data_MDO
#
_chem_comp.id MDO
_chem_comp.name "{2-[(1S)-1-aminoethyl]-4-methylidene-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid"
_chem_comp.type "L-PEPTIDE LINKING"
_chem_comp.pdbx_type ATOMP
_chem_comp.formula "C8 H11 N3 O3"
_chem_comp.mon_nstd_parent_comp_id "ALA, SER, GLY"
_chem_comp.pdbx_synonyms "4-METHYLIDENE-5-ONE; PEPTIDE DERIVED CHROMOPHORE"
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2001-08-15
_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 197.191
_chem_comp.one_letter_code ASG
_chem_comp.three_letter_code MDO
_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 ?
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site EBI
_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
MDO N1 N N 0 1 N N N Y Y N 9.572 -16.772 11.295 1.449 2.956 0.692 N MDO 1
MDO CA1 CA C 0 1 N N S Y N N 8.875 -17.955 11.764 0.310 2.112 0.305 CA MDO 2
MDO C1 C1 C 0 1 N N N Y N N 9.734 -19.120 12.142 0.767 0.682 0.174 C1 MDO 3
MDO CB CB C 0 1 N N N N N N 7.629 -18.311 10.979 -0.249 2.593 -1.035 CB MDO 4
MDO N2 N2 N 0 1 N N N Y N N 9.457 -20.352 11.804 1.933 0.326 -0.263 N2 MDO 5
MDO CA2 CA2 C 0 1 N N N Y N N 10.456 -21.099 12.313 2.022 -1.043 -0.255 CA2 MDO 6
MDO C2 C2 C 0 1 N N N Y N N 11.353 -20.178 13.006 0.719 -1.522 0.261 C2 MDO 7
MDO O2 O2 O 0 1 N N N Y N N 12.379 -20.498 13.613 0.371 -2.675 0.431 O2 MDO 8
MDO CB2 CB2 C 0 1 N N N N N N 10.517 -22.450 12.200 3.074 -1.793 -0.636 CB2 MDO 9
MDO N3 N3 N 0 1 N N N Y N N 10.818 -18.994 12.871 0.004 -0.403 0.507 N3 MDO 10
MDO CA3 CA3 C 0 1 N N N Y N N 11.490 -17.821 13.363 -1.361 -0.358 1.039 CA3 MDO 11
MDO C3 C C 0 1 N N N Y N Y 12.608 -17.314 12.388 -2.345 -0.386 -0.101 C MDO 12
MDO O3 O O 0 1 N N N Y N Y 12.424 -17.522 11.169 -1.948 -0.438 -1.241 O MDO 13
MDO OXT OXT O 0 1 N Y N Y N Y 13.784 -16.953 12.812 -3.664 -0.354 0.149 OXT MDO 14
MDO H H H 0 1 N N N Y Y N 8.907 -16.059 11.071 1.168 3.920 0.786 H MDO 15
MDO H2 H2 H 0 1 N Y N Y Y N 10.186 -16.441 12.011 1.876 2.618 1.542 H2 MDO 16
MDO HA1 HCA H 0 1 N N N Y N N 8.490 -17.626 12.740 -0.466 2.177 1.067 HCA MDO 17
MDO HB1 HB1 H 0 1 N N N N N N 7.172 -19.216 11.406 -0.579 3.628 -0.940 HB1 MDO 18
MDO HB2 HB2 H 0 1 N N N N N N 6.912 -17.478 11.032 0.527 2.528 -1.797 HB2 MDO 19
MDO HB3 HB3 H 0 1 N N N N N N 7.898 -18.497 9.929 -1.094 1.967 -1.322 HB3 MDO 20
MDO HB21 HB21 H 0 0 N N N N N N 9.736 -22.984 11.679 3.974 -1.317 -0.996 HB21 MDO 21
MDO HB22 HB22 H 0 0 N N N N N N 11.346 -22.991 12.631 3.017 -2.870 -0.581 HB22 MDO 22
MDO HA31 HA31 H 0 0 N N N Y N N 10.746 -17.020 13.486 -1.528 -1.221 1.684 HA31 MDO 23
MDO HA32 HA32 H 0 0 N N N Y N N 11.956 -18.066 14.329 -1.497 0.557 1.614 HA32 MDO 24
MDO HXT HXT H 0 1 N Y N Y N Y 14.382 -16.894 12.076 -4.256 -0.373 -0.615 HXT MDO 25
#
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
MDO N1 CA1 SING N N 1
MDO CA1 C1 SING N N 2
MDO CA1 CB SING N N 3
MDO C1 N2 DOUB N N 4
MDO C1 N3 SING N N 5
MDO N2 CA2 SING N N 6
MDO CA2 C2 SING N N 7
MDO CA2 CB2 DOUB N N 8
MDO C2 O2 DOUB N N 9
MDO C2 N3 SING N N 10
MDO N3 CA3 SING N N 11
MDO CA3 C3 SING N N 12
MDO C3 O3 DOUB N N 13
MDO C3 OXT SING N N 14
MDO N1 H SING N N 15
MDO N1 H2 SING N N 16
MDO CA1 HA1 SING N N 17
MDO CB HB1 SING N N 18
MDO CB HB2 SING N N 19
MDO CB HB3 SING N N 20
MDO CB2 HB21 SING N N 21
MDO CB2 HB22 SING N N 22
MDO CA3 HA31 SING N N 23
MDO CA3 HA32 SING N N 24
MDO OXT HXT SING N N 25
#
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
MDO SMILES ACDLabs 12.01 "O=C1C(\N=C(N1CC(=O)O)C(N)C)=C"
MDO InChI InChI 1.03 "InChI=1S/C8H11N3O3/c1-4(9)7-10-5(2)8(14)11(7)3-6(12)13/h4H,2-3,9H2,1H3,(H,12,13)/t4-/m0/s1"
MDO InChIKey InChI 1.03 OVDQQXSNYCENRU-BYPYZUCNSA-N
MDO SMILES_CANONICAL CACTVS 3.370 "C[C@H](N)C1=NC(=C)C(=O)N1CC(O)=O"
MDO SMILES CACTVS 3.370 "C[CH](N)C1=NC(=C)C(=O)N1CC(O)=O"
MDO SMILES_CANONICAL "OpenEye OEToolkits" 1.7.2 "C[C@@H](C1=NC(=C)C(=O)N1CC(=O)O)N"
MDO SMILES "OpenEye OEToolkits" 1.7.2 "CC(C1=NC(=C)C(=O)N1CC(=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
MDO "SYSTEMATIC NAME" ACDLabs 12.01 "{2-[(1S)-1-aminoethyl]-4-methylidene-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid"
MDO "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.2 "2-[2-[(1S)-1-azanylethyl]-4-methylidene-5-oxidanylidene-imidazol-1-yl]ethanoic 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
MDO "Create component" 2001-08-15 EBI
MDO "Other modification" 2011-05-18 RCSB
MDO "Modify parent residue" 2011-05-19 RCSB
MDO "Modify descriptor" 2011-06-04 RCSB
MDO "Modify one letter code" 2011-08-18 RCSB
MDO "Modify synonyms" 2020-06-05 PDBE
MDO "Modify backbone" 2023-11-03 PDBE
MDO "Modify PCM" 2024-09-27 PDBE
#
loop_
_pdbx_chem_comp_synonyms.ordinal
_pdbx_chem_comp_synonyms.comp_id
_pdbx_chem_comp_synonyms.name
_pdbx_chem_comp_synonyms.provenance
_pdbx_chem_comp_synonyms.type
1 MDO 4-METHYLIDENE-5-ONE ? ?
2 MDO "PEPTIDE DERIVED CHROMOPHORE" ? ?
#
_pdbx_chem_comp_pcm.pcm_id 1
_pdbx_chem_comp_pcm.comp_id MDO
_pdbx_chem_comp_pcm.modified_residue_id "ALA, SER, GLY"
_pdbx_chem_comp_pcm.type None
_pdbx_chem_comp_pcm.category Chromophore/chromophore-like
_pdbx_chem_comp_pcm.position "Amino-acid side chain and backbone"
_pdbx_chem_comp_pcm.polypeptide_position "Any 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 ?
#