data_CRX
#
_chem_comp.id CRX
_chem_comp.name '[2-(1-AMINOETHYL)-2-HYDROXY-4-METHYLENE-5-OXOIMIDAZOLIDIN-1-YL]ACETIC ACID'
_chem_comp.type 'L-PEPTIDE LINKING'
_chem_comp.pdbx_type ATOMP
_chem_comp.formula 'C8 H13 N3 O4'
_chem_comp.mon_nstd_parent_comp_id 'ALA, SER, GLY'
_chem_comp.pdbx_synonyms 'CHROMOPHORE (ALA-SER-GLY)'
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2005-01-28
_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 215.207
_chem_comp.one_letter_code ASG
_chem_comp.three_letter_code CRX
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag Y
_chem_comp.pdbx_ideal_coordinates_details ?
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code 1YJ2
_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
CRX N1 N1 N 0 1 N N N Y Y N 23.812 27.127 1.467 2.871 -1.543 3.961 N1 CRX 1
CRX CA1 CA1 C 0 1 N N S Y N N 24.759 26.115 1.691 3.854 -0.439 3.842 CA1 CRX 2
CRX CB1 CB1 C 0 1 N N N N N N 25.661 26.184 0.523 5.154 -0.989 3.274 CB1 CRX 3
CRX C1 C1 C 0 1 N N R Y N N 25.614 26.186 2.957 3.267 0.650 2.955 C1 CRX 4
CRX N2 N2 N 0 1 N N N Y N N 26.674 27.188 2.901 2.991 0.122 1.637 N2 CRX 5
CRX N3 N3 N 0 1 N N N Y N N 24.841 26.551 4.127 1.937 1.090 3.372 N3 CRX 6
CRX C2 C2 C 0 1 N N N Y N N 25.694 27.277 5.035 0.952 0.860 2.402 C2 CRX 7
CRX O2 O2 O 0 1 N N N Y N N 25.398 27.528 6.212 -0.240 1.111 2.436 O2 CRX 8
CRX CA2 CA2 C 0 1 N N N Y N N 26.744 27.713 4.184 1.681 0.220 1.269 CA2 CRX 9
CRX CA3 CA3 C 0 1 N N N Y N N 23.555 26.081 4.468 1.681 1.714 4.657 CA3 CRX 10
CRX C3 C3 C 0 1 N N N Y N Y 23.446 24.753 5.064 1.871 3.193 4.518 C3 CRX 11
CRX O3 O3 O 0 1 N N N Y N Y 22.553 24.472 5.882 1.666 3.861 3.515 O3 CRX 12
CRX CB2 CB2 C 0 1 N N N N N N 27.732 28.497 4.533 1.065 -0.148 0.145 CB2 CRX 13
CRX O1 O1 O 0 1 N N N N N N 26.233 24.883 3.002 4.149 1.760 2.875 O1 CRX 14
CRX OXT OXT O 0 1 N Y N Y N Y ? ? ? 2.314 3.716 5.691 OXT CRX 15
CRX H HN11 H 0 0 N N N Y Y N 23.334 27.058 0.568 2.813 -2.172 3.203 HN11 CRX 16
CRX H2 HN12 H 0 0 N Y N Y Y N 23.189 27.079 2.273 2.201 -1.469 4.681 HN12 CRX 17
CRX HA1 HA1 H 0 1 N N N Y N N 24.184 25.170 1.833 4.033 -0.035 4.844 HA1 CRX 18
CRX HB11 HB11 H 0 0 N N N N N N 26.105 27.192 0.351 5.067 -2.060 3.066 HB11 CRX 19
CRX HB12 HB12 H 0 0 N N N N N N 26.413 25.380 0.701 5.429 -0.482 2.342 HB12 CRX 20
CRX HB13 HB13 H 0 0 N N N N N N 25.139 26.108 -0.459 5.978 -0.846 3.981 HB13 CRX 21
CRX HN2 HN2 H 0 1 N N N Y N N 26.539 27.891 2.175 3.693 -0.266 1.022 HN2 CRX 22
CRX HA31 HA31 H 0 0 N N N Y N N 22.897 26.133 3.570 2.390 1.320 5.390 HA31 CRX 23
CRX HA32 HA32 H 0 0 N N N Y N N 23.060 26.823 5.137 0.654 1.498 4.962 HA32 CRX 24
CRX HB21 HB21 H 0 0 N N N N N N 27.788 28.914 5.553 1.618 -0.611 -0.664 HB21 CRX 25
CRX HB22 HB22 H 0 0 N N N N N N 28.548 28.836 3.872 -0.000 0.011 0.020 HB22 CRX 26
CRX HO1 HO1 H 0 1 N N N N N N 26.764 24.927 3.788 4.733 1.602 2.116 HO1 CRX 27
CRX HXT HXT H 0 1 N Y N Y N Y -0.071 -0.864 0.388 2.448 4.686 5.632 HXT CRX 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
CRX N1 CA1 SING N N 1
CRX N1 H SING N N 2
CRX N1 H2 SING N N 3
CRX CA1 CB1 SING N N 4
CRX CA1 C1 SING N N 5
CRX CA1 HA1 SING N N 6
CRX CB1 HB11 SING N N 7
CRX CB1 HB12 SING N N 8
CRX CB1 HB13 SING N N 9
CRX C1 N2 SING N N 10
CRX C1 N3 SING N N 11
CRX C1 O1 SING N N 12
CRX N2 CA2 SING N N 13
CRX N2 HN2 SING N N 14
CRX N3 C2 SING N N 15
CRX N3 CA3 SING N N 16
CRX C2 O2 DOUB N N 17
CRX C2 CA2 SING N N 18
CRX CA2 CB2 DOUB N N 19
CRX CA3 C3 SING N N 20
CRX CA3 HA31 SING N N 21
CRX CA3 HA32 SING N N 22
CRX C3 O3 DOUB N N 23
CRX C3 OXT SING N N 24
CRX CB2 HB21 SING N N 25
CRX CB2 HB22 SING N N 26
CRX O1 HO1 SING N N 27
CRX OXT HXT SING N N 28
#
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
CRX SMILES ACDLabs 10.04 'O=C(O)CN1C(=O)/C(NC1(O)C(N)C)=C'
CRX SMILES_CANONICAL CACTVS 3.341 'C[C@H](N)[C@@]1(O)NC(=C)C(=O)N1CC(O)=O'
CRX SMILES CACTVS 3.341 'C[CH](N)[C]1(O)NC(=C)C(=O)N1CC(O)=O'
CRX SMILES_CANONICAL 'OpenEye OEToolkits' 1.5.0 'C[C@@H]([C@]1(NC(=C)C(=O)N1CC(=O)O)O)N'
CRX SMILES 'OpenEye OEToolkits' 1.5.0 'CC(C1(NC(=C)C(=O)N1CC(=O)O)O)N'
CRX InChI InChI 1.03 'InChI=1S/C8H13N3O4/c1-4-7(14)11(3-6(12)13)8(15,10-4)5(2)9/h5,10,15H,1,3,9H2,2H3,(H,12,13)/t5-,8+/m0/s1'
CRX InChIKey InChI 1.03 KGHMLYAJQPCDLM-YLWLKBPMSA-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
CRX 'SYSTEMATIC NAME' ACDLabs 10.04 '{(2R)-2-[(1S)-1-aminoethyl]-2-hydroxy-4-methylidene-5-oxoimidazolidin-1-yl}acetic acid'
CRX 'SYSTEMATIC NAME' 'OpenEye OEToolkits' 1.5.0 '2-[(2R)-2-[(1S)-1-aminoethyl]-2-hydroxy-4-methylidene-5-oxo-imidazolidin-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
CRX 'Create component' 2005-01-28 RCSB
CRX 'Modify descriptor' 2011-06-04 RCSB
CRX 'Modify synonyms' 2020-06-05 PDBE
CRX 'Modify backbone' 2023-11-03 PDBE
CRX 'Modify PCM' 2024-09-27 PDBE
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id CRX
_pdbx_chem_comp_synonyms.name 'CHROMOPHORE (ALA-SER-GLY)'
_pdbx_chem_comp_synonyms.provenance ?
_pdbx_chem_comp_synonyms.type ?
#
_pdbx_chem_comp_pcm.pcm_id 1
_pdbx_chem_comp_pcm.comp_id CRX
_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 ?
_pdbx_chem_comp_pcm.first_instance_model_db_code 1YJ2
#
_pdbe_chem_comp_synonyms.comp_id CRX
_pdbe_chem_comp_synonyms.name 'CHROMOPHORE (ALA-SER-GLY)'
_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
CRX N1 N 9.144 2.677 1
CRX CA1 C 9.754 1.306 2
CRX CB1 C 11.246 1.149 3
CRX C1 C 8.873 0.093 4
CRX N2 N 10.086 -0.789 5
CRX N3 N 7.659 -0.789 6
CRX C2 C 8.123 -2.216 7
CRX O2 O 7.241 -3.429 8
CRX CA2 C 9.623 -2.216 9
CRX CA3 C 6.232 -0.325 10
CRX C3 C 5.118 -1.329 11
CRX O3 O 3.691 -0.866 12
CRX CB2 C 10.504 -3.429 13
CRX O1 O 7.991 1.306 14
CRX OXT O 5.429 -2.796 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
CRX N1 CA1 SINGLE NONE 1
CRX CA1 CB1 SINGLE BEGINWEDGE 2
CRX CA1 C1 SINGLE NONE 3
CRX C1 N2 SINGLE NONE 4
CRX C1 N3 SINGLE NONE 5
CRX C1 O1 SINGLE BEGINDASH 6
CRX N2 CA2 SINGLE NONE 7
CRX N3 C2 SINGLE NONE 8
CRX N3 CA3 SINGLE NONE 9
CRX C2 O2 DOUBLE NONE 10
CRX C2 CA2 SINGLE NONE 11
CRX CA2 CB2 DOUBLE NONE 12
CRX CA3 C3 SINGLE NONE 13
CRX C3 O3 DOUBLE NONE 14
CRX C3 OXT SINGLE 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
CRX MurckoScaffold S1 scaffold C=C1NCNC1=O InChI=1S/C4H6N2O/c1-3-4(7)6-2-5-3/h5H,1-2H2,(H,6,7) BKTBOPBQVTXOFL-UHFFFAOYSA-N
CRX amide F1 fragment CC(N)=O InChI=1S/C2H5NO/c1-2(3)4/h1H3,(H2,3,4) DLFVBJFMPXGRIB-UHFFFAOYSA-N
CRX 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
CRX C1 S1 1
CRX N2 S1 1
CRX N3 S1 1
CRX C2 S1 1
CRX O2 S1 1
CRX CA2 S1 1
CRX CB2 S1 1
CRX N3 F1 1
CRX C2 F1 1
CRX O2 F1 1
CRX CA2 F1 1
CRX O2 F2 1
CRX C2 F2 1
CRX CA2 F2 1
CRX N2 F2 1
CRX O3 F2 2
CRX C3 F2 2
CRX CA3 F2 2
CRX N3 F2 2
#
_pdbe_chem_comp_rdkit_properties.comp_id CRX
_pdbe_chem_comp_rdkit_properties.exactmw 215.091
_pdbe_chem_comp_rdkit_properties.amw 215.209
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 7
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 5
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 6
_pdbe_chem_comp_rdkit_properties.NumHBD 4
_pdbe_chem_comp_rdkit_properties.NumHBA 6
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 15
_pdbe_chem_comp_rdkit_properties.NumAtoms 28
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 7
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 1
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.500
_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 2
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 104.772
_pdbe_chem_comp_rdkit_properties.tpsa 115.890
_pdbe_chem_comp_rdkit_properties.CrippenClogP -1.990
_pdbe_chem_comp_rdkit_properties.CrippenMR 50.224
_pdbe_chem_comp_rdkit_properties.chi0v 6.975
_pdbe_chem_comp_rdkit_properties.chi1v 3.408
_pdbe_chem_comp_rdkit_properties.chi2v 1.484
_pdbe_chem_comp_rdkit_properties.chi3v 1.484
_pdbe_chem_comp_rdkit_properties.chi4v 0.870
_pdbe_chem_comp_rdkit_properties.chi0n 19.975
_pdbe_chem_comp_rdkit_properties.chi1n 9.566
_pdbe_chem_comp_rdkit_properties.chi2n 1.484
_pdbe_chem_comp_rdkit_properties.chi3n 1.484
_pdbe_chem_comp_rdkit_properties.chi4n 0.870
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.600
_pdbe_chem_comp_rdkit_properties.kappa1 2.956
_pdbe_chem_comp_rdkit_properties.kappa2 3.519
_pdbe_chem_comp_rdkit_properties.kappa3 1.786
_pdbe_chem_comp_rdkit_properties.Phi 0.694
#
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
CRX UniChem PDBe CRX
CRX UniChem ZINC ZINC000103537280
CRX UniChem PubChem 49866832
#
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
CRX N1 -2.821 -0.312 0.127 ETKDGv3 1
CRX CA1 -1.474 -0.861 -0.071 ETKDGv3 2
CRX CB1 -1.480 -1.765 -1.319 ETKDGv3 3
CRX C1 -0.401 0.282 -0.165 ETKDGv3 4
CRX N2 -0.810 1.464 0.620 ETKDGv3 5
CRX N3 0.879 -0.149 0.447 ETKDGv3 6
CRX C2 1.202 0.754 1.498 ETKDGv3 7
CRX O2 2.245 0.690 2.202 ETKDGv3 8
CRX CA2 0.167 1.741 1.610 ETKDGv3 9
CRX CA3 1.772 -1.212 -0.023 ETKDGv3 10
CRX C3 2.412 -0.824 -1.317 ETKDGv3 11
CRX O3 2.166 -1.476 -2.367 ETKDGv3 12
CRX CB2 0.113 2.758 2.465 ETKDGv3 13
CRX O1 -0.174 0.675 -1.496 ETKDGv3 14
CRX OXT 3.276 0.266 -1.361 ETKDGv3 15
CRX H -2.888 0.054 1.104 ETKDGv3 16
CRX H2 -3.516 -1.093 0.086 ETKDGv3 17
CRX HA1 -1.228 -1.503 0.807 ETKDGv3 18
CRX HB11 -2.099 -2.668 -1.127 ETKDGv3 19
CRX HB12 -1.914 -1.226 -2.187 ETKDGv3 20
CRX HB13 -0.463 -2.102 -1.592 ETKDGv3 21
CRX HN2 -1.628 2.078 0.406 ETKDGv3 22
CRX HA31 1.213 -2.164 -0.122 ETKDGv3 23
CRX HA32 2.574 -1.397 0.723 ETKDGv3 24
CRX HB21 -0.724 3.444 2.445 ETKDGv3 25
CRX HB22 0.901 2.912 3.191 ETKDGv3 26
CRX HO1 -1.014 1.087 -1.827 ETKDGv3 27
CRX HXT 3.714 0.546 -2.230 ETKDGv3 28
#