data_CCD
#
_chem_comp.id CCD
_chem_comp.name '(4R)-4-HYDROXY-N,N,N-TRIMETHYLPENTAN-1-AMINIUM'
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula 'C8 H20 N O'
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 1
_chem_comp.pdbx_initial_date 2006-06-15
_chem_comp.pdbx_modified_date 2024-09-27
_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 146.250
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code CCD
_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 RCSB
_chem_comp.pdbx_pcm Y
#
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
CCD O7 O7 O 0 1 N N N N N N 29.567 14.907 13.499 2.790 1.334 -0.095 O7 CCD 1
CCD C5 C5 C 0 1 N N R N N N 28.862 15.269 12.319 2.688 -0.019 0.355 C5 CCD 2
CCD C6 C6 C 0 1 N N N N N N 29.754 14.989 11.103 3.959 -0.780 -0.029 C6 CCD 3
CCD C4 C4 C 0 1 N N N N N N 28.385 16.740 12.383 1.477 -0.685 -0.300 C4 CCD 4
CCD C3 C3 C 0 1 N N N N N N 27.642 17.144 13.663 0.196 0.000 0.182 C3 CCD 5
CCD C2 C2 C 0 1 N N N N N N 27.584 18.677 13.726 -1.016 -0.666 -0.473 C2 CCD 6
CCD N1 N1 N 1 1 N N N N N N 26.828 19.282 14.848 -2.245 -0.010 -0.010 N1 CCD 7
CCD C9 C9 C 0 1 N N N N N N 27.414 18.947 16.136 -2.209 1.412 -0.379 C9 CCD 8
CCD C10 C10 C 0 1 N N N N N N 25.403 18.886 14.824 -3.409 -0.649 -0.639 C10 CCD 9
CCD C8 C8 C 0 1 N N N N N N 26.934 20.749 14.694 -2.347 -0.135 1.450 C8 CCD 10
CCD HO7 HO7 H 0 1 N N N N N N 30.493 14.826 13.303 2.894 1.302 -1.056 HO7 CCD 11
CCD HXT HXT H 0 1 N N N N N N 27.950 14.661 12.226 2.569 -0.033 1.438 HXT CCD 12
CCD H61 1H6 H 0 1 N N N N N N 30.288 14.039 11.251 4.822 -0.306 0.438 H61 CCD 13
CCD H62 2H6 H 0 1 N N N N N N 30.482 15.805 10.987 3.881 -1.812 0.315 H62 CCD 14
CCD H63 3H6 H 0 1 N N N N N N 29.131 14.922 10.199 4.078 -0.766 -1.112 H63 CCD 15
CCD H41 1H4 H 0 1 N N N N N N 27.663 16.860 11.562 1.553 -0.592 -1.384 H41 CCD 16
CCD H42 2H4 H 0 1 N N N N N N 29.277 17.379 12.304 1.450 -1.739 -0.027 H42 CCD 17
CCD H31 1H3 H 0 1 N N N N N N 28.168 16.750 14.545 0.120 -0.093 1.265 H31 CCD 18
CCD H32 2H3 H 0 1 N N N N N N 26.622 16.732 13.648 0.223 1.054 -0.091 H32 CCD 19
CCD H21 1H2 H 0 1 N N N N N N 27.044 18.982 12.818 -0.940 -0.574 -1.557 H21 CCD 20
CCD H22 2H2 H 0 1 N N N N N N 28.621 19.034 13.809 -1.042 -1.721 -0.200 H22 CCD 21
CCD H91 1H9 H 0 1 N N N N N N 27.004 17.988 16.487 -2.134 1.505 -1.462 H91 CCD 22
CCD H92 2H9 H 0 1 N N N N N N 27.175 19.737 16.864 -3.122 1.900 -0.035 H92 CCD 23
CCD H93 3H9 H 0 1 N N N N N N 28.506 18.862 16.032 -1.346 1.887 0.088 H93 CCD 24
CCD H101 1H10 H 0 0 N N N N N N 25.299 17.922 14.304 -3.435 -1.704 -0.366 H101 CCD 25
CCD H102 2H10 H 0 0 N N N N N N 24.818 19.653 14.296 -4.321 -0.162 -0.296 H102 CCD 26
CCD H103 3H10 H 0 0 N N N N N N 25.032 18.788 15.855 -3.333 -0.556 -1.723 H103 CCD 27
CCD H81 1H8 H 0 1 N N N N N N 26.064 21.122 14.134 -1.484 0.340 1.916 H81 CCD 28
CCD H82 2H8 H 0 1 N N N N N N 27.856 20.994 14.147 -3.260 0.353 1.793 H82 CCD 29
CCD H83 3H8 H 0 1 N N N N N N 26.960 21.221 15.687 -2.374 -1.190 1.723 H83 CCD 30
#
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
CCD O7 C5 SING N N 1
CCD O7 HO7 SING N N 2
CCD C5 C6 SING N N 3
CCD C5 C4 SING N N 4
CCD C5 HXT SING N N 5
CCD C6 H61 SING N N 6
CCD C6 H62 SING N N 7
CCD C6 H63 SING N N 8
CCD C4 C3 SING N N 9
CCD C4 H41 SING N N 10
CCD C4 H42 SING N N 11
CCD C3 C2 SING N N 12
CCD C3 H31 SING N N 13
CCD C3 H32 SING N N 14
CCD C2 N1 SING N N 15
CCD C2 H21 SING N N 16
CCD C2 H22 SING N N 17
CCD N1 C9 SING N N 18
CCD N1 C10 SING N N 19
CCD N1 C8 SING N N 20
CCD C9 H91 SING N N 21
CCD C9 H92 SING N N 22
CCD C9 H93 SING N N 23
CCD C10 H101 SING N N 24
CCD C10 H102 SING N N 25
CCD C10 H103 SING N N 26
CCD C8 H81 SING N N 27
CCD C8 H82 SING N N 28
CCD C8 H83 SING N N 29
#
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
CCD SMILES ACDLabs 10.04 'OC(C)CCC[N+](C)(C)C'
CCD SMILES_CANONICAL CACTVS 3.341 'C[C@@H](O)CCC[N+](C)(C)C'
CCD SMILES CACTVS 3.341 'C[CH](O)CCC[N+](C)(C)C'
CCD SMILES_CANONICAL 'OpenEye OEToolkits' 1.5.0 'C[C@H](CCC[N+](C)(C)C)O'
CCD SMILES 'OpenEye OEToolkits' 1.5.0 'CC(CCC[N+](C)(C)C)O'
CCD InChI InChI 1.03 'InChI=1S/C8H20NO/c1-8(10)6-5-7-9(2,3)4/h8,10H,5-7H2,1-4H3/q+1/t8-/m1/s1'
CCD InChIKey InChI 1.03 HSBSNRZAOXKTSK-MRVPVSSYSA-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
CCD 'SYSTEMATIC NAME' ACDLabs 10.04 '(4R)-4-hydroxy-N,N,N-trimethylpentan-1-aminium'
CCD 'SYSTEMATIC NAME' 'OpenEye OEToolkits' 1.5.0 '[(4R)-4-hydroxypentyl]-trimethyl-azanium'
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
CCD 'Create component' 2006-06-15 RCSB
CCD 'Modify descriptor' 2011-06-04 RCSB
CCD 'Modify PCM' 2024-09-27 PDBE
#
_pdbx_chem_comp_pcm.pcm_id 1
_pdbx_chem_comp_pcm.comp_id CCD
_pdbx_chem_comp_pcm.modified_residue_id SER
_pdbx_chem_comp_pcm.type None
_pdbx_chem_comp_pcm.category 'Covalent chemical modification'
_pdbx_chem_comp_pcm.position 'Amino-acid side chain'
_pdbx_chem_comp_pcm.polypeptide_position 'Any position'
_pdbx_chem_comp_pcm.comp_id_linking_atom C5
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom OG
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession ?
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession ?
#
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
CCD O7 O 10.794 0.851 1
CCD C5 C 9.495 0.101 2
CCD C6 C 9.495 -1.399 3
CCD C4 C 8.196 0.851 4
CCD C3 C 6.897 0.101 5
CCD C2 C 5.598 0.851 6
CCD N1 N 4.299 0.101 7
CCD C9 C 3.000 -0.649 8
CCD C10 C 3.549 1.399 9
CCD C8 C 5.049 -1.198 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
CCD O7 C5 SINGLE NONE 1
CCD C5 C6 SINGLE BEGINDASH 2
CCD C5 C4 SINGLE NONE 3
CCD C4 C3 SINGLE NONE 4
CCD C3 C2 SINGLE NONE 5
CCD C2 N1 SINGLE NONE 6
CCD N1 C9 SINGLE NONE 7
CCD N1 C10 SINGLE NONE 8
CCD N1 C8 SINGLE NONE 9
#
#
#
_pdbe_chem_comp_rdkit_properties.comp_id CCD
_pdbe_chem_comp_rdkit_properties.exactmw 146.154
_pdbe_chem_comp_rdkit_properties.amw 146.254
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 2
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 1
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 9
_pdbe_chem_comp_rdkit_properties.NumHBD 1
_pdbe_chem_comp_rdkit_properties.NumHBA 1
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 10
_pdbe_chem_comp_rdkit_properties.NumAtoms 30
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 2
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 1
_pdbe_chem_comp_rdkit_properties.NumRings 0
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 0
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 0
_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 1
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 92.244
_pdbe_chem_comp_rdkit_properties.tpsa 20.230
_pdbe_chem_comp_rdkit_properties.CrippenClogP 0.854
_pdbe_chem_comp_rdkit_properties.CrippenMR 43.814
_pdbe_chem_comp_rdkit_properties.chi0v 4.855
_pdbe_chem_comp_rdkit_properties.chi1v 2.099
_pdbe_chem_comp_rdkit_properties.chi2v 0.400
_pdbe_chem_comp_rdkit_properties.chi3v 0.400
_pdbe_chem_comp_rdkit_properties.chi4v 0.169
_pdbe_chem_comp_rdkit_properties.chi0n 24.855
_pdbe_chem_comp_rdkit_properties.chi1n 12.007
_pdbe_chem_comp_rdkit_properties.chi2n 0.400
_pdbe_chem_comp_rdkit_properties.chi3n 0.400
_pdbe_chem_comp_rdkit_properties.chi4n 0.169
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.080
_pdbe_chem_comp_rdkit_properties.kappa1 0.944
_pdbe_chem_comp_rdkit_properties.kappa2 3.938
_pdbe_chem_comp_rdkit_properties.kappa3 7.920
_pdbe_chem_comp_rdkit_properties.Phi 0.372
#
_pdbe_chem_comp_external_mappings.comp_id CCD
_pdbe_chem_comp_external_mappings.source UniChem
_pdbe_chem_comp_external_mappings.resource PubChem
_pdbe_chem_comp_external_mappings.resource_id 24916842
#
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
CCD O7 1.992 -1.558 1.072 ETKDGv3 1
CCD C5 2.558 -0.721 0.097 ETKDGv3 2
CCD C6 4.067 -0.623 0.337 ETKDGv3 3
CCD C4 1.908 0.675 0.169 ETKDGv3 4
CCD C3 0.508 0.739 -0.471 ETKDGv3 5
CCD C2 -0.559 -0.049 0.330 ETKDGv3 6
CCD N1 -1.974 0.188 -0.093 ETKDGv3 7
CCD C9 -2.843 -0.728 0.686 ETKDGv3 8
CCD C10 -2.162 -0.105 -1.535 ETKDGv3 9
CCD C8 -2.398 1.581 0.192 ETKDGv3 10
CCD HO7 2.181 -2.492 0.794 ETKDGv3 11
CCD HXT 2.393 -1.147 -0.921 ETKDGv3 12
CCD H61 4.272 -0.181 1.336 ETKDGv3 13
CCD H62 4.524 -1.634 0.293 ETKDGv3 14
CCD H63 4.543 0.007 -0.445 ETKDGv3 15
CCD H41 1.859 1.019 1.226 ETKDGv3 16
CCD H42 2.549 1.401 -0.379 ETKDGv3 17
CCD H31 0.233 1.810 -0.527 ETKDGv3 18
CCD H32 0.572 0.351 -1.510 ETKDGv3 19
CCD H21 -0.444 0.200 1.411 ETKDGv3 20
CCD H22 -0.321 -1.131 0.225 ETKDGv3 21
CCD H91 -2.741 -0.544 1.779 ETKDGv3 22
CCD H92 -3.916 -0.594 0.420 ETKDGv3 23
CCD H93 -2.582 -1.793 0.491 ETKDGv3 24
CCD H101 -1.781 -1.120 -1.788 ETKDGv3 25
CCD H102 -3.238 -0.060 -1.815 ETKDGv3 26
CCD H103 -1.633 0.636 -2.173 ETKDGv3 27
CCD H81 -1.902 2.311 -0.481 ETKDGv3 28
CCD H82 -3.493 1.705 0.035 ETKDGv3 29
CCD H83 -2.170 1.861 1.245 ETKDGv3 30
#