 5.096 0.432 -0.991 ETKDGv3 37
GBM H5 5.450 -0.671 -3.175 ETKDGv3 38
GBM H6 7.006 -1.379 -2.614 ETKDGv3 39
GBM H7 6.649 0.040 0.931 ETKDGv3 40
GBM H8 7.727 -0.954 -0.108 ETKDGv3 41
GBM H9 6.344 1.624 -2.939 ETKDGv3 42
GBM H10 7.437 0.638 -3.972 ETKDGv3 43
GBM H11 7.078 2.054 -0.431 ETKDGv3 44
GBM H12 8.632 1.335 0.119 ETKDGv3 45
GBM H13 8.993 0.270 -2.084 ETKDGv3 46
GBM H14 8.699 2.031 -2.299 ETKDGv3 47
GBM H15 -2.144 0.970 0.278 ETKDGv3 48
GBM H16 -2.348 1.218 2.038 ETKDGv3 49
GBM H17 1.227 -2.286 -0.284 ETKDGv3 50
GBM H18 0.902 -1.692 3.989 ETKDGv3 51
GBM H19 -0.687 -0.872 -0.662 ETKDGv3 52
GBM H20 -1.117 -0.221 3.597 ETKDGv3 53
GBM H21 -3.446 -1.206 0.443 ETKDGv3 54
GBM H22 -3.621 -0.938 2.212 ETKDGv3 55
GBM H23 -5.375 3.098 -1.907 ETKDGv3 56
GBM H24 -9.652 1.803 0.288 ETKDGv3 57
GBM H25 -9.573 3.711 -1.162 ETKDGv3 58
GBM H26 -8.439 -1.301 2.078 ETKDGv3 59
GBM H27 -9.070 0.381 2.234 ETKDGv3 60
GBM H28 -9.477 -0.622 0.769 ETKDGv3 61
#