data_12N
#
_chem_comp.id 12N
_chem_comp.name "(2R,3S)-3-amino-4-cyclobutyl-2-hydroxybutanoic acid"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C8 H15 N O3"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2012-10-01
_chem_comp.pdbx_modified_date 2012-10-01
_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 173.210
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code 12N
_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 3LOX
_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
12N N29 N29 N 0 1 N N N N N N 196.466 -6.372 51.373 -0.207 -0.489 -1.233 N29 12N 1
12N C30 C30 C 0 1 N N S N N N 197.345 -5.279 50.984 -0.252 -0.285 0.221 C30 12N 2
12N C31 C31 C 0 1 N N N N N N 196.550 -4.243 50.185 0.998 0.475 0.669 C31 12N 3
12N C32 C32 C 0 1 N N N N N N 195.965 -4.717 48.828 2.236 -0.387 0.419 C32 12N 4
12N C33 C33 C 0 1 N N N N N N 196.924 -4.911 47.617 3.543 0.254 0.914 C33 12N 5
12N C34 C34 C 0 1 N N N N N N 195.203 -3.651 48.015 2.801 -0.256 -1.005 C34 12N 6
12N C35 C35 C 0 1 N N N N N N 195.971 -4.065 46.749 4.201 -0.286 -0.366 C35 12N 7
12N O36 O36 O 0 1 N N N N N N 198.609 -5.653 53.043 -1.452 1.791 -0.073 O36 12N 8
12N C37 C37 C 0 1 N N R N N N 198.092 -4.608 52.168 -1.499 0.523 0.584 C37 12N 9
12N O38 O38 O 0 1 N N N N N N 199.023 -2.596 51.336 -3.441 0.234 -0.718 O38 12N 10
12N C40 C40 C 0 1 N N N N N N 199.251 -3.782 51.548 -2.730 -0.226 0.143 C40 12N 11
12N H37 H37 H 0 1 N N N N N N 196.986 -7.049 51.895 -0.989 -1.045 -1.545 H37 12N 12
12N H38 H38 H 0 1 N N N N N N 198.115 -5.685 50.311 -0.288 -1.253 0.722 H38 12N 13
12N H39 H39 H 0 1 N N N N N N 197.218 -3.393 49.983 1.080 1.403 0.103 H39 12N 14
12N H40 H40 H 0 1 N N N N N N 195.711 -3.909 50.813 0.922 0.704 1.732 H40 12N 15
12N H41 H41 H 0 1 N N N N N N 195.342 -5.613 48.970 2.106 -1.420 0.744 H41 12N 16
12N H42 H42 H 0 1 N N N N N N 197.029 -5.955 47.287 3.506 1.342 0.960 H42 12N 17
12N H43 H43 H 0 1 N N N N N N 197.921 -4.468 47.755 3.931 -0.195 1.829 H43 12N 18
12N H44 H44 H 0 1 N N N N N N 195.395 -2.617 48.339 2.591 -1.118 -1.639 H44 12N 19
12N H45 H45 H 0 1 N N N N N N 194.118 -3.821 47.957 2.559 0.692 -1.486 H45 12N 20
12N H46 H46 H 0 1 N N N N N N 196.460 -3.230 46.225 4.905 0.410 -0.822 H46 12N 21
12N H47 H47 H 0 1 N N N N N N 195.376 -4.650 46.032 4.609 -1.291 -0.257 H47 12N 22
12N H48 H48 H 0 1 N N N N N N 199.069 -5.256 53.773 -1.421 1.734 -1.037 H48 12N 23
12N H49 H49 H 0 1 N N N N N N 197.407 -3.940 52.710 -1.533 0.674 1.663 H49 12N 24
12N H2 H2 H 0 1 N Y N N N N 195.721 -6.016 51.937 -0.174 0.394 -1.721 H2 12N 25
12N OXT OXT O 0 1 N Y N N N N ? ? ? -3.036 -1.405 0.708 OXT 12N 26
12N HXT HXT H 0 1 N Y N N N N ? ? ? -3.836 -1.848 0.392 HXT 12N 27
#
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
12N C35 C33 SING N N 1
12N C35 C34 SING N N 2
12N C33 C32 SING N N 3
12N C34 C32 SING N N 4
12N C32 C31 SING N N 5
12N C31 C30 SING N N 6
12N C30 N29 SING N N 7
12N C30 C37 SING N N 8
12N O38 C40 DOUB N N 9
12N C40 C37 SING N N 10
12N C37 O36 SING N N 11
12N N29 H37 SING N N 12
12N C30 H38 SING N N 13
12N C31 H39 SING N N 14
12N C31 H40 SING N N 15
12N C32 H41 SING N N 16
12N C33 H42 SING N N 17
12N C33 H43 SING N N 18
12N C34 H44 SING N N 19
12N C34 H45 SING N N 20
12N C35 H46 SING N N 21
12N C35 H47 SING N N 22
12N O36 H48 SING N N 23
12N C37 H49 SING N N 24
12N N29 H2 SING N N 25
12N C40 OXT SING N N 26
12N OXT HXT SING N N 27
#
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
12N SMILES ACDLabs 12.01 O=C(O)C(O)C(N)CC1CCC1
12N InChI InChI 1.03 InChI=1S/C8H15NO3/c9-6(7(10)8(11)12)4-5-2-1-3-5/h5-7,10H,1-4,9H2,(H,11,12)/t6-,7+/m0/s1
12N InChIKey InChI 1.03 GKGGRKROASKKFG-NKWVEPMBSA-N
12N SMILES_CANONICAL CACTVS 3.370 N[C@@H](CC1CCC1)[C@@H](O)C(O)=O
12N SMILES CACTVS 3.370 N[CH](CC1CCC1)[CH](O)C(O)=O
12N SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 C1CC(C1)C[C@@H]([C@H](C(=O)O)O)N
12N SMILES "OpenEye OEToolkits" 1.7.6 C1CC(C1)CC(C(C(=O)O)O)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
12N "SYSTEMATIC NAME" ACDLabs 12.01 "(2R,3S)-3-amino-4-cyclobutyl-2-hydroxybutanoic acid"
12N "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "(2R,3S)-3-azanyl-4-cyclobutyl-2-oxidanyl-butanoic acid"
#
_pdbx_chem_comp_audit.comp_id 12N
_pdbx_chem_comp_audit.action_type 'Create component'
_pdbx_chem_comp_audit.date 2012-10-01
_pdbx_chem_comp_audit.processing_site 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
12N N29 N 7.398 -1.946 1
12N C30 C 7.010 -0.497 2
12N C31 C 5.561 -0.109 3
12N C32 C 4.500 -1.170 4
12N C33 C 4.500 -2.670 5
12N C34 C 3.000 -1.170 6
12N C35 C 3.000 -2.670 7
12N O36 O 7.682 2.012 8
12N C37 C 8.070 0.563 9
12N O38 O 10.580 1.236 10
12N C40 C 9.519 0.175 11
12N OXT O 9.907 -1.274 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
12N C35 C33 SINGLE NONE 1
12N C35 C34 SINGLE NONE 2
12N C33 C32 SINGLE NONE 3
12N C34 C32 SINGLE NONE 4
12N C32 C31 SINGLE NONE 5
12N C31 C30 SINGLE NONE 6
12N C30 N29 SINGLE BEGINWEDGE 7
12N C30 C37 SINGLE NONE 8
12N O38 C40 DOUBLE NONE 9
12N C40 C37 SINGLE NONE 10
12N C37 O36 SINGLE BEGINWEDGE 11
12N C40 OXT SINGLE NONE 12
#
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
12N MurckoScaffold S1 scaffold C1CCC1 InChI=1S/C4H8/c1-2-4-3-1/h1-4H2 PMPVIKIVABFJJI-UHFFFAOYSA-N
12N cyclobutane F1 fragment C1CCC1 InChI=1S/C4H8/c1-2-4-3-1/h1-4H2 PMPVIKIVABFJJI-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
12N C32 S1 1
12N C33 S1 1
12N C34 S1 1
12N C35 S1 1
12N C32 F1 1
12N C33 F1 1
12N C35 F1 1
12N C34 F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id 12N
_pdbe_chem_comp_rdkit_properties.exactmw 173.105
_pdbe_chem_comp_rdkit_properties.amw 173.212
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 4
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 4
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 6
_pdbe_chem_comp_rdkit_properties.NumHBD 3
_pdbe_chem_comp_rdkit_properties.NumHBA 4
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 12
_pdbe_chem_comp_rdkit_properties.NumAtoms 27
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 4
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.875
_pdbe_chem_comp_rdkit_properties.NumRings 1
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 0
_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 2
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 92.742
_pdbe_chem_comp_rdkit_properties.tpsa 83.550
_pdbe_chem_comp_rdkit_properties.CrippenClogP -0.051
_pdbe_chem_comp_rdkit_properties.CrippenMR 43.576
_pdbe_chem_comp_rdkit_properties.chi0v 5.672
_pdbe_chem_comp_rdkit_properties.chi1v 2.836
_pdbe_chem_comp_rdkit_properties.chi2v 1.019
_pdbe_chem_comp_rdkit_properties.chi3v 1.019
_pdbe_chem_comp_rdkit_properties.chi4v 0.459
_pdbe_chem_comp_rdkit_properties.chi0n 20.672
_pdbe_chem_comp_rdkit_properties.chi1n 10.047
_pdbe_chem_comp_rdkit_properties.chi2n 1.019
_pdbe_chem_comp_rdkit_properties.chi3n 1.019
_pdbe_chem_comp_rdkit_properties.chi4n 0.459
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.610
_pdbe_chem_comp_rdkit_properties.kappa1 1.766
_pdbe_chem_comp_rdkit_properties.kappa2 3.868
_pdbe_chem_comp_rdkit_properties.kappa3 2.186
_pdbe_chem_comp_rdkit_properties.Phi 0.569
#
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
12N UniChem PDBe 12N
12N UniChem ZINC ZINC000098207911
12N UniChem SureChEMBL SCHEMBL8212276
12N UniChem PubChem 59318585
#
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
12N N29 0.944 1.450 -0.063 ETKDGv3 1
12N C30 1.071 0.012 0.202 ETKDGv3 2
12N C31 -0.237 -0.754 -0.118 ETKDGv3 3
12N C32 -1.395 -0.373 0.828 ETKDGv3 4
12N C33 -2.625 -1.267 0.664 ETKDGv3 5
12N C34 -2.225 0.832 0.378 ETKDGv3 6
12N C35 -3.448 -0.062 0.232 ETKDGv3 7
12N O36 2.059 -0.541 -1.974 ETKDGv3 8
12N C37 2.266 -0.584 -0.583 ETKDGv3 9
12N O38 4.312 -0.437 0.660 ETKDGv3 10
12N C40 3.563 0.086 -0.208 ETKDGv3 11
12N H37 0.354 1.883 0.684 ETKDGv3 12
12N H38 1.293 -0.128 1.285 ETKDGv3 13
12N H39 -0.530 -0.602 -1.180 ETKDGv3 14
12N H40 -0.042 -1.841 0.015 ETKDGv3 15
12N H41 -1.085 -0.302 1.895 ETKDGv3 16
12N H42 -2.534 -2.024 -0.147 ETKDGv3 17
12N H43 -2.973 -1.692 1.631 ETKDGv3 18
12N H44 -1.914 1.268 -0.596 ETKDGv3 19
12N H45 -2.346 1.587 1.184 ETKDGv3 20
12N H46 -3.797 -0.139 -0.821 ETKDGv3 21
12N H47 -4.250 0.191 0.960 ETKDGv3 22
12N H48 2.022 0.410 -2.254 ETKDGv3 23
12N H49 2.355 -1.657 -0.300 ETKDGv3 24
12N H2 0.465 1.607 -0.978 ETKDGv3 25
12N OXT 3.917 1.304 -0.782 ETKDGv3 26
12N HXT 4.779 1.770 -0.522 ETKDGv3 27
#