data_PQ0
#
_chem_comp.id PQ0
_chem_comp.name 2-AMINO-4-OXO-4,7-DIHYDRO-3H-PYRROLO[2,3-D]PYRIMIDINE-5-CARBONITRILE
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C7 H5 N5 O"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms 7-DEAZA-7-CYANO-GUANINE
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2002-01-22
_chem_comp.pdbx_modified_date 2020-06-17
_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 175.147
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code PQ0
_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 1IT8
_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
PQ0 N1 N1 N 0 1 Y N N N N N 34.509 36.982 79.328 -1.252 -0.003 1.665 N1 PQ0 1
PQ0 C2 C2 C 0 1 Y N N N N N 35.594 37.844 79.555 -0.081 0.001 2.363 C2 PQ0 2
PQ0 N3 N3 N 0 1 Y N N N N N 36.006 38.645 78.603 1.087 0.000 1.764 N3 PQ0 3
PQ0 C4 C4 C 0 1 Y N N N N N 35.345 38.659 77.278 1.183 -0.000 0.427 C4 PQ0 4
PQ0 C5 C5 C 0 1 Y N N N N N 34.303 37.845 77.020 0.013 0.000 -0.339 C5 PQ0 5
PQ0 C6 C6 C 0 1 Y N N N N N 33.838 36.938 78.105 -1.236 0.000 0.313 C6 PQ0 6
PQ0 O6 O6 O 0 1 N N N N N N 32.905 36.208 77.877 -2.275 0.000 -0.325 O6 PQ0 7
PQ0 C7 C7 C 0 1 Y N N N N N 33.955 38.164 75.623 0.443 0.000 -1.746 C7 PQ0 8
PQ0 C10 C10 C 0 1 N N N N N N 32.921 37.581 74.839 -0.399 0.000 -2.903 C10 PQ0 9
PQ0 N11 N11 N 0 1 N N N N N N 32.151 37.026 74.153 -1.069 0.000 -3.821 N11 PQ0 10
PQ0 C8 C8 C 0 1 Y N N N N N 34.807 39.097 75.252 1.806 -0.000 -1.727 C8 PQ0 11
PQ0 N9 N9 N 0 1 Y N N N N N 35.609 39.371 76.230 2.242 -0.000 -0.437 N9 PQ0 12
PQ0 N2 N2 N 0 1 N N N N N N 36.160 37.820 80.711 -0.125 0.001 3.734 N2 PQ0 13
PQ0 HN1 HN1 H 0 1 N N N N N N 34.197 36.366 80.079 -2.098 -0.003 2.139 HN1 PQ0 14
PQ0 H8 H8 H 0 1 N N N N N N 34.844 39.581 74.262 2.442 0.000 -2.600 H8 PQ0 15
PQ0 HN9 HN9 H 0 1 N N N N N N 36.357 40.063 76.181 3.174 -0.001 -0.169 HN9 PQ0 16
PQ0 HN21 1HN2 H 0 0 N N N N N N 36.445 36.864 80.922 0.698 0.000 4.246 HN21 PQ0 17
PQ0 HN22 2HN2 H 0 0 N N N N N N 36.948 38.446 80.876 -0.981 0.006 4.192 HN22 PQ0 18
#
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
PQ0 N1 C2 SING Y N 1
PQ0 N1 C6 SING Y N 2
PQ0 N1 HN1 SING N N 3
PQ0 C2 N3 DOUB Y N 4
PQ0 C2 N2 SING N N 5
PQ0 N3 C4 SING Y N 6
PQ0 C4 C5 DOUB Y N 7
PQ0 C4 N9 SING Y N 8
PQ0 C5 C6 SING Y N 9
PQ0 C5 C7 SING Y N 10
PQ0 C6 O6 DOUB N N 11
PQ0 C7 C10 SING N N 12
PQ0 C7 C8 DOUB Y N 13
PQ0 C10 N11 TRIP N N 14
PQ0 C8 N9 SING Y N 15
PQ0 C8 H8 SING N N 16
PQ0 N9 HN9 SING N N 17
PQ0 N2 HN21 SING N N 18
PQ0 N2 HN22 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
PQ0 SMILES ACDLabs 10.04 "N#Cc1cnc2N=C(NC(=O)c12)N"
PQ0 SMILES_CANONICAL CACTVS 3.341 "NC1=Nc2[nH]cc(C#N)c2C(=O)N1"
PQ0 SMILES CACTVS 3.341 "NC1=Nc2[nH]cc(C#N)c2C(=O)N1"
PQ0 SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "c1c(c2c([nH]1)N=C(NC2=O)N)C#N"
PQ0 SMILES "OpenEye OEToolkits" 1.5.0 "c1c(c2c([nH]1)N=C(NC2=O)N)C#N"
PQ0 InChI InChI 1.03 InChI=1S/C7H5N5O/c8-1-3-2-10-5-4(3)6(13)12-7(9)11-5/h2H,(H4,9,10,11,12,13)
PQ0 InChIKey InChI 1.03 FMKSMYDYKXQYRV-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
PQ0 "SYSTEMATIC NAME" ACDLabs 10.04 2-amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidine-5-carbonitrile
PQ0 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 2-amino-4-oxo-3,7-dihydropyrrolo[5,4-d]pyrimidine-5-carbonitrile
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
PQ0 'Create component' 2002-01-22 RCSB
PQ0 'Modify descriptor' 2011-06-04 RCSB
PQ0 'Modify synonyms' 2020-06-05 PDBE
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id PQ0
_pdbx_chem_comp_synonyms.name 7-DEAZA-7-CYANO-GUANINE
_pdbx_chem_comp_synonyms.provenance ?
_pdbx_chem_comp_synonyms.type ?
#
_pdbe_chem_comp_drugbank_details.comp_id PQ0
_pdbe_chem_comp_drugbank_details.drugbank_id DB03074
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name 7-cyano-7-deazaguanine
_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
PQ0 7-DEAZA-7-CYANO-GUANINE wwPDB ?
PQ0 7-CN-7-deazaG DrugBank ?
PQ0 7-Cyano-7-carbaguanine DrugBank ?
#
_pdbe_chem_comp_drugbank_classification.comp_id PQ0
_pdbe_chem_comp_drugbank_classification.drugbank_id DB03074
_pdbe_chem_comp_drugbank_classification.parent 'Pyrrolo[2,3-d]pyrimidines'
_pdbe_chem_comp_drugbank_classification.kingdom 'Organic compounds'
_pdbe_chem_comp_drugbank_classification.class Pyrrolopyrimidines
_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 pyrrolo[2,3-d]pyrimidines. These are aromatic heteropolycyclic compounds containing a pyrrolo[2,3-d]pyrimidine ring system, which is an pyrrolopyrimidine isomers having the 3 ring nitrogen atoms at the 1-, 5-, and 7-positions.'
#
_pdbe_chem_comp_drugbank_targets.comp_id PQ0
_pdbe_chem_comp_drugbank_targets.drugbank_id DB03074
_pdbe_chem_comp_drugbank_targets.name 'Queuine tRNA-ribosyltransferase'
_pdbe_chem_comp_drugbank_targets.organism 'Zymomonas mobilis subsp. mobilis (strain ATCC 31821 / ZM4 / CP4)'
_pdbe_chem_comp_drugbank_targets.uniprot_id P28720
_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
PQ0 N1 N 5.104 -0.064 1
PQ0 C2 C 5.104 -1.564 2
PQ0 N3 N 6.404 -2.314 3
PQ0 C4 C 7.702 -1.564 4
PQ0 C5 C 7.702 -0.064 5
PQ0 C6 C 6.404 0.686 6
PQ0 O6 O 6.404 2.186 7
PQ0 C7 C 9.122 0.393 8
PQ0 C10 C 9.588 1.819 9
PQ0 N11 N 10.054 3.244 10
PQ0 C8 C 9.997 -0.814 11
PQ0 N9 N 9.122 -2.021 12
PQ0 N2 N 3.805 -2.314 13
#
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
PQ0 N1 C2 SINGLE NONE 1
PQ0 N1 C6 SINGLE NONE 2
PQ0 C2 N3 DOUBLE NONE 3
PQ0 C2 N2 SINGLE NONE 4
PQ0 N3 C4 SINGLE NONE 5
PQ0 C4 C5 DOUBLE NONE 6
PQ0 C4 N9 SINGLE NONE 7
PQ0 C5 C6 SINGLE NONE 8
PQ0 C5 C7 SINGLE NONE 9
PQ0 C6 O6 DOUBLE NONE 10
PQ0 C7 C10 SINGLE NONE 11
PQ0 C7 C8 DOUBLE NONE 12
PQ0 C10 N11 TRIPLE NONE 13
PQ0 C8 N9 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
PQ0 MurckoScaffold S1 scaffold 'O=c1[nH]cnc2[nH]ccc12' InChI=1S/C6H5N3O/c10-6-4-1-2-7-5(4)8-3-9-6/h1-3H,(H2,7,8,9,10) FBMZEITWVNHWJW-UHFFFAOYSA-N
PQ0 pyrimidine F1 fragment c1cncnc1 InChI=1S/C4H4N2/c1-2-5-4-6-3-1/h1-4H CZPWVGJYEJSRLH-UHFFFAOYSA-N
PQ0 pyrrole F2 fragment 'c1cc[nH]c1' InChI=1S/C4H5N/c1-2-4-5-3-1/h1-5H KAESVJOAVNADME-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
PQ0 N1 S1 1
PQ0 C2 S1 1
PQ0 N3 S1 1
PQ0 C4 S1 1
PQ0 C5 S1 1
PQ0 C6 S1 1
PQ0 O6 S1 1
PQ0 C7 S1 1
PQ0 C8 S1 1
PQ0 N9 S1 1
PQ0 C5 F1 1
PQ0 C4 F1 1
PQ0 N3 F1 1
PQ0 C2 F1 1
PQ0 N1 F1 1
PQ0 C6 F1 1
PQ0 C4 F2 1
PQ0 C5 F2 1
PQ0 C7 F2 1
PQ0 C8 F2 1
PQ0 N9 F2 1
#
_pdbe_chem_comp_rdkit_properties.comp_id PQ0
_pdbe_chem_comp_rdkit_properties.exactmw 175.049
_pdbe_chem_comp_rdkit_properties.amw 175.151
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 6
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 4
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 1
_pdbe_chem_comp_rdkit_properties.NumHBD 3
_pdbe_chem_comp_rdkit_properties.NumHBA 4
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 13
_pdbe_chem_comp_rdkit_properties.NumAtoms 18
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 6
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0
_pdbe_chem_comp_rdkit_properties.NumRings 2
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 2
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 0
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 2
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 2
_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 79.278
_pdbe_chem_comp_rdkit_properties.tpsa 111.350
_pdbe_chem_comp_rdkit_properties.CrippenClogP -0.259
_pdbe_chem_comp_rdkit_properties.CrippenMR 42.654
_pdbe_chem_comp_rdkit_properties.chi0v 6.144
_pdbe_chem_comp_rdkit_properties.chi1v 3.243
_pdbe_chem_comp_rdkit_properties.chi2v 1.480
_pdbe_chem_comp_rdkit_properties.chi3v 1.480
_pdbe_chem_comp_rdkit_properties.chi4v 0.963
_pdbe_chem_comp_rdkit_properties.chi0n 11.144
_pdbe_chem_comp_rdkit_properties.chi1n 5.532
_pdbe_chem_comp_rdkit_properties.chi2n 1.480
_pdbe_chem_comp_rdkit_properties.chi3n 1.480
_pdbe_chem_comp_rdkit_properties.chi4n 0.963
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -2.290
_pdbe_chem_comp_rdkit_properties.kappa1 3.616
_pdbe_chem_comp_rdkit_properties.kappa2 2.349
_pdbe_chem_comp_rdkit_properties.kappa3 0.945
_pdbe_chem_comp_rdkit_properties.Phi 0.653
#
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
PQ0 UniChem ChEMBL CHEMBL577120
PQ0 UniChem DrugBank DB03074
PQ0 UniChem PDBe PQ0
PQ0 UniChem 'KEGG LIGAND' C15996
PQ0 UniChem ChEBI 45075
PQ0 UniChem ZINC ZINC000005973818
PQ0 UniChem NMRShiftDB 60023365
PQ0 UniChem 'EPA CompTox Dashboard' DTXSID10332223
PQ0 UniChem MetaboLights MTBLC45075
PQ0 UniChem BRENDA 115059
PQ0 UniChem BRENDA 17838
PQ0 UniChem BRENDA 17839
PQ0 UniChem BRENDA 18723
PQ0 UniChem BRENDA 27752
PQ0 UniChem BRENDA 42627
PQ0 UniChem Rhea 45075
PQ0 UniChem ChemicalBook CB91509248
PQ0 UniChem 'Probes And Drugs' PD039210
PQ0 UniChem BindingDb 50303507
PQ0 UniChem SureChEMBL SCHEMBL94358
PQ0 UniChem 'PubChem TPHARMA' 15636958
PQ0 UniChem 'PubChem TPHARMA' 163437126
PQ0 UniChem PubChem 135446206
PQ0 UniChem Nikkaji J879.780C
#
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
PQ0 N1 1.518 0.508 1.186 ETKDGv3 1
PQ0 C2 2.056 -0.083 -0.020 ETKDGv3 2
PQ0 N3 1.256 -0.502 -0.966 ETKDGv3 3
PQ0 C4 -0.167 -0.384 -0.822 ETKDGv3 4
PQ0 C5 -0.732 0.141 0.242 ETKDGv3 5
PQ0 C6 0.096 0.631 1.339 ETKDGv3 6
PQ0 O6 -0.407 1.140 2.375 ETKDGv3 7
PQ0 C7 -2.175 0.094 0.034 ETKDGv3 8
PQ0 C10 -3.195 0.557 0.935 ETKDGv3 9
PQ0 N11 -4.016 0.930 1.660 ETKDGv3 10
PQ0 C8 -2.381 -0.464 -1.158 ETKDGv3 11
PQ0 N9 -1.135 -0.800 -1.773 ETKDGv3 12
PQ0 N2 3.468 -0.210 -0.181 ETKDGv3 13
PQ0 HN1 2.157 0.843 1.941 ETKDGv3 14
PQ0 H8 -3.349 -0.642 -1.608 ETKDGv3 15
PQ0 HN9 -0.976 -1.246 -2.703 ETKDGv3 16
PQ0 HN21 4.118 0.121 0.566 ETKDGv3 17
PQ0 HN22 3.867 -0.634 -1.048 ETKDGv3 18
#