data_SLA
#
_chem_comp.id SLA
_chem_comp.name 'Omuralide, open form'
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula 'C10 H17 N O4'
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms
'(2R,3S,4R)-3-hydroxy-2-[(1S)-1-hydroxy-2-methylpropyl]-4-methyl-5-oxopyrrolidine-2-carbaldehyde'
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2011-06-04
_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 215.246
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code SLA
_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 3DY4
_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
SLA C1 C1 C 0 1 N N S N N N 62.612 -138.518 41.594 -0.636 0.657 0.753 C1 SLA 1
SLA C2 C2 C 0 1 N N R N N N 61.523 -138.699 40.478 -1.817 -0.307 1.011 C2 SLA 2
SLA C3 C3 C 0 1 N N N N N N 60.615 -137.527 40.786 -2.030 -0.997 -0.318 C3 SLA 3
SLA N4 N4 N 0 1 N N N N N N 61.249 -136.639 41.578 -0.956 -0.821 -1.107 N4 SLA 4
SLA C5 C5 C 0 1 N N R N N N 62.627 -136.976 41.966 0.079 -0.030 -0.431 C5 SLA 5
SLA C6 C6 C 0 1 N N N N N N 62.838 -136.820 43.459 0.642 1.004 -1.371 C6 SLA 6
SLA O7 O7 O 0 1 N N N N N N 61.900 -136.451 44.170 0.397 2.174 -1.199 O7 SLA 7
SLA O8 O8 O 0 1 N N N N N N 62.292 -139.296 42.798 -1.106 1.955 0.384 O8 SLA 8
SLA C9 C9 C 0 1 N N N N N N 60.766 -140.072 40.522 -3.068 0.475 1.416 C9 SLA 9
SLA O10 O10 O 0 1 N N N N N N 59.471 -137.410 40.363 -3.025 -1.618 -0.627 O10 SLA 10
SLA C11 C11 C 0 1 N N S N N N 63.708 -136.145 41.125 1.194 -0.945 0.081 C11 SLA 11
SLA O12 O12 O 0 1 N N N N N N 63.402 -136.249 39.720 1.895 -1.509 -1.029 O12 SLA 12
SLA C13 C13 C 0 1 N N N N N N 63.859 -134.606 41.548 2.166 -0.132 0.939 C13 SLA 13
SLA C14 C14 C 0 1 N N N N N N 64.913 -133.861 40.678 3.192 -1.072 1.575 C14 SLA 14
SLA C15 C15 C 0 1 N N N N N N 62.529 -133.793 41.472 2.888 0.891 0.060 C15 SLA 15
SLA H18 H18 H 0 1 N Y N N N N 63.803 -137.030 43.897 1.265 0.699 -2.199 H18 SLA 16
SLA H1 H1 H 0 1 N N N N N N 63.596 -138.803 41.194 0.019 0.715 1.623 H1 SLA 17
SLA H2 H2 H 0 1 N N N N N N 61.988 -138.569 39.489 -1.556 -1.032 1.782 H2 SLA 18
SLA H3 H3 H 0 1 N N N N N N 60.806 -135.797 41.885 -0.876 -1.172 -2.008 H3 SLA 19
SLA H4 H4 H 0 1 N N N N N N 62.970 -139.164 43.451 -1.562 2.425 1.095 H4 SLA 20
SLA H5 H5 H 0 1 N N N N N N 61.469 -140.886 40.292 -3.906 -0.213 1.528 H5 SLA 21
SLA H6 H6 H 0 1 N N N N N N 60.343 -140.225 41.526 -2.887 0.986 2.362 H6 SLA 22
SLA H7 H7 H 0 1 N N N N N N 59.955 -140.067 39.779 -3.302 1.210 0.645 H7 SLA 23
SLA H8 H8 H 0 1 N N N N N N 64.683 -136.620 41.308 0.760 -1.744 0.681 H8 SLA 24
SLA H9 H9 H 0 1 N N N N N N 63.315 -137.164 39.481 2.307 -0.853 -1.608 H9 SLA 25
SLA H10 H10 H 0 1 N N N N N N 64.207 -134.585 42.591 1.613 0.386 1.722 H10 SLA 26
SLA H11 H11 H 0 1 N N N N N N 64.982 -132.812 41.003 3.687 -1.651 0.796 H11 SLA 27
SLA H12 H12 H 0 1 N N N N N N 65.893 -134.346 40.794 3.933 -0.486 2.118 H12 SLA 28
SLA H13 H13 H 0 1 N N N N N N 64.608 -133.898 39.622 2.687 -1.748 2.265 H13 SLA 29
SLA H14 H14 H 0 1 N N N N N N 61.758 -134.292 42.078 2.210 1.712 -0.173 H14 SLA 30
SLA H15 H15 H 0 1 N N N N N N 62.698 -132.777 41.859 3.757 1.278 0.593 H15 SLA 31
SLA H16 H16 H 0 1 N N N N N N 62.193 -133.736 40.426 3.212 0.413 -0.864 H16 SLA 32
#
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
SLA O12 C11 SING N N 1
SLA O10 C3 DOUB N N 2
SLA C2 C9 SING N N 3
SLA C2 C3 SING N N 4
SLA C2 C1 SING N N 5
SLA C14 C13 SING N N 6
SLA C3 N4 SING N N 7
SLA C11 C13 SING N N 8
SLA C11 C5 SING N N 9
SLA C15 C13 SING N N 10
SLA N4 C5 SING N N 11
SLA C1 C5 SING N N 12
SLA C1 O8 SING N N 13
SLA C5 C6 SING N N 14
SLA C6 O7 DOUB N N 15
SLA C6 H18 SING N N 16
SLA C1 H1 SING N N 17
SLA C2 H2 SING N N 18
SLA N4 H3 SING N N 19
SLA O8 H4 SING N N 20
SLA C9 H5 SING N N 21
SLA C9 H6 SING N N 22
SLA C9 H7 SING N N 23
SLA C11 H8 SING N N 24
SLA O12 H9 SING N N 25
SLA C13 H10 SING N N 26
SLA C14 H11 SING N N 27
SLA C14 H12 SING N N 28
SLA C14 H13 SING N N 29
SLA C15 H14 SING N N 30
SLA C15 H15 SING N N 31
SLA C15 H16 SING N N 32
#
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
SLA SMILES ACDLabs 12.01 'O=CC1(NC(=O)C(C1O)C)C(O)C(C)C'
SLA InChI InChI 1.03 'InChI=1S/C10H17NO4/c1-5(2)7(13)10(4-12)8(14)6(3)9(15)11-10/h4-8,13-14H,1-3H3,(H,11,15)/t6-,7+,8+,10-/m1/s1'
SLA InChIKey InChI 1.03 NREVXJAQSWMFJZ-CHIQAWFVSA-N
SLA SMILES_CANONICAL CACTVS 3.385 'CC(C)[C@H](O)[C@]1(NC(=O)[C@H](C)[C@@H]1O)C=O'
SLA SMILES CACTVS 3.385 'CC(C)[CH](O)[C]1(NC(=O)[CH](C)[CH]1O)C=O'
SLA SMILES_CANONICAL 'OpenEye OEToolkits' 1.7.6 'C[C@@H]1[C@@H]([C@@](NC1=O)(C=O)[C@H](C(C)C)O)O'
SLA SMILES 'OpenEye OEToolkits' 1.7.6 'CC1C(C(NC1=O)(C=O)C(C(C)C)O)O'
#
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
SLA 'SYSTEMATIC NAME' ACDLabs 12.01 '(2R,3S,4R)-3-hydroxy-2-[(1S)-1-hydroxy-2-methylpropyl]-4-methyl-5-oxopyrrolidine-2-carbaldehyde'
SLA 'SYSTEMATIC NAME' 'OpenEye OEToolkits' 1.7.6 '(2R,3S,4R)-4-methyl-2-[(1S)-2-methyl-1-oxidanyl-propyl]-3-oxidanyl-5-oxidanylidene-pyrrolidine-2-carbaldehyde'
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
SLA 'Create component' 2011-06-04 RCSB
SLA 'Other modification' 2014-08-04 RCSB
SLA 'Modify synonyms' 2020-06-05 PDBE
SLA 'Modify PCM' 2024-09-27 PDBE
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id SLA
_pdbx_chem_comp_synonyms.name
'(2R,3S,4R)-3-hydroxy-2-[(1S)-1-hydroxy-2-methylpropyl]-4-methyl-5-oxopyrrolidine-2-carbaldehyde'
_pdbx_chem_comp_synonyms.provenance ?
_pdbx_chem_comp_synonyms.type ?
#
loop_
_pdbx_chem_comp_pcm.pcm_id
_pdbx_chem_comp_pcm.comp_id
_pdbx_chem_comp_pcm.modified_residue_id
_pdbx_chem_comp_pcm.type
_pdbx_chem_comp_pcm.category
_pdbx_chem_comp_pcm.position
_pdbx_chem_comp_pcm.polypeptide_position
_pdbx_chem_comp_pcm.comp_id_linking_atom
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession
_pdbx_chem_comp_pcm.first_instance_model_db_code
1 SLA SER None 'Covalent chemical modification' 'Amino-acid side chain' 'Any position' C6 OG ? ? 4FWG
2 SLA THR None 'Covalent chemical modification' 'Amino-acid side chain' 'Any position' C6 OG1 ? ? 3DY4
#
_pdbe_chem_comp_synonyms.comp_id SLA
_pdbe_chem_comp_synonyms.name
'(2R,3S,4R)-3-hydroxy-2-[(1S)-1-hydroxy-2-methylpropyl]-4-methyl-5-oxopyrrolidine-2-carbaldehyde'
_pdbe_chem_comp_synonyms.provenance wwPDB
_pdbe_chem_comp_synonyms.type ?
#
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
SLA C1 C 5.118 -1.019 1
SLA C2 C 5.581 -2.446 2
SLA C3 C 7.081 -2.446 3
SLA N4 N 7.545 -1.019 4
SLA C5 C 6.331 -0.138 5
SLA C6 C 5.449 1.076 6
SLA O7 O 3.958 0.919 7
SLA O8 O 3.691 -0.556 8
SLA C9 C 4.699 -3.660 9
SLA O10 O 7.963 -3.660 10
SLA C11 C 7.213 1.076 11
SLA O12 O 8.705 0.919 12
SLA C13 C 6.603 2.446 13
SLA C14 C 7.485 3.660 14
SLA C15 C 5.111 2.603 15
#
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
SLA C11 O12 SINGLE BEGINDASH 1
SLA O10 C3 DOUBLE NONE 2
SLA C2 C9 SINGLE BEGINDASH 3
SLA C2 C3 SINGLE NONE 4
SLA C2 C1 SINGLE NONE 5
SLA C14 C13 SINGLE NONE 6
SLA C3 N4 SINGLE NONE 7
SLA C11 C13 SINGLE NONE 8
SLA C11 C5 SINGLE NONE 9
SLA C15 C13 SINGLE NONE 10
SLA N4 C5 SINGLE NONE 11
SLA C1 C5 SINGLE NONE 12
SLA C1 O8 SINGLE BEGINDASH 13
SLA C5 C6 SINGLE BEGINDASH 14
SLA C6 O7 DOUBLE NONE 15
#
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
SLA MurckoScaffold S1 scaffold O=C1CCCN1 InChI=1S/C4H7NO/c6-4-2-1-3-5-4/h1-3H2,(H,5,6) HNJBEVLQSNELDL-UHFFFAOYSA-N
SLA amide F1 fragment CC(N)=O InChI=1S/C2H5NO/c1-2(3)4/h1H3,(H2,3,4) DLFVBJFMPXGRIB-UHFFFAOYSA-N
SLA peptide F2 fragment NCC=O InChI=1S/C2H5NO/c3-1-2-4/h2H,1,3H2 LYIIBVSRGJSHAV-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
SLA C1 S1 1
SLA C2 S1 1
SLA C3 S1 1
SLA N4 S1 1
SLA C5 S1 1
SLA O10 S1 1
SLA N4 F1 1
SLA C3 F1 1
SLA O10 F1 1
SLA C2 F1 1
SLA O7 F2 1
SLA C6 F2 1
SLA C5 F2 1
SLA N4 F2 1
#
_pdbe_chem_comp_rdkit_properties.comp_id SLA
_pdbe_chem_comp_rdkit_properties.exactmw 215.116
_pdbe_chem_comp_rdkit_properties.amw 215.249
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 5
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 3
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 8
_pdbe_chem_comp_rdkit_properties.NumHBD 3
_pdbe_chem_comp_rdkit_properties.NumHBA 4
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 15
_pdbe_chem_comp_rdkit_properties.NumAtoms 32
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 5
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 1
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.800
_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 1
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumSpiroAtoms 0
_pdbe_chem_comp_rdkit_properties.NumBridgeheadAtoms 0
_pdbe_chem_comp_rdkit_properties.NumAtomStereoCenters 4
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 112.595
_pdbe_chem_comp_rdkit_properties.tpsa 86.630
_pdbe_chem_comp_rdkit_properties.CrippenClogP -0.932
_pdbe_chem_comp_rdkit_properties.CrippenMR 52.953
_pdbe_chem_comp_rdkit_properties.chi0v 7.080
_pdbe_chem_comp_rdkit_properties.chi1v 3.514
_pdbe_chem_comp_rdkit_properties.chi2v 1.742
_pdbe_chem_comp_rdkit_properties.chi3v 1.742
_pdbe_chem_comp_rdkit_properties.chi4v 0.987
_pdbe_chem_comp_rdkit_properties.chi0n 24.080
_pdbe_chem_comp_rdkit_properties.chi1n 11.777
_pdbe_chem_comp_rdkit_properties.chi2n 1.742
_pdbe_chem_comp_rdkit_properties.chi3n 1.742
_pdbe_chem_comp_rdkit_properties.chi4n 0.987
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.940
_pdbe_chem_comp_rdkit_properties.kappa1 2.486
_pdbe_chem_comp_rdkit_properties.kappa2 3.903
_pdbe_chem_comp_rdkit_properties.kappa3 1.656
_pdbe_chem_comp_rdkit_properties.Phi 0.647
#
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
SLA UniChem PDBe SLA
SLA UniChem ZINC ZINC000098209411
SLA UniChem PubChem 137350010
#
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
SLA C1 0.911 -0.703 0.154 ETKDGv3 1
SLA C2 2.417 -0.488 0.455 ETKDGv3 2
SLA C3 2.392 0.789 1.200 ETKDGv3 3
SLA N4 1.147 1.451 1.122 ETKDGv3 4
SLA C5 0.223 0.703 0.274 ETKDGv3 5
SLA C6 0.157 1.427 -1.062 ETKDGv3 6
SLA O7 -0.085 2.623 -1.111 ETKDGv3 7
SLA O8 0.690 -1.318 -1.092 ETKDGv3 8
SLA C9 3.288 -0.352 -0.802 ETKDGv3 9
SLA O10 3.376 1.262 1.828 ETKDGv3 10
SLA C11 -1.173 0.634 0.994 ETKDGv3 11
SLA O12 -1.630 1.930 1.301 ETKDGv3 12
SLA C13 -2.328 -0.212 0.345 ETKDGv3 13
SLA C14 -2.225 -1.718 0.635 ETKDGv3 14
SLA C15 -2.550 0.026 -1.156 ETKDGv3 15
SLA H18 0.347 0.907 -1.994 ETKDGv3 16
SLA H1 0.521 -1.362 0.964 ETKDGv3 17
SLA H2 2.811 -1.304 1.099 ETKDGv3 18
SLA H3 0.979 2.414 1.491 ETKDGv3 19
SLA H4 0.966 -2.266 -0.993 ETKDGv3 20
SLA H5 4.332 -0.102 -0.515 ETKDGv3 21
SLA H6 2.901 0.446 -1.472 ETKDGv3 22
SLA H7 3.309 -1.313 -1.358 ETKDGv3 23
SLA H8 -0.975 0.169 1.986 ETKDGv3 24
SLA H9 -2.026 2.322 0.482 ETKDGv3 25
SLA H10 -3.265 0.115 0.849 ETKDGv3 26
SLA H11 -3.194 -2.210 0.403 ETKDGv3 27
SLA H12 -2.003 -1.902 1.707 ETKDGv3 28
SLA H13 -1.450 -2.204 0.011 ETKDGv3 29
SLA H14 -2.636 1.108 -1.382 ETKDGv3 30
SLA H15 -1.729 -0.415 -1.757 ETKDGv3 31
SLA H16 -3.498 -0.458 -1.475 ETKDGv3 32
#