data_EA1
#
_chem_comp.id EA1
_chem_comp.name 3H-IMIDAZO[2,1-I]PURINE
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C7 H5 N5"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms 1,N6-ETHENOADENINE
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2003-07-07
_chem_comp.pdbx_modified_date 2021-03-13
_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 159.148
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code EA1
_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 1PU8
_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
EA1 N7 N7 N 0 1 Y N N N N N 116.487 8.437 47.655 1.499 0.002 -1.663 N7 EA1 1
EA1 C8 C8 C 0 1 Y N N N N N 115.405 9.135 47.168 0.936 -0.001 -2.838 C8 EA1 2
EA1 C5 C5 C 0 1 Y N N N N N 117.552 8.951 47.019 0.544 0.001 -0.708 C5 EA1 3
EA1 C4 C4 C 0 1 Y N N N N N 117.042 9.993 46.125 -0.694 0.002 -1.355 C4 EA1 4
EA1 N3 N3 N 0 1 Y N N N N N 117.900 10.778 45.270 -1.821 0.001 -0.632 N3 EA1 5
EA1 N9 N9 N 0 1 Y N N N N N 115.728 10.088 46.232 -0.417 -0.005 -2.700 N9 EA1 6
EA1 C6 C6 C 0 1 Y N N N N N 118.927 8.788 46.961 0.550 0.005 0.753 C6 EA1 7
EA1 N6 N6 N 0 1 Y N N N N N 119.688 7.917 47.661 1.499 -0.001 1.666 N6 EA1 8
EA1 C11 C11 C 0 1 Y N N N N N 121.097 8.096 47.286 0.940 -0.002 2.882 C11 EA1 9
EA1 N1 N1 N 0 1 Y N N N N N 119.719 9.586 46.116 -0.665 -0.000 1.396 N1 EA1 10
EA1 C10 C10 C 0 1 Y N N N N N 121.022 9.213 46.254 -0.400 -0.002 2.740 C10 EA1 11
EA1 C2 C2 C 0 1 Y N N N N N 119.223 10.540 45.299 -1.816 0.000 0.668 C2 EA1 12
EA1 H8 H8 H 0 1 N N N N N N 114.369 8.947 47.498 1.464 -0.002 -3.780 H8 EA1 13
EA1 HN9 HN9 H 0 1 N N N N N N 115.120 10.730 45.723 -1.068 -0.008 -3.419 HN9 EA1 14
EA1 H11 H11 H 0 1 N N N N N N 121.970 7.544 47.672 1.474 -0.003 3.821 H11 EA1 15
EA1 H10 H10 H 0 1 N N N N N N 121.822 9.698 45.671 -1.130 -0.002 3.537 H10 EA1 16
EA1 H2 H2 H 0 1 N N N N N N 119.899 11.125 44.654 -2.761 -0.000 1.191 H2 EA1 17
#
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
EA1 N7 C8 DOUB Y N 1
EA1 N7 C5 SING Y N 2
EA1 C8 N9 SING Y N 3
EA1 C8 H8 SING N N 4
EA1 C5 C4 DOUB Y N 5
EA1 C5 C6 SING Y N 6
EA1 C4 N3 SING Y N 7
EA1 C4 N9 SING Y N 8
EA1 N3 C2 DOUB Y N 9
EA1 N9 HN9 SING N N 10
EA1 C6 N6 DOUB Y N 11
EA1 C6 N1 SING Y N 12
EA1 N6 C11 SING Y N 13
EA1 C11 C10 DOUB Y N 14
EA1 C11 H11 SING N N 15
EA1 N1 C10 SING Y N 16
EA1 N1 C2 SING Y N 17
EA1 C10 H10 SING N N 18
EA1 C2 H2 SING N N 19
#
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
EA1 SMILES ACDLabs 10.04 n2cnc3ncn1c(ncc1)c23
EA1 SMILES_CANONICAL CACTVS 3.341 "[nH]1cnc2c1ncn3ccnc23"
EA1 SMILES CACTVS 3.341 "[nH]1cnc2c1ncn3ccnc23"
EA1 SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 c1cn2cnc3c(c2n1)nc[nH]3
EA1 SMILES "OpenEye OEToolkits" 1.5.0 c1cn2cnc3c(c2n1)nc[nH]3
EA1 InChI InChI 1.03 InChI=1S/C7H5N5/c1-2-12-4-11-6-5(7(12)8-1)9-3-10-6/h1-4H,(H,9,10)
EA1 InChIKey InChI 1.03 OGVOXGPIHFKUGM-UHFFFAOYSA-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
EA1 "SYSTEMATIC NAME" ACDLabs 10.04 3H-imidazo[2,1-i]purine
EA1 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 3H-imidazo[2,1-f]purine
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
EA1 'Create component' 2003-07-07 RCSB
EA1 'Modify descriptor' 2011-06-04 RCSB
EA1 'Modify synonyms' 2021-03-13 RCSB
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id EA1
_pdbx_chem_comp_synonyms.name 1,N6-ETHENOADENINE
_pdbx_chem_comp_synonyms.provenance PDB
_pdbx_chem_comp_synonyms.type ?
#
_pdbe_chem_comp_drugbank_details.comp_id EA1
_pdbe_chem_comp_drugbank_details.drugbank_id DB01952
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name 1,N6-Ethenoadenine
_pdbe_chem_comp_drugbank_details.description ?
_pdbe_chem_comp_drugbank_details.cas_number 13875-63-3
_pdbe_chem_comp_drugbank_details.mechanism_of_action ?
#
_pdbe_chem_comp_synonyms.comp_id EA1
_pdbe_chem_comp_synonyms.name 1,N6-ETHENOADENINE
_pdbe_chem_comp_synonyms.provenance wwPDB
_pdbe_chem_comp_synonyms.type ?
#
_pdbe_chem_comp_drugbank_classification.comp_id EA1
_pdbe_chem_comp_drugbank_classification.drugbank_id DB01952
_pdbe_chem_comp_drugbank_classification.parent 'Purines and purine derivatives'
_pdbe_chem_comp_drugbank_classification.kingdom 'Organic compounds'
_pdbe_chem_comp_drugbank_classification.class Imidazopyrimidines
_pdbe_chem_comp_drugbank_classification.superclass 'Organoheterocyclic compounds'
_pdbe_chem_comp_drugbank_classification.description
'This compound belongs to the class of organic compounds known as purines and purine derivatives. These are aromatic heterocyclic compounds containing a purine moiety, which is formed a pyrimidine-ring ring fused to an imidazole ring.'
#
_pdbe_chem_comp_drugbank_targets.comp_id EA1
_pdbe_chem_comp_drugbank_targets.drugbank_id DB01952
_pdbe_chem_comp_drugbank_targets.name 'Endonuclease III'
_pdbe_chem_comp_drugbank_targets.organism 'Helicobacter pylori (strain ATCC 700392 / 26695)'
_pdbe_chem_comp_drugbank_targets.uniprot_id O25323
_pdbe_chem_comp_drugbank_targets.pharmacologically_active unknown
_pdbe_chem_comp_drugbank_targets.ordinal 1
#
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
EA1 N7 N 3.875 -0.132 1
EA1 C8 C 3.000 1.075 2
EA1 C5 C 5.295 0.325 3
EA1 C4 C 5.295 1.825 4
EA1 N3 N 6.594 2.575 5
EA1 N9 N 3.875 2.282 6
EA1 C6 C 6.594 -0.425 7
EA1 N6 N 6.908 -1.883 8
EA1 C11 C 8.391 -2.037 9
EA1 N1 N 7.893 0.325 10
EA1 C10 C 8.998 -0.676 11
EA1 C2 C 7.893 1.825 12
#
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
EA1 N7 C8 DOUBLE NONE 1
EA1 N7 C5 SINGLE NONE 2
EA1 C8 N9 SINGLE NONE 3
EA1 C5 C4 DOUBLE NONE 4
EA1 C5 C6 SINGLE NONE 5
EA1 C4 N3 SINGLE NONE 6
EA1 C4 N9 SINGLE NONE 7
EA1 N3 C2 DOUBLE NONE 8
EA1 C6 N6 DOUBLE NONE 9
EA1 C6 N1 SINGLE NONE 10
EA1 N6 C11 SINGLE NONE 11
EA1 C11 C10 DOUBLE NONE 12
EA1 N1 C10 SINGLE NONE 13
EA1 N1 C2 SINGLE NONE 14
#
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
EA1 MurckoScaffold S1 scaffold 'c1cn2cnc3[nH]cnc3c2n1' InChI=1S/C7H5N5/c1-2-12-4-11-6-5(7(12)8-1)9-3-10-6/h1-4H,(H,9,10) OGVOXGPIHFKUGM-UHFFFAOYSA-N
EA1 imidazole F1 fragment 'c1c[nH]cn1' InChI=1S/C3H4N2/c1-2-5-3-4-1/h1-3H,(H,4,5) RAXXELZNTBOGNW-UHFFFAOYSA-N
EA1 purine F2 fragment 'c1ncc2[nH]cnc2n1' InChI=1S/C5H4N4/c1-4-5(8-2-6-1)9-3-7-4/h1-3H,(H,6,7,8,9) KDCGOANMDULRCW-UHFFFAOYSA-N
EA1 pyrimidine F3 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
EA1 N7 S1 1
EA1 C8 S1 1
EA1 C5 S1 1
EA1 C4 S1 1
EA1 N3 S1 1
EA1 N9 S1 1
EA1 C6 S1 1
EA1 N6 S1 1
EA1 C11 S1 1
EA1 N1 S1 1
EA1 C10 S1 1
EA1 C2 S1 1
EA1 C5 F1 1
EA1 C4 F1 1
EA1 N9 F1 1
EA1 C8 F1 1
EA1 N7 F1 1
EA1 C11 F1 2
EA1 C10 F1 2
EA1 N1 F1 2
EA1 C6 F1 2
EA1 N6 F1 2
EA1 N7 F2 1
EA1 C8 F2 1
EA1 N9 F2 1
EA1 C4 F2 1
EA1 C5 F2 1
EA1 C6 F2 1
EA1 N1 F2 1
EA1 C2 F2 1
EA1 N3 F2 1
EA1 C5 F3 1
EA1 C4 F3 1
EA1 N3 F3 1
EA1 C2 F3 1
EA1 N1 F3 1
EA1 C6 F3 1
#
_pdbe_chem_comp_rdkit_properties.comp_id EA1
_pdbe_chem_comp_rdkit_properties.exactmw 159.054
_pdbe_chem_comp_rdkit_properties.amw 159.152
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 5
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 1
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 0
_pdbe_chem_comp_rdkit_properties.NumHBD 1
_pdbe_chem_comp_rdkit_properties.NumHBA 4
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 12
_pdbe_chem_comp_rdkit_properties.NumAtoms 17
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 5
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0
_pdbe_chem_comp_rdkit_properties.NumRings 3
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 3
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 0
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 3
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 3
_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 0
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 74.182
_pdbe_chem_comp_rdkit_properties.tpsa 58.870
_pdbe_chem_comp_rdkit_properties.CrippenClogP -0.037
_pdbe_chem_comp_rdkit_properties.CrippenMR 39.330
_pdbe_chem_comp_rdkit_properties.chi0v 5.736
_pdbe_chem_comp_rdkit_properties.chi1v 3.210
_pdbe_chem_comp_rdkit_properties.chi2v 1.533
_pdbe_chem_comp_rdkit_properties.chi3v 1.533
_pdbe_chem_comp_rdkit_properties.chi4v 1.013
_pdbe_chem_comp_rdkit_properties.chi0n 10.736
_pdbe_chem_comp_rdkit_properties.chi1n 5.657
_pdbe_chem_comp_rdkit_properties.chi2n 1.533
_pdbe_chem_comp_rdkit_properties.chi3n 1.533
_pdbe_chem_comp_rdkit_properties.chi4n 1.013
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.910
_pdbe_chem_comp_rdkit_properties.kappa1 2.855
_pdbe_chem_comp_rdkit_properties.kappa2 1.818
_pdbe_chem_comp_rdkit_properties.kappa3 0.554
_pdbe_chem_comp_rdkit_properties.Phi 0.432
#
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
EA1 UniChem DrugBank DB01952
EA1 UniChem PDBe EA1
EA1 UniChem ChEBI 29146
EA1 UniChem ChEBI 42173
EA1 UniChem ZINC ZINC000012501389
EA1 UniChem fdasrs SIN7411HG7
EA1 UniChem HMDB HMDB0244259
EA1 UniChem ACTor 13875-63-3
EA1 UniChem Nikkaji J396.647J
EA1 UniChem 'EPA CompTox Dashboard' DTXSID90160768
EA1 UniChem BRENDA 37374
EA1 UniChem 'Probes And Drugs' PD060208
EA1 UniChem PubChem 104994
EA1 UniChem SureChEMBL SCHEMBL8127207
#
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
EA1 N7 -1.716 1.651 0.575 ETKDGv3 1
EA1 C8 -2.879 1.101 0.367 ETKDGv3 2
EA1 C5 -0.793 0.612 0.276 ETKDGv3 3
EA1 C4 -1.414 -0.487 -0.088 ETKDGv3 4
EA1 N3 -0.733 -1.711 -0.452 ETKDGv3 5
EA1 N9 -2.808 -0.267 -0.061 ETKDGv3 6
EA1 C6 0.659 0.606 0.319 ETKDGv3 7
EA1 N6 1.458 1.567 0.645 ETKDGv3 8
EA1 C11 2.765 0.983 0.501 ETKDGv3 9
EA1 N1 1.310 -0.590 -0.038 ETKDGv3 10
EA1 C10 2.681 -0.285 0.100 ETKDGv3 11
EA1 C2 0.578 -1.763 -0.429 ETKDGv3 12
EA1 H8 -3.810 1.632 0.506 ETKDGv3 13
EA1 HN9 -3.584 -0.925 -0.292 ETKDGv3 14
EA1 H11 3.689 1.511 0.696 ETKDGv3 15
EA1 H10 3.503 -0.962 -0.088 ETKDGv3 16
EA1 H2 1.096 -2.673 -0.700 ETKDGv3 17
#