data_M1A
#
_chem_comp.id M1A
_chem_comp.name 6-AMINO-1-METHYLPURINE
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C6 H8 N5"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 1
_chem_comp.pdbx_initial_date 1999-07-08
_chem_comp.pdbx_modified_date 2011-06-04
_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 150.161
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code M1A
_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 1B42
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site PDBJ
#
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
M1A N9 N9 N 0 1 Y N N N N N 18.584 12.314 19.680 -2.396 0.744 -0.002 N9 M1A 1
M1A C8 C8 C 0 1 Y N N N N N 18.952 13.395 18.924 -2.734 -0.577 0.001 C8 M1A 2
M1A N7 N7 N 0 1 Y N N N N N 18.339 14.504 19.246 -1.658 -1.310 0.004 N7 M1A 3
M1A C5 C5 C 0 1 Y N N N N N 17.497 14.142 20.305 -0.566 -0.509 0.003 C5 M1A 4
M1A C6 C6 C 0 1 Y N N N N N 16.574 14.880 21.107 0.822 -0.730 -0.001 C6 M1A 5
M1A N6 N6 N 0 1 N N N N N N 16.346 16.176 20.985 1.334 -2.016 -0.005 N6 M1A 6
M1A N1 N1 N 1 1 Y N N N N N 15.914 14.217 22.059 1.631 0.324 0.002 N1 M1A 7
M1A C2 C2 C 0 1 Y N N N N N 16.158 12.912 22.220 1.151 1.555 -0.001 C2 M1A 8
M1A N3 N3 N 0 1 Y N N N N N 16.998 12.094 21.561 -0.141 1.809 -0.002 N3 M1A 9
M1A C4 C4 C 0 1 Y N N N N N 17.644 12.798 20.581 -1.026 0.819 -0.001 C4 M1A 10
M1A CN1 CN1 C 0 1 N N N N N N 14.978 14.984 22.858 3.081 0.118 0.004 CN1 M1A 11
M1A HN9 HN9 H 0 1 N N N N N N 18.932 11.359 19.591 -3.012 1.493 -0.004 HN9 M1A 12
M1A H8 H8 H 0 1 N N N N N N 19.694 13.373 18.108 -3.744 -0.958 0.002 H8 M1A 13
M1A HN61 1HN6 H 0 0 N N N N N N 15.686 16.703 21.557 0.733 -2.777 -0.005 HN61 M1A 14
M1A HN62 2HN6 H 0 0 N N N N N N 16.091 16.341 20.011 2.294 -2.155 -0.008 HN62 M1A 15
M1A H2 H2 H 0 1 N N N N N N 15.573 12.434 23.024 1.844 2.383 -0.002 H2 M1A 16
M1A H11 1H1 H 0 1 N N N N N N 14.426 14.430 23.653 3.440 0.069 1.032 H11 M1A 17
M1A H12 2H1 H 0 1 N N N N N N 15.500 15.860 23.306 3.316 -0.816 -0.508 H12 M1A 18
M1A H13 3H1 H 0 1 N N N N N N 14.250 15.499 22.188 3.567 0.947 -0.512 H13 M1A 19
#
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
M1A N9 C8 SING Y N 1
M1A N9 C4 SING Y N 2
M1A N9 HN9 SING N N 3
M1A C8 N7 DOUB Y N 4
M1A C8 H8 SING N N 5
M1A N7 C5 SING Y N 6
M1A C5 C6 SING Y N 7
M1A C5 C4 DOUB Y N 8
M1A C6 N6 SING N N 9
M1A C6 N1 DOUB Y N 10
M1A N6 HN61 SING N N 11
M1A N6 HN62 SING N N 12
M1A N1 C2 SING Y N 13
M1A N1 CN1 SING N N 14
M1A C2 N3 DOUB Y N 15
M1A C2 H2 SING N N 16
M1A N3 C4 SING Y N 17
M1A CN1 H11 SING N N 18
M1A CN1 H12 SING N N 19
M1A CN1 H13 SING N N 20
#
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
M1A SMILES ACDLabs 10.04 n1c[n+](c(c2ncnc12)N)C
M1A SMILES_CANONICAL CACTVS 3.341 C[n+]1cnc2[nH]cnc2c1N
M1A SMILES CACTVS 3.341 C[n+]1cnc2[nH]cnc2c1N
M1A SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 C[n+]1cnc2c(c1N)nc[nH]2
M1A SMILES "OpenEye OEToolkits" 1.5.0 C[n+]1cnc2c(c1N)nc[nH]2
M1A InChI InChI 1.03 InChI=1S/C6H7N5/c1-11-3-10-6-4(5(11)7)8-2-9-6/h2-3H,1H3,(H2,7,8,9)/p+1
M1A InChIKey InChI 1.03 DYGBIJOMQSXREB-UHFFFAOYSA-O
#
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
M1A "SYSTEMATIC NAME" ACDLabs 10.04 6-amino-1-methyl-9H-purin-1-ium
M1A "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 1-methyl-9H-purin-1-ium-6-amine
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
M1A 'Create component' 1999-07-08 PDBJ
M1A 'Modify descriptor' 2011-06-04 RCSB
#
_pdbe_chem_comp_drugbank_details.comp_id M1A
_pdbe_chem_comp_drugbank_details.drugbank_id DB03164
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name 6-amino-1-methyl-7H-purin-1-ium
_pdbe_chem_comp_drugbank_details.description ?
_pdbe_chem_comp_drugbank_details.cas_number ?
_pdbe_chem_comp_drugbank_details.mechanism_of_action ?
#
_pdbe_chem_comp_synonyms.comp_id M1A
_pdbe_chem_comp_synonyms.name 6-amino-1-methylpurine
_pdbe_chem_comp_synonyms.provenance DrugBank
_pdbe_chem_comp_synonyms.type ?
#
_pdbe_chem_comp_drugbank_classification.comp_id M1A
_pdbe_chem_comp_drugbank_classification.drugbank_id DB03164
_pdbe_chem_comp_drugbank_classification.parent 6-aminopurines
_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 6-aminopurines. These are purines that carry an amino group at position 6. Purine is a bicyclic aromatic compound made up of a pyrimidine ring fused to an imidazole ring.'
#
_pdbe_chem_comp_drugbank_targets.comp_id M1A
_pdbe_chem_comp_drugbank_targets.drugbank_id DB03164
_pdbe_chem_comp_drugbank_targets.name "Cap-specific mRNA (nucleoside-2'-O-)-methyltransferase"
_pdbe_chem_comp_drugbank_targets.organism VACV
_pdbe_chem_comp_drugbank_targets.uniprot_id P07617
_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
M1A N9 N 8.316 -2.190 1
M1A C8 C 9.192 -0.983 2
M1A N7 N 8.316 0.225 3
M1A C5 C 6.897 -0.233 4
M1A C6 C 5.598 0.517 5
M1A N6 N 5.598 2.018 6
M1A N1 N 4.299 -0.233 7
M1A C2 C 4.299 -1.732 8
M1A N3 N 5.598 -2.482 9
M1A C4 C 6.897 -1.732 10
M1A CN1 C 3.000 0.517 11
#
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
M1A N9 C8 SINGLE NONE 1
M1A N9 C4 SINGLE NONE 2
M1A C8 N7 DOUBLE NONE 3
M1A N7 C5 SINGLE NONE 4
M1A C5 C6 SINGLE NONE 5
M1A C5 C4 DOUBLE NONE 6
M1A C6 N6 SINGLE NONE 7
M1A C6 N1 DOUBLE NONE 8
M1A N1 C2 SINGLE NONE 9
M1A N1 CN1 SINGLE NONE 10
M1A C2 N3 DOUBLE NONE 11
M1A N3 C4 SINGLE NONE 12
#
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
M1A MurckoScaffold S1 scaffold 'c1nc2c[nH+]cnc2[nH]1' InChI=1S/C5H4N4/c1-4-5(8-2-6-1)9-3-7-4/h1-3H,(H,6,7,8,9)/p+1 KDCGOANMDULRCW-UHFFFAOYSA-O
M1A adenine F1 fragment 'Nc1ncnc2nc[nH]c12' InChI=1S/C5H5N5/c6-4-3-5(9-1-7-3)10-2-8-4/h1-2H,(H3,6,7,8,9,10) GFFGJBXGBJISGV-UHFFFAOYSA-N
M1A imidazole F2 fragment 'c1c[nH]cn1' InChI=1S/C3H4N2/c1-2-5-3-4-1/h1-3H,(H,4,5) RAXXELZNTBOGNW-UHFFFAOYSA-N
M1A purine F3 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
M1A pyrimidine F4 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
M1A N9 S1 1
M1A C8 S1 1
M1A N7 S1 1
M1A C5 S1 1
M1A C6 S1 1
M1A N1 S1 1
M1A C2 S1 1
M1A N3 S1 1
M1A C4 S1 1
M1A N1 F1 1
M1A C6 F1 1
M1A C5 F1 1
M1A C4 F1 1
M1A N3 F1 1
M1A C2 F1 1
M1A N9 F1 1
M1A C8 F1 1
M1A N7 F1 1
M1A N6 F1 1
M1A C5 F2 1
M1A C4 F2 1
M1A N9 F2 1
M1A C8 F2 1
M1A N7 F2 1
M1A N7 F3 1
M1A C8 F3 1
M1A N9 F3 1
M1A C4 F3 1
M1A C5 F3 1
M1A C6 F3 1
M1A N1 F3 1
M1A C2 F3 1
M1A N3 F3 1
M1A C5 F4 1
M1A C6 F4 1
M1A N1 F4 1
M1A C2 F4 1
M1A N3 F4 1
M1A C4 F4 1
#
_pdbe_chem_comp_rdkit_properties.comp_id M1A
_pdbe_chem_comp_rdkit_properties.exactmw 150.077
_pdbe_chem_comp_rdkit_properties.amw 150.165
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 5
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 3
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 2
_pdbe_chem_comp_rdkit_properties.NumHBD 2
_pdbe_chem_comp_rdkit_properties.NumHBA 3
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 11
_pdbe_chem_comp_rdkit_properties.NumAtoms 19
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 5
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.167
_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 74.310
_pdbe_chem_comp_rdkit_properties.tpsa 71.470
_pdbe_chem_comp_rdkit_properties.CrippenClogP -1.444
_pdbe_chem_comp_rdkit_properties.CrippenMR 36.447
_pdbe_chem_comp_rdkit_properties.chi0v 5.236
_pdbe_chem_comp_rdkit_properties.chi1v 2.736
_pdbe_chem_comp_rdkit_properties.chi2v 1.209
_pdbe_chem_comp_rdkit_properties.chi3v 1.209
_pdbe_chem_comp_rdkit_properties.chi4v 0.704
_pdbe_chem_comp_rdkit_properties.chi0n 13.236
_pdbe_chem_comp_rdkit_properties.chi1n 6.578
_pdbe_chem_comp_rdkit_properties.chi2n 1.209
_pdbe_chem_comp_rdkit_properties.chi3n 1.209
_pdbe_chem_comp_rdkit_properties.chi4n 0.704
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.650
_pdbe_chem_comp_rdkit_properties.kappa1 1.936
_pdbe_chem_comp_rdkit_properties.kappa2 1.914
_pdbe_chem_comp_rdkit_properties.kappa3 0.739
_pdbe_chem_comp_rdkit_properties.Phi 0.337
#
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
M1A UniChem DrugBank DB03164
M1A UniChem PDBe M1A
M1A UniChem ZINC ZINC000012503143
M1A UniChem PubChem 444453
M1A UniChem 'Probes And Drugs' PD059837
M1A UniChem Nikkaji J2.356.728H
M1A UniChem Nikkaji J2.356.727J
#
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
M1A N9 2.879 -0.784 0.166 ETKDGv3 1
M1A C8 3.126 0.618 0.328 ETKDGv3 2
M1A N7 2.046 1.347 0.309 ETKDGv3 3
M1A C5 0.996 0.403 0.125 ETKDGv3 4
M1A C6 -0.452 0.630 0.025 ETKDGv3 5
M1A N6 -0.966 1.967 0.115 ETKDGv3 6
M1A N1 -1.235 -0.421 -0.147 ETKDGv3 7
M1A C2 -0.656 -1.760 -0.232 ETKDGv3 8
M1A N3 0.634 -1.943 -0.141 ETKDGv3 9
M1A C4 1.473 -0.803 0.045 ETKDGv3 10
M1A CN1 -2.692 -0.287 -0.258 ETKDGv3 11
M1A HN9 3.557 -1.577 0.145 ETKDGv3 12
M1A H8 4.114 1.038 0.454 ETKDGv3 13
M1A HN61 -0.312 2.770 0.251 ETKDGv3 14
M1A HN62 -1.983 2.187 0.051 ETKDGv3 15
M1A H2 -1.294 -2.622 -0.373 ETKDGv3 16
M1A H11 -2.950 0.345 -1.134 ETKDGv3 17
M1A H12 -3.182 -1.274 -0.399 ETKDGv3 18
M1A H13 -3.104 0.164 0.670 ETKDGv3 19
#