data_IWD
#
_chem_comp.id IWD
_chem_comp.name "2-AMINO-3-(5-IODO-2,4-DIOXO-3,4-DIHYDRO-2H-PYRIMIDIN-1-YL)-PROPIONIC ACID"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C7 H8 I N3 O4"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms IODO-WILLARDIINE
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2002-09-18
_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 325.061
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code IWD
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag N
_chem_comp.pdbx_ideal_coordinates_details ?
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code 1MQG
_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
IWD N1 N1 N 0 1 Y N N N N N 18.712 3.098 21.051 -0.685 -0.451 1.255 N1 IWD 1
IWD C2 C2 C 0 1 Y N N N N N 17.841 3.776 20.157 -1.995 -0.156 1.161 C2 IWD 2
IWD O2 O2 O 0 1 N N N N N N 18.194 4.334 19.147 -2.689 -0.186 2.159 O2 IWD 3
IWD N3 N3 N 0 1 Y N N N N N 16.484 3.743 20.552 -2.544 0.183 -0.019 N3 IWD 4
IWD C4 C4 C 0 1 Y N N N N N 15.935 3.145 21.655 -1.789 0.222 -1.135 C4 IWD 5
IWD O4 O4 O 0 1 N N N N N N 14.744 3.197 21.902 -2.287 0.524 -2.204 O4 IWD 6
IWD C5 C5 C 0 1 Y N N N N N 16.967 2.446 22.536 -0.410 -0.092 -1.052 C5 IWD 7
IWD I5 I5 I 0 1 N N N N N N 16.375 1.420 24.242 0.794 -0.043 -2.765 I5 IWD 8
IWD C6 C6 C 0 1 Y N N N N N 18.258 2.462 22.152 0.116 -0.424 0.146 C6 IWD 9
IWD C7 C7 C 0 1 N N N N N N 20.153 2.981 20.749 -0.114 -0.812 2.555 C7 IWD 10
IWD C8 C8 C 0 1 N N S N N N 20.456 2.073 19.569 0.385 0.450 3.259 C8 IWD 11
IWD N8 N8 N 0 1 N N N N N N 20.160 0.651 19.960 1.415 1.096 2.434 N8 IWD 12
IWD C9 C9 C 0 1 N N N N N N 21.879 2.194 18.997 0.973 0.079 4.597 C9 IWD 13
IWD O91 O91 O 0 1 N N N N N N 22.564 1.189 18.891 2.147 -0.191 4.686 O91 IWD 14
IWD O92 O92 O 0 1 N N N N N N 22.235 3.398 18.714 0.192 0.051 5.688 O92 IWD 15
IWD H3 H3 H 0 1 N N N N N N 15.805 4.217 19.957 -3.489 0.397 -0.068 H3 IWD 16
IWD H6 H6 H 0 1 N N N N N N 18.988 1.921 22.777 1.165 -0.666 0.229 H6 IWD 17
IWD H71 1H7 H 0 1 N N N N N N 20.606 3.988 20.597 0.717 -1.500 2.408 H71 IWD 18
IWD H72 2H7 H 0 1 N N N N N N 20.719 2.655 21.652 -0.878 -1.291 3.167 H72 IWD 19
IWD H8 H8 H 0 1 N N N N N N 19.794 2.409 18.737 -0.446 1.138 3.406 H8 IWD 20
IWD H81 1H8 H 0 1 N N N N N N 20.363 0.041 19.167 2.161 0.426 2.325 H81 IWD 21
IWD H82 2H8 H 0 1 N N N N N N 19.208 0.533 20.307 1.010 1.232 1.520 H82 IWD 22
IWD H92O OH92 H 0 0 N N N N N N 23.113 3.472 18.360 0.569 -0.186 6.546 H92O IWD 23
#
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
IWD N1 C2 SING Y N 1
IWD N1 C6 SING Y N 2
IWD N1 C7 SING N N 3
IWD C2 O2 DOUB N N 4
IWD C2 N3 SING Y N 5
IWD N3 C4 SING Y N 6
IWD N3 H3 SING N N 7
IWD C4 O4 DOUB N N 8
IWD C4 C5 SING Y N 9
IWD C5 I5 SING N N 10
IWD C5 C6 DOUB Y N 11
IWD C6 H6 SING N N 12
IWD C7 C8 SING N N 13
IWD C7 H71 SING N N 14
IWD C7 H72 SING N N 15
IWD C8 N8 SING N N 16
IWD C8 C9 SING N N 17
IWD C8 H8 SING N N 18
IWD N8 H81 SING N N 19
IWD N8 H82 SING N N 20
IWD C9 O91 DOUB N N 21
IWD C9 O92 SING N N 22
IWD O92 H92O SING N N 23
#
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
IWD SMILES ACDLabs 10.04 O=C(O)C(N)CN1C=C(I)C(=O)NC1=O
IWD SMILES_CANONICAL CACTVS 3.341 N[C@@H](CN1C=C(I)C(=O)NC1=O)C(O)=O
IWD SMILES CACTVS 3.341 N[CH](CN1C=C(I)C(=O)NC1=O)C(O)=O
IWD SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 C1=C(C(=O)NC(=O)N1C[C@@H](C(=O)O)N)I
IWD SMILES "OpenEye OEToolkits" 1.5.0 C1=C(C(=O)NC(=O)N1CC(C(=O)O)N)I
IWD InChI InChI 1.03 InChI=1S/C7H8IN3O4/c8-3-1-11(2-4(9)6(13)14)7(15)10-5(3)12/h1,4H,2,9H2,(H,13,14)(H,10,12,15)/t4-/m0/s1
IWD InChIKey InChI 1.03 AXXYLTBQIQBTES-BYPYZUCNSA-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
IWD "SYSTEMATIC NAME" ACDLabs 10.04 3-(5-iodo-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-L-alanine
IWD "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "(2S)-2-amino-3-(5-iodo-2,4-dioxo-pyrimidin-1-yl)propanoic 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
IWD 'Create component' 2002-09-18 RCSB
IWD 'Modify descriptor' 2011-06-04 RCSB
IWD 'Modify synonyms' 2021-03-01 PDBE
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id IWD
_pdbx_chem_comp_synonyms.name IODO-WILLARDIINE
_pdbx_chem_comp_synonyms.provenance ?
_pdbx_chem_comp_synonyms.type ?
#
_pdbe_chem_comp_drugbank_details.comp_id IWD
_pdbe_chem_comp_drugbank_details.drugbank_id DB02818
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name Iodo-Willardiine
_pdbe_chem_comp_drugbank_details.description ?
_pdbe_chem_comp_drugbank_details.cas_number ?
_pdbe_chem_comp_drugbank_details.mechanism_of_action ?
#
loop_
_pdbe_chem_comp_synonyms.comp_id
_pdbe_chem_comp_synonyms.name
_pdbe_chem_comp_synonyms.provenance
_pdbe_chem_comp_synonyms.type
IWD IODO-WILLARDIINE wwPDB ?
IWD Iodo-Willardiine DrugBank ?
#
_pdbe_chem_comp_drugbank_classification.comp_id IWD
_pdbe_chem_comp_drugbank_classification.drugbank_id DB02818
_pdbe_chem_comp_drugbank_classification.parent 'L-alpha-amino acids'
_pdbe_chem_comp_drugbank_classification.kingdom 'Organic compounds'
_pdbe_chem_comp_drugbank_classification.class 'Carboxylic acids and derivatives'
_pdbe_chem_comp_drugbank_classification.superclass 'Organic acids and derivatives'
_pdbe_chem_comp_drugbank_classification.description
'This compound belongs to the class of organic compounds known as l-alpha-amino acids. These are alpha amino acids which have the L-configuration of the alpha-carbon atom.'
#
loop_
_pdbe_chem_comp_drugbank_targets.comp_id
_pdbe_chem_comp_drugbank_targets.drugbank_id
_pdbe_chem_comp_drugbank_targets.name
_pdbe_chem_comp_drugbank_targets.organism
_pdbe_chem_comp_drugbank_targets.uniprot_id
_pdbe_chem_comp_drugbank_targets.pharmacologically_active
_pdbe_chem_comp_drugbank_targets.ordinal
IWD DB02818 'Glutamate receptor ionotropic, kainate 1' Humans P39086 unknown 1
IWD DB02818 'Glutamate receptor 2' Humans P42262 unknown 2
#
loop_
_software.name
_software.version
_software.description
rdkit 2025.03.3 'Core functionality.'
pdbeccdutils 1.0.0 '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
IWD N1 N 6.404 0.465 1
IWD C2 C 7.702 1.215 2
IWD O2 O 9.002 0.465 3
IWD N3 N 7.702 2.715 4
IWD C4 C 6.404 3.465 5
IWD O4 O 6.404 4.965 6
IWD C5 C 5.104 2.715 7
IWD I5 I 3.805 3.465 8
IWD C6 C 5.104 1.215 9
IWD C7 C 6.404 -1.035 10
IWD C8 C 5.104 -1.785 11
IWD N8 N 3.805 -1.035 12
IWD C9 C 5.104 -3.285 13
IWD O91 O 3.805 -4.035 14
IWD O92 O 6.404 -4.035 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
IWD N1 C2 SINGLE NONE 1
IWD N1 C6 SINGLE NONE 2
IWD N1 C7 SINGLE NONE 3
IWD C2 O2 DOUBLE NONE 4
IWD C2 N3 SINGLE NONE 5
IWD N3 C4 SINGLE NONE 6
IWD C4 O4 DOUBLE NONE 7
IWD C4 C5 SINGLE NONE 8
IWD C5 I5 SINGLE NONE 9
IWD C5 C6 DOUBLE NONE 10
IWD C7 C8 SINGLE NONE 11
IWD C8 N8 SINGLE BEGINWEDGE 12
IWD C8 C9 SINGLE NONE 13
IWD C9 O91 DOUBLE NONE 14
IWD C9 O92 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
IWD MurckoScaffold S1 scaffold 'O=c1cc[nH]c(=O)[nH]1' InChI=1S/C4H4N2O2/c7-3-1-2-5-4(8)6-3/h1-2H,(H2,5,6,7,8) ISAKRJDGNUQOIC-UHFFFAOYSA-N
IWD peptide F1 fragment NCC=O InChI=1S/C2H5NO/c3-1-2-4/h2H,1,3H2 LYIIBVSRGJSHAV-UHFFFAOYSA-N
IWD pyrimidine F2 fragment c1cncnc1 InChI=1S/C4H4N2/c1-2-5-4-6-3-1/h1-4H CZPWVGJYEJSRLH-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
IWD N1 S1 1
IWD C2 S1 1
IWD O2 S1 1
IWD N3 S1 1
IWD C4 S1 1
IWD O4 S1 1
IWD C5 S1 1
IWD C6 S1 1
IWD O91 F1 1
IWD C9 F1 1
IWD C8 F1 1
IWD N8 F1 1
IWD C5 F2 1
IWD C4 F2 1
IWD N3 F2 1
IWD C2 F2 1
IWD N1 F2 1
IWD C6 F2 1
#
_pdbe_chem_comp_rdkit_properties.comp_id IWD
_pdbe_chem_comp_rdkit_properties.exactmw 324.956
_pdbe_chem_comp_rdkit_properties.amw 325.062
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 7
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 4
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 4
_pdbe_chem_comp_rdkit_properties.NumHBD 3
_pdbe_chem_comp_rdkit_properties.NumHBA 6
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 15
_pdbe_chem_comp_rdkit_properties.NumAtoms 23
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 8
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.286
_pdbe_chem_comp_rdkit_properties.NumRings 1
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 1
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 0
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 1
_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 108.557
_pdbe_chem_comp_rdkit_properties.tpsa 118.180
_pdbe_chem_comp_rdkit_properties.CrippenClogP 0.353
_pdbe_chem_comp_rdkit_properties.CrippenMR 59.867
_pdbe_chem_comp_rdkit_properties.chi0v 9.010
_pdbe_chem_comp_rdkit_properties.chi1v 4.426
_pdbe_chem_comp_rdkit_properties.chi2v 1.900
_pdbe_chem_comp_rdkit_properties.chi3v 1.900
_pdbe_chem_comp_rdkit_properties.chi4v 0.969
_pdbe_chem_comp_rdkit_properties.chi0n 14.853
_pdbe_chem_comp_rdkit_properties.chi1n 7.097
_pdbe_chem_comp_rdkit_properties.chi2n 1.197
_pdbe_chem_comp_rdkit_properties.chi3n 1.197
_pdbe_chem_comp_rdkit_properties.chi4n 0.607
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.160
_pdbe_chem_comp_rdkit_properties.kappa1 4.784
_pdbe_chem_comp_rdkit_properties.kappa2 4.573
_pdbe_chem_comp_rdkit_properties.kappa3 2.892
_pdbe_chem_comp_rdkit_properties.Phi 1.458
#
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
IWD UniChem DrugBank DB02818
IWD UniChem 'Guide to Pharmacology' 4071
IWD UniChem ZINC ZINC000002047688
IWD UniChem 'PubChem TPHARMA' 136973113
IWD UniChem BindingDb 50060627
IWD UniChem 'EPA CompTox Dashboard' DTXSID90332246
IWD UniChem 'Probes And Drugs' PD007614
IWD UniChem Nikkaji J669.187K
IWD UniChem eMolecules 36500523
IWD UniChem SureChEMBL SCHEMBL401659
IWD UniChem PubChem 447196
#
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
IWD N1 0.396 0.537 -0.451 ETKDGv3 1
IWD C2 0.965 1.601 0.339 ETKDGv3 2
IWD O2 0.332 2.674 0.531 ETKDGv3 3
IWD N3 2.263 1.434 0.911 ETKDGv3 4
IWD C4 2.983 0.223 0.675 ETKDGv3 5
IWD O4 4.126 0.063 1.180 ETKDGv3 6
IWD C5 2.383 -0.829 -0.161 ETKDGv3 7
IWD I5 3.438 -2.622 -0.543 ETKDGv3 8
IWD C6 1.165 -0.660 -0.688 ETKDGv3 9
IWD C7 -0.949 0.657 -1.036 ETKDGv3 10
IWD C8 -2.045 0.037 -0.139 ETKDGv3 11
IWD N8 -2.146 0.708 1.161 ETKDGv3 12
IWD C9 -1.853 -1.445 0.035 ETKDGv3 13
IWD O91 -1.231 -1.901 1.033 ETKDGv3 14
IWD O92 -2.324 -2.316 -0.941 ETKDGv3 15
IWD H3 2.683 2.192 1.495 ETKDGv3 16
IWD H6 0.749 -1.448 -1.303 ETKDGv3 17
IWD H71 -1.192 1.724 -1.229 ETKDGv3 18
IWD H72 -0.969 0.160 -2.031 ETKDGv3 19
IWD H8 -3.016 0.178 -0.663 ETKDGv3 20
IWD H81 -2.328 1.725 1.002 ETKDGv3 21
IWD H82 -1.241 0.626 1.678 ETKDGv3 22
IWD H92O -2.188 -3.316 -0.855 ETKDGv3 23
#