data_CCB
#
_chem_comp.id CCB
_chem_comp.name CYCLOBUTYL(CYCLOPENTYL)FORMAMIDE
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C10 H17 N O"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms N-CYCLOPENTYL-N-CYCLOBUTYLFORMAMIDE
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2004-07-26
_chem_comp.pdbx_modified_date 2020-06-17
_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 167.248
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code CCB
_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 1U3T
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site RCSB
#
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
CCB N1 N1 N 0 1 N N N N N N 10.613 -0.522 0.819 -0.538 0.074 0.289 N1 CCB 1
CCB C2 C2 C 0 1 N N N N N N 11.651 -0.607 -0.017 -1.816 0.128 -0.135 C2 CCB 2
CCB O3 O3 O 0 1 N N N N N N 12.306 -1.634 -0.168 -2.724 0.093 0.668 O3 CCB 3
CCB C5 C5 C 0 1 N N N N N N 10.181 -1.654 1.603 0.554 0.005 -0.683 C5 CCB 4
CCB C6 C6 C 0 1 N N N N N N 9.946 0.721 0.894 -0.242 0.085 1.724 C6 CCB 5
CCB C7 C7 C 0 1 N N N N N N 8.957 -2.364 1.135 0.484 1.211 -1.643 C7 CCB 6
CCB C8 C8 C 0 1 N N N N N N 8.549 -3.181 2.347 0.908 0.630 -3.015 C8 CCB 7
CCB C9 C9 C 0 1 N N N N N N 9.174 -2.513 3.559 0.253 -0.773 -3.009 C9 CCB 8
CCB C10 C10 C 0 1 N N N N N N 9.913 -1.312 3.030 0.407 -1.256 -1.552 C10 CCB 9
CCB C20 C20 C 0 1 N N N N N N 9.614 1.694 1.966 0.935 0.998 2.102 C20 CCB 10
CCB C21 C21 C 0 1 N N N N N N 8.793 2.424 0.961 1.366 -0.098 3.090 C21 CCB 11
CCB C22 C22 C 0 1 N N N N N N 8.642 1.121 0.261 0.628 -1.096 2.182 C22 CCB 12
CCB H2 H2 H 0 1 N N N N N N 11.996 0.240 -0.633 -2.032 0.198 -1.191 H2 CCB 13
CCB H5 H5 H 0 1 N N N N N N 11.061 -2.328 1.478 1.513 -0.006 -0.167 H5 CCB 14
CCB H6 H6 H 0 1 N N N N N N 10.979 0.652 0.480 -1.129 0.238 2.338 H6 CCB 15
CCB H71 1H7 H 0 1 N N N N N N 9.092 -2.956 0.200 -0.532 1.601 -1.692 H71 CCB 16
CCB H72 2H7 H 0 1 N N N N N N 8.158 -1.698 0.733 1.178 1.990 -1.328 H72 CCB 17
CCB H81 1H8 H 0 1 N N N N N N 8.811 -4.261 2.257 1.993 0.550 -3.081 H81 CCB 18
CCB H82 2H8 H 0 1 N N N N N N 7.445 -3.311 2.438 0.514 1.237 -3.830 H82 CCB 19
CCB H91 1H9 H 0 1 N N N N N N 9.811 -3.197 4.166 0.779 -1.442 -3.690 H91 CCB 20
CCB H92 2H9 H 0 1 N N N N N N 8.440 -2.267 4.361 -0.800 -0.703 -3.278 H92 CCB 21
CCB H101 1H10 H 0 0 N N N N N N 9.380 -0.344 3.177 1.296 -1.880 -1.457 H101 CCB 22
CCB H102 2H10 H 0 0 N N N N N N 10.822 -1.039 3.615 -0.476 -1.817 -1.249 H102 CCB 23
CCB H201 1H20 H 0 0 N N N N N N 10.416 2.213 2.540 1.644 1.157 1.289 H201 CCB 24
CCB H202 2H20 H 0 0 N N N N N N 9.174 1.357 2.933 0.630 1.926 2.586 H202 CCB 25
CCB H211 1H21 H 0 0 N N N N N N 9.185 3.325 0.434 0.919 0.004 4.079 H211 CCB 26
CCB H212 2H21 H 0 0 N N N N N N 7.906 3.027 1.264 2.444 -0.254 3.126 H212 CCB 27
CCB H221 1H22 H 0 0 N N N N N N 7.724 0.500 0.383 0.076 -1.859 2.729 H221 CCB 28
CCB H222 2H22 H 0 0 N N N N N N 8.493 1.070 -0.843 1.253 -1.510 1.390 H222 CCB 29
#
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
CCB N1 C2 SING N N 1
CCB N1 C5 SING N N 2
CCB N1 C6 SING N N 3
CCB C2 O3 DOUB N N 4
CCB C2 H2 SING N N 5
CCB C5 C7 SING N N 6
CCB C5 C10 SING N N 7
CCB C5 H5 SING N N 8
CCB C6 C20 SING N N 9
CCB C6 C22 SING N N 10
CCB C6 H6 SING N N 11
CCB C7 C8 SING N N 12
CCB C7 H71 SING N N 13
CCB C7 H72 SING N N 14
CCB C8 C9 SING N N 15
CCB C8 H81 SING N N 16
CCB C8 H82 SING N N 17
CCB C9 C10 SING N N 18
CCB C9 H91 SING N N 19
CCB C9 H92 SING N N 20
CCB C10 H101 SING N N 21
CCB C10 H102 SING N N 22
CCB C20 C21 SING N N 23
CCB C20 H201 SING N N 24
CCB C20 H202 SING N N 25
CCB C21 C22 SING N N 26
CCB C21 H211 SING N N 27
CCB C21 H212 SING N N 28
CCB C22 H221 SING N N 29
CCB C22 H222 SING N N 30
#
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
CCB SMILES ACDLabs 10.04 O=CN(C1CCC1)C2CCCC2
CCB SMILES_CANONICAL CACTVS 3.341 O=CN(C1CCCC1)C2CCC2
CCB SMILES CACTVS 3.341 O=CN(C1CCCC1)C2CCC2
CCB SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 C1CCC(C1)N(C=O)C2CCC2
CCB SMILES "OpenEye OEToolkits" 1.5.0 C1CCC(C1)N(C=O)C2CCC2
CCB InChI InChI 1.03 InChI=1S/C10H17NO/c12-8-11(10-6-3-7-10)9-4-1-2-5-9/h8-10H,1-7H2
CCB InChIKey InChI 1.03 DWGVYBRKKSJLNS-UHFFFAOYSA-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
CCB "SYSTEMATIC NAME" ACDLabs 10.04 N-cyclobutyl-N-cyclopentylformamide
CCB "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 N-cyclobutyl-N-cyclopentyl-methanamide
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
CCB 'Create component' 2004-07-26 RCSB
CCB 'Modify descriptor' 2011-06-04 RCSB
CCB 'Modify synonyms' 2020-06-05 PDBE
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id CCB
_pdbx_chem_comp_synonyms.name N-CYCLOPENTYL-N-CYCLOBUTYLFORMAMIDE
_pdbx_chem_comp_synonyms.provenance ?
_pdbx_chem_comp_synonyms.type ?
#
_pdbe_chem_comp_drugbank_details.comp_id CCB
_pdbe_chem_comp_drugbank_details.drugbank_id DB04065
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name N-Cyclopentyl-N-Cyclobutylformamide
_pdbe_chem_comp_drugbank_details.description ?
_pdbe_chem_comp_drugbank_details.cas_number ?
_pdbe_chem_comp_drugbank_details.mechanism_of_action ?
#
_pdbe_chem_comp_synonyms.comp_id CCB
_pdbe_chem_comp_synonyms.name N-CYCLOPENTYL-N-CYCLOBUTYLFORMAMIDE
_pdbe_chem_comp_synonyms.provenance wwPDB
_pdbe_chem_comp_synonyms.type ?
#
_pdbe_chem_comp_drugbank_classification.comp_id CCB
_pdbe_chem_comp_drugbank_classification.drugbank_id DB04065
_pdbe_chem_comp_drugbank_classification.parent 'Tertiary carboxylic acid amides'
_pdbe_chem_comp_drugbank_classification.kingdom 'Organic compounds'
_pdbe_chem_comp_drugbank_classification.class 'Carboxylic acids and derivatives'
_pdbe_chem_comp_drugbank_classification.superclass 'Organic acids and derivatives'
_pdbe_chem_comp_drugbank_classification.description
'This compound belongs to the class of organic compounds known as tertiary carboxylic acid amides. These are compounds containing an amide derivative of carboxylic acid, with the general structure RN(R1)C(R2)=O (R1-R2 any atom but H).'
#
_pdbe_chem_comp_drugbank_targets.comp_id CCB
_pdbe_chem_comp_drugbank_targets.drugbank_id DB04065
_pdbe_chem_comp_drugbank_targets.name 'Alcohol dehydrogenase 1A'
_pdbe_chem_comp_drugbank_targets.organism Humans
_pdbe_chem_comp_drugbank_targets.uniprot_id P07327
_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
CCB N1 N 5.104 0.779 1
CCB C2 C 3.805 1.529 2
CCB O3 O 3.805 3.029 3
CCB C5 C 5.104 -0.721 4
CCB C6 C 6.404 1.529 5
CCB C7 C 3.891 -1.603 6
CCB C8 C 4.354 -3.029 7
CCB C9 C 5.854 -3.029 8
CCB C10 C 6.318 -1.603 9
CCB C20 C 7.852 1.141 10
CCB C21 C 8.241 2.590 11
CCB C22 C 6.792 2.978 12
#
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
CCB N1 C2 SINGLE NONE 1
CCB N1 C5 SINGLE NONE 2
CCB N1 C6 SINGLE NONE 3
CCB C2 O3 DOUBLE NONE 4
CCB C5 C7 SINGLE NONE 5
CCB C5 C10 SINGLE NONE 6
CCB C6 C20 SINGLE NONE 7
CCB C6 C22 SINGLE NONE 8
CCB C7 C8 SINGLE NONE 9
CCB C8 C9 SINGLE NONE 10
CCB C9 C10 SINGLE NONE 11
CCB C20 C21 SINGLE NONE 12
CCB C21 C22 SINGLE NONE 13
#
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
CCB MurckoScaffold S1 scaffold C1CCC(NC2CCC2)C1 InChI=1S/C9H17N/c1-2-5-8(4-1)10-9-6-3-7-9/h8-10H,1-7H2 UHUUCQADKIMNQD-UHFFFAOYSA-N
CCB cyclobutane F1 fragment C1CCC1 InChI=1S/C4H8/c1-2-4-3-1/h1-4H2 PMPVIKIVABFJJI-UHFFFAOYSA-N
CCB cyclopentane F2 fragment C1CCCC1 InChI=1S/C5H10/c1-2-4-5-3-1/h1-5H2 RGSFGYAAUTVSQA-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
CCB N1 S1 1
CCB C5 S1 1
CCB C6 S1 1
CCB C7 S1 1
CCB C8 S1 1
CCB C9 S1 1
CCB C10 S1 1
CCB C20 S1 1
CCB C21 S1 1
CCB C22 S1 1
CCB C6 F1 1
CCB C20 F1 1
CCB C21 F1 1
CCB C22 F1 1
CCB C5 F2 1
CCB C7 F2 1
CCB C8 F2 1
CCB C9 F2 1
CCB C10 F2 1
#
_pdbe_chem_comp_rdkit_properties.comp_id CCB
_pdbe_chem_comp_rdkit_properties.exactmw 167.131
_pdbe_chem_comp_rdkit_properties.amw 167.252
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 2
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 0
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 2
_pdbe_chem_comp_rdkit_properties.NumHBD 0
_pdbe_chem_comp_rdkit_properties.NumHBA 1
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 12
_pdbe_chem_comp_rdkit_properties.NumAtoms 29
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 2
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 1
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.900
_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 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 97.818
_pdbe_chem_comp_rdkit_properties.tpsa 20.310
_pdbe_chem_comp_rdkit_properties.CrippenClogP 1.940
_pdbe_chem_comp_rdkit_properties.CrippenMR 47.798
_pdbe_chem_comp_rdkit_properties.chi0v 5.855
_pdbe_chem_comp_rdkit_properties.chi1v 3.125
_pdbe_chem_comp_rdkit_properties.chi2v 1.325
_pdbe_chem_comp_rdkit_properties.chi3v 1.325
_pdbe_chem_comp_rdkit_properties.chi4v 0.757
_pdbe_chem_comp_rdkit_properties.chi0n 22.855
_pdbe_chem_comp_rdkit_properties.chi1n 11.625
_pdbe_chem_comp_rdkit_properties.chi2n 1.325
_pdbe_chem_comp_rdkit_properties.chi3n 1.325
_pdbe_chem_comp_rdkit_properties.chi4n 0.757
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.530
_pdbe_chem_comp_rdkit_properties.kappa1 1.448
_pdbe_chem_comp_rdkit_properties.kappa2 3.461
_pdbe_chem_comp_rdkit_properties.kappa3 1.346
_pdbe_chem_comp_rdkit_properties.Phi 0.418
#
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
CCB UniChem ChEMBL CHEMBL45844
CCB UniChem DrugBank DB04065
CCB UniChem PDBe CCB
CCB UniChem ChEBI 191227
CCB UniChem SureChEMBL SCHEMBL4315833
CCB UniChem BindingDb 50064286
CCB UniChem BRENDA 122876
CCB UniChem 'Probes And Drugs' PD006509
CCB UniChem Nikkaji J962.590I
CCB UniChem 'PubChem TPHARMA' 15462353
CCB UniChem PubChem 5287890
#
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
CCB N1 0.370 -0.860 -0.407 ETKDGv3 1
CCB C2 -0.142 -2.151 -0.801 ETKDGv3 2
CCB O3 -1.357 -2.448 -0.658 ETKDGv3 3
CCB C5 -0.517 0.183 0.169 ETKDGv3 4
CCB C6 1.822 -0.635 -0.582 ETKDGv3 5
CCB C7 -1.230 -0.290 1.445 ETKDGv3 6
CCB C8 -2.724 -0.136 1.189 ETKDGv3 7
CCB C9 -2.855 0.829 0.023 ETKDGv3 8
CCB C10 -1.602 0.633 -0.814 ETKDGv3 9
CCB C20 2.171 0.668 -1.297 ETKDGv3 10
CCB C21 2.875 1.161 -0.037 ETKDGv3 11
CCB C22 2.530 -0.142 0.678 ETKDGv3 12
CCB H2 0.521 -2.893 -1.229 ETKDGv3 13
CCB H5 0.069 1.087 0.440 ETKDGv3 14
CCB H6 2.351 -1.504 -1.036 ETKDGv3 15
CCB H71 -0.982 -1.339 1.714 ETKDGv3 16
CCB H72 -0.934 0.356 2.301 ETKDGv3 17
CCB H81 -3.253 0.248 2.088 ETKDGv3 18
CCB H82 -3.161 -1.119 0.907 ETKDGv3 19
CCB H91 -3.774 0.630 -0.568 ETKDGv3 20
CCB H92 -2.885 1.873 0.408 ETKDGv3 21
CCB H101 -1.797 -0.131 -1.596 ETKDGv3 22
CCB H102 -1.316 1.580 -1.322 ETKDGv3 23
CCB H201 2.881 0.509 -2.138 ETKDGv3 24
CCB H202 1.297 1.293 -1.578 ETKDGv3 25
CCB H211 2.374 2.044 0.416 ETKDGv3 26
CCB H212 3.970 1.290 -0.183 ETKDGv3 27
CCB H221 3.435 -0.743 0.914 ETKDGv3 28
CCB H222 1.864 0.008 1.555 ETKDGv3 29
#