data_SMZ
#
_chem_comp.id SMZ
_chem_comp.name N~5~-[(E)-imino(methylsulfanyl)methyl]-L-ornithine
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C7 H15 N3 O2 S"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms S-methyl-L-thiocitrulline
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2008-01-15
_chem_comp.pdbx_modified_date 2021-03-01
_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 205.278
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code SMZ
_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 3BPB
_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
SMZ C8 C8 C 0 1 N N N N N N 17.004 45.629 -13.658 5.715 0.502 -0.249 C8 SMZ 1
SMZ S1 S1 S 0 1 N N N N N N 17.037 47.240 -14.538 4.472 -0.663 0.361 S1 SMZ 2
SMZ C2 C2 C 0 1 N N S N N N 21.898 48.838 -11.123 -3.169 -0.502 0.337 C2 SMZ 3
SMZ O2 O2 O 0 1 N N N N N N 23.680 50.372 -11.069 -4.803 1.250 0.937 O2 SMZ 4
SMZ C4 C4 C 0 1 N N N N N N 20.675 49.003 -13.357 -0.672 -0.437 0.284 C4 SMZ 5
SMZ C5 C5 C 0 1 N N N N N N 19.960 47.654 -13.502 0.548 0.380 -0.147 C5 SMZ 6
SMZ O1 O1 O 0 1 N N N N N N 23.694 48.844 -12.700 -5.088 0.067 -0.908 O1 SMZ 7
SMZ C1 C1 C 0 1 N N N N N N 23.194 49.393 -11.684 -4.423 0.292 0.076 C1 SMZ 8
SMZ N2 N2 N 0 1 N N N N N N 21.852 49.223 -9.701 -3.215 -1.755 -0.429 N2 SMZ 9
SMZ C3 C3 C 0 1 N N N N N N 20.733 49.476 -11.894 -1.950 0.315 -0.094 C3 SMZ 10
SMZ N6 N6 N 0 1 N N N N N N 19.735 47.416 -14.928 1.771 -0.341 0.216 N6 SMZ 11
SMZ C7 C7 C 0 1 N N N N N N 18.541 47.246 -15.461 3.001 0.203 -0.074 C7 SMZ 12
SMZ N8 N8 N 0 1 N N N N N N 18.491 47.045 -16.758 3.078 1.360 -0.672 N8 SMZ 13
SMZ H8 H8 H 0 1 N N N N N N 16.997 44.810 -14.392 5.585 0.642 -1.322 H8 SMZ 14
SMZ H8A H8A H 0 1 N N N N N N 17.895 45.542 -13.019 5.597 1.458 0.259 H8A SMZ 15
SMZ H8B H8B H 0 1 N N N N N N 16.099 45.570 -13.035 6.711 0.106 -0.053 H8B SMZ 16
SMZ H2 H2 H 0 1 N N N N N N 21.830 47.744 -11.221 -3.097 -0.729 1.401 H2 SMZ 17
SMZ HO2 HO2 H 0 1 N N N N N N 24.489 50.640 -11.488 -5.614 1.732 0.727 HO2 SMZ 18
SMZ H4 H4 H 0 1 N N N N N N 21.704 48.896 -13.732 -0.658 -1.404 -0.218 H4 SMZ 19
SMZ H4A H4A H 0 1 N N N N N N 20.109 49.750 -13.933 -0.646 -0.588 1.363 H4A SMZ 20
SMZ H5 H5 H 0 1 N N N N N N 20.582 46.851 -13.080 0.521 0.530 -1.226 H5 SMZ 21
SMZ H5A H5A H 0 1 N N N N N N 19.003 47.668 -12.961 0.533 1.347 0.356 H5A SMZ 22
SMZ HN2 HN2 H 0 1 N N N N N N 21.842 48.400 -9.133 -3.975 -2.341 -0.117 HN2 SMZ 23
SMZ HN2A HN2A H 0 0 N N N N N N 22.658 49.772 -9.478 -3.282 -1.571 -1.419 HN2A SMZ 24
SMZ H3 H3 H 0 1 N N N N N N 19.791 49.198 -11.398 -1.976 0.466 -1.173 H3 SMZ 25
SMZ H3A H3A H 0 1 N N N N N N 20.884 50.566 -11.896 -1.964 1.282 0.408 H3A SMZ 26
SMZ HN6 HN6 H 0 1 N N N N N N 20.531 47.380 -15.532 1.713 -1.201 0.660 HN6 SMZ 27
SMZ HN8 HN8 H 0 1 N N N N N N 17.526 46.927 -16.993 3.945 1.743 -0.877 HN8 SMZ 28
#
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
SMZ S1 C8 SING N N 1
SMZ C8 H8 SING N N 2
SMZ C8 H8A SING N N 3
SMZ C8 H8B SING N N 4
SMZ C7 S1 SING N N 5
SMZ C3 C2 SING N N 6
SMZ C1 C2 SING N N 7
SMZ C2 N2 SING N N 8
SMZ C2 H2 SING N N 9
SMZ C1 O2 SING N N 10
SMZ O2 HO2 SING N N 11
SMZ C5 C4 SING N N 12
SMZ C4 C3 SING N N 13
SMZ C4 H4 SING N N 14
SMZ C4 H4A SING N N 15
SMZ N6 C5 SING N N 16
SMZ C5 H5 SING N N 17
SMZ C5 H5A SING N N 18
SMZ O1 C1 DOUB N N 19
SMZ N2 HN2 SING N N 20
SMZ N2 HN2A SING N N 21
SMZ C3 H3 SING N N 22
SMZ C3 H3A SING N N 23
SMZ C7 N6 SING N N 24
SMZ N6 HN6 SING N N 25
SMZ N8 C7 DOUB N N 26
SMZ N8 HN8 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
SMZ SMILES ACDLabs 10.04 O=C(O)C(N)CCCNC(=[N@H])SC
SMZ SMILES_CANONICAL CACTVS 3.341 CSC(=N)NCCC[C@H](N)C(O)=O
SMZ SMILES CACTVS 3.341 CSC(=N)NCCC[CH](N)C(O)=O
SMZ SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "[H]/N=C(/NCCC[C@@H](C(=O)O)N)\SC"
SMZ SMILES "OpenEye OEToolkits" 1.5.0 "[H]N=C(NCCCC(C(=O)O)N)SC"
SMZ InChI InChI 1.03 InChI=1S/C7H15N3O2S/c1-13-7(9)10-4-2-3-5(8)6(11)12/h5H,2-4,8H2,1H3,(H2,9,10)(H,11,12)/t5-/m0/s1
SMZ InChIKey InChI 1.03 NGVMVBQRKZPFLB-YFKPBYRVSA-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
SMZ "SYSTEMATIC NAME" ACDLabs 10.04 N~5~-[(Z)-imino(methylsulfanyl)methyl]-L-ornithine
SMZ "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "(2S)-2-amino-5-[(methylsulfanylcarbonimidoyl)amino]pentanoic acid"
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
SMZ 'Create component' 2008-01-15 RCSB
SMZ 'Modify descriptor' 2011-06-04 RCSB
SMZ 'Modify synonyms' 2021-03-01 PDBE
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id SMZ
_pdbx_chem_comp_synonyms.name S-methyl-L-thiocitrulline
_pdbx_chem_comp_synonyms.provenance ?
_pdbx_chem_comp_synonyms.type ?
#
_pdbe_chem_comp_synonyms.comp_id SMZ
_pdbe_chem_comp_synonyms.name S-methyl-L-thiocitrulline
_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
SMZ C8 C 6.404 -5.250 1
SMZ S1 S 6.404 -3.750 2
SMZ C2 C 5.104 3.000 3
SMZ O2 O 7.702 3.000 4
SMZ C4 C 6.404 0.750 5
SMZ C5 C 6.404 -0.750 6
SMZ O1 O 6.404 5.250 7
SMZ C1 C 6.404 3.750 8
SMZ N2 N 3.805 3.750 9
SMZ C3 C 5.104 1.500 10
SMZ N6 N 7.702 -1.500 11
SMZ C7 C 7.702 -3.000 12
SMZ N8 N 9.002 -3.750 13
SMZ HN8 H 10.301 -3.000 14
#
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
SMZ S1 C8 SINGLE NONE 1
SMZ C7 S1 SINGLE ENDDOWNRIGHT 2
SMZ C3 C2 SINGLE NONE 3
SMZ C1 C2 SINGLE NONE 4
SMZ C2 N2 SINGLE BEGINDASH 5
SMZ C1 O2 SINGLE NONE 6
SMZ C5 C4 SINGLE NONE 7
SMZ C4 C3 SINGLE NONE 8
SMZ N6 C5 SINGLE NONE 9
SMZ O1 C1 DOUBLE NONE 10
SMZ C7 N6 SINGLE ENDUPRIGHT 11
SMZ N8 C7 DOUBLE NONE 12
#
_pdbe_chem_comp_substructure.comp_id SMZ
_pdbe_chem_comp_substructure.substructure_name peptide
_pdbe_chem_comp_substructure.id F1
_pdbe_chem_comp_substructure.substructure_type fragment
_pdbe_chem_comp_substructure.substructure_smiles NCC=O
_pdbe_chem_comp_substructure.substructure_inchis InChI=1S/C2H5NO/c3-1-2-4/h2H,1,3H2
_pdbe_chem_comp_substructure.substructure_inchikeys 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
SMZ O1 F1 1
SMZ C1 F1 1
SMZ C2 F1 1
SMZ N2 F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id SMZ
_pdbe_chem_comp_rdkit_properties.exactmw 205.088
_pdbe_chem_comp_rdkit_properties.amw 205.283
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 5
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 5
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 7
_pdbe_chem_comp_rdkit_properties.NumHBD 4
_pdbe_chem_comp_rdkit_properties.NumHBA 5
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 13
_pdbe_chem_comp_rdkit_properties.NumAtoms 28
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 6
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.714
_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 102.976
_pdbe_chem_comp_rdkit_properties.tpsa 99.200
_pdbe_chem_comp_rdkit_properties.CrippenClogP 0.066
_pdbe_chem_comp_rdkit_properties.CrippenMR 54.090
_pdbe_chem_comp_rdkit_properties.chi0v 6.883
_pdbe_chem_comp_rdkit_properties.chi1v 3.527
_pdbe_chem_comp_rdkit_properties.chi2v 0.947
_pdbe_chem_comp_rdkit_properties.chi3v 0.947
_pdbe_chem_comp_rdkit_properties.chi4v 0.328
_pdbe_chem_comp_rdkit_properties.chi0n 21.066
_pdbe_chem_comp_rdkit_properties.chi1n 9.908
_pdbe_chem_comp_rdkit_properties.chi2n 0.673
_pdbe_chem_comp_rdkit_properties.chi3n 0.673
_pdbe_chem_comp_rdkit_properties.chi4n 0.237
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.750
_pdbe_chem_comp_rdkit_properties.kappa1 2.250
_pdbe_chem_comp_rdkit_properties.kappa2 6.732
_pdbe_chem_comp_rdkit_properties.kappa3 6.415
_pdbe_chem_comp_rdkit_properties.Phi 1.165
#
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
SMZ UniChem ChEMBL CHEMBL106516
SMZ UniChem PDBe SMZ
SMZ UniChem ChEBI 90712
SMZ UniChem ZINC ZINC000006019622
SMZ UniChem fdasrs M790X706JV
SMZ UniChem ACTor 156719-41-4
SMZ UniChem Nikkaji J587.761J
SMZ UniChem MetaboLights MTBLC90712
SMZ UniChem BRENDA 4690
SMZ UniChem MedChemExpress HY-U00432
SMZ UniChem 'Probes And Drugs' PD099554
SMZ UniChem BindingDb 50138983
SMZ UniChem eMolecules 6878408
SMZ UniChem SureChEMBL SCHEMBL940520
SMZ UniChem 'PubChem TPHARMA' 15171805
SMZ UniChem 'PubChem TPHARMA' 15220109
SMZ UniChem PubChem 107968
SMZ UniChem PubChem 7048562
#
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
SMZ C8 4.273 -1.376 0.176 ETKDGv3 1
SMZ S1 4.496 0.296 -0.506 ETKDGv3 2
SMZ C2 -2.689 0.447 0.179 ETKDGv3 3
SMZ O2 -3.219 -2.007 0.308 ETKDGv3 4
SMZ C4 -0.172 -0.009 0.587 ETKDGv3 5
SMZ C5 0.387 1.046 -0.377 ETKDGv3 6
SMZ O1 -2.838 -1.008 -1.723 ETKDGv3 7
SMZ C1 -2.918 -0.894 -0.471 ETKDGv3 8
SMZ N2 -3.909 0.901 0.851 ETKDGv3 9
SMZ C3 -1.529 0.395 1.195 ETKDGv3 10
SMZ N6 1.745 0.691 -0.788 ETKDGv3 11
SMZ C7 2.889 0.860 0.059 ETKDGv3 12
SMZ N8 2.775 1.424 1.220 ETKDGv3 13
SMZ H8 4.138 -1.323 1.277 ETKDGv3 14
SMZ H8A 5.175 -1.982 -0.047 ETKDGv3 15
SMZ H8B 3.389 -1.862 -0.287 ETKDGv3 16
SMZ H2 -2.442 1.195 -0.605 ETKDGv3 17
SMZ HO2 -3.374 -2.913 -0.118 ETKDGv3 18
SMZ H4 -0.257 -0.985 0.063 ETKDGv3 19
SMZ H4A 0.544 -0.150 1.425 ETKDGv3 20
SMZ H5 0.389 2.052 0.097 ETKDGv3 21
SMZ H5A -0.253 1.096 -1.283 ETKDGv3 22
SMZ HN2 -4.671 0.990 0.139 ETKDGv3 23
SMZ HN2A -4.214 0.182 1.548 ETKDGv3 24
SMZ H3 -1.425 1.390 1.681 ETKDGv3 25
SMZ H3A -1.781 -0.332 1.999 ETKDGv3 26
SMZ HN6 1.891 0.322 -1.754 ETKDGv3 27
SMZ HN8 3.602 1.555 1.844 ETKDGv3 28
#