data_B61
#
_chem_comp.id B61
_chem_comp.name 2-amino-6-(2-hydroxy-2-methylpropyl)-8-methyl-7,8-dihydropteridin-4(3H)-one
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C11 H17 N5 O2"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2009-04-23
_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 251.285
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code B61
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag N
_chem_comp.pdbx_ideal_coordinates_details Corina
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code 3H2M
_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
B61 O2 O2 O 0 1 N N N N N N -64.616 57.765 138.437 0.588 -2.646 -0.089 O2 B61 1
B61 C1 C1 C 0 1 N N N N N N -64.792 58.957 138.113 1.259 -1.628 -0.054 C1 B61 2
B61 C4 C4 C 0 1 N N N N N N -64.075 59.508 136.937 0.646 -0.359 -0.062 C4 B61 3
B61 C7 C7 C 0 1 N N N N N N -64.291 60.924 136.604 1.465 0.779 -0.026 C7 B61 4
B61 N6 N6 N 0 1 N N N N N N -65.132 61.631 137.406 2.788 0.646 0.024 N6 B61 5
B61 C5 C5 C 0 1 N N N N N N -65.774 61.080 138.487 3.349 -0.547 0.035 C5 B61 6
B61 N8 N8 N 0 1 N N N N N N -66.575 61.827 139.266 4.713 -0.641 0.087 N8 B61 7
B61 N3 N3 N 0 1 N N N N N N -65.619 59.780 138.800 2.608 -1.688 0.000 N3 B61 8
B61 N9 N9 N 0 1 N N N N N N -63.257 58.766 136.172 -0.710 -0.222 -0.095 N9 B61 9
B61 C10 C10 C 0 1 N N N N N N -62.603 59.243 135.076 -1.267 0.902 -0.390 C10 B61 10
B61 C17 C17 C 0 1 N N N N N N -61.730 58.133 134.487 -2.770 1.001 -0.398 C17 B61 11
B61 C23 C23 C 0 1 N N N N N N -61.675 57.803 132.996 -3.370 -0.306 0.123 C23 B61 12
B61 O24 O24 O 0 1 N N N N N N -63.069 57.577 132.532 -2.956 -1.387 -0.715 O24 B61 13
B61 C25 C25 C 0 1 N N N N N N -61.000 59.039 132.338 -2.886 -0.555 1.553 C25 B61 14
B61 C26 C26 C 0 1 N N N N N N -60.826 56.505 132.749 -4.897 -0.207 0.111 C26 B61 15
B61 C11 C11 C 0 1 N N N N N N -62.697 60.712 134.600 -0.445 2.120 -0.727 C11 B61 16
B61 N12 N12 N 0 1 N N N N N N -63.627 61.474 135.482 0.859 2.021 -0.053 N12 B61 17
B61 C13 C13 C 0 1 N N N N N N -63.913 62.877 135.256 1.488 3.190 0.566 C13 B61 18
B61 HN8 HN8 H 0 1 N N N N N N -66.603 62.768 138.927 5.254 0.163 0.116 HN8 B61 19
B61 HN8A HN8A H 0 0 N N N N N N -67.071 61.491 140.067 5.140 -1.513 0.095 HN8A B61 20
B61 H17 H17 H 0 1 N N N N N N -60.699 58.408 134.756 -3.083 1.825 0.243 H17 B61 21
B61 H17A H17A H 0 0 N N N N N N -62.208 57.231 134.898 -3.117 1.180 -1.416 H17A B61 22
B61 HO24 HO24 H 0 0 N N N N N N -63.649 57.529 133.283 -3.300 -2.249 -0.444 HO24 B61 23
B61 H25 H25 H 0 1 N N N N N N -60.841 59.818 133.098 -3.202 0.269 2.192 H25 B61 24
B61 H25A H25A H 0 0 N N N N N N -60.032 58.742 131.908 -3.314 -1.487 1.924 H25A B61 25
B61 H25B H25B H 0 0 N N N N N N -61.650 59.431 131.542 -1.798 -0.626 1.561 H25B B61 26
B61 H26 H26 H 0 1 N N N N N N -60.628 56.395 131.673 -5.247 -0.114 -0.917 H26 B61 27
B61 H26A H26A H 0 0 N N N N N N -59.872 56.582 133.292 -5.323 -1.105 0.559 H26A B61 28
B61 H26B H26B H 0 0 N N N N N N -61.384 55.628 133.110 -5.209 0.667 0.682 H26B B61 29
B61 H11 H11 H 0 1 N N N N N N -61.699 61.172 134.640 -0.295 2.172 -1.806 H11 B61 30
B61 H13 H13 H 0 1 N N N N N N -63.985 63.397 136.222 1.170 3.267 1.606 H13 B61 31
B61 H13A H13A H 0 0 N N N N N N -63.105 63.324 134.659 2.572 3.084 0.525 H13A B61 32
B61 H13B H13B H 0 0 N N N N N N -64.866 62.974 134.715 1.191 4.090 0.028 H13B B61 33
B61 H16 H16 H 0 1 N N N N N N -66.135 59.407 139.571 3.051 -2.551 0.010 H16 B61 34
B61 H171 H171 H 0 0 N N N N N N -63.077 60.734 133.568 -0.965 3.016 -0.387 H171 B61 35
#
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
B61 C1 O2 DOUB N N 1
B61 C1 N3 SING N N 2
B61 C4 C1 SING N N 3
B61 C7 C4 DOUB N N 4
B61 C7 N6 SING N N 5
B61 N6 C5 DOUB N N 6
B61 C5 N3 SING N N 7
B61 C5 N8 SING N N 8
B61 N8 HN8 SING N N 9
B61 N8 HN8A SING N N 10
B61 N9 C4 SING N N 11
B61 C10 N9 DOUB N N 12
B61 C17 C10 SING N N 13
B61 C17 H17 SING N N 14
B61 C17 H17A SING N N 15
B61 C23 C17 SING N N 16
B61 O24 C23 SING N N 17
B61 O24 HO24 SING N N 18
B61 C25 C23 SING N N 19
B61 C25 H25 SING N N 20
B61 C25 H25A SING N N 21
B61 C25 H25B SING N N 22
B61 C26 C23 SING N N 23
B61 C26 H26 SING N N 24
B61 C26 H26A SING N N 25
B61 C26 H26B SING N N 26
B61 C11 C10 SING N N 27
B61 C11 N12 SING N N 28
B61 C11 H11 SING N N 29
B61 N12 C7 SING N N 30
B61 C13 N12 SING N N 31
B61 C13 H13 SING N N 32
B61 C13 H13A SING N N 33
B61 C13 H13B SING N N 34
B61 N3 H16 SING N N 35
B61 C11 H171 SING N N 36
#
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
B61 SMILES ACDLabs 10.04 O=C1NC(=NC=2N(CC(=NC1=2)CC(O)(C)C)C)N
B61 SMILES_CANONICAL CACTVS 3.341 CN1CC(=NC2=C1N=C(N)NC2=O)CC(C)(C)O
B61 SMILES CACTVS 3.341 CN1CC(=NC2=C1N=C(N)NC2=O)CC(C)(C)O
B61 SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 CC(C)(CC1=NC2=C(N=C(NC2=O)N)N(C1)C)O
B61 SMILES "OpenEye OEToolkits" 1.5.0 CC(C)(CC1=NC2=C(N=C(NC2=O)N)N(C1)C)O
B61 InChI InChI 1.03 InChI=1S/C11H17N5O2/c1-11(2,18)4-6-5-16(3)8-7(13-6)9(17)15-10(12)14-8/h18H,4-5H2,1-3H3,(H3,12,14,15,17)
B61 InChIKey InChI 1.03 WRSJTVSFGTWZBM-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
B61 "SYSTEMATIC NAME" ACDLabs 10.04 2-amino-6-(2-hydroxy-2-methylpropyl)-8-methyl-7,8-dihydropteridin-4(3H)-one
B61 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 2-amino-6-(2-hydroxy-2-methyl-propyl)-8-methyl-3,7-dihydropteridin-4-one
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
B61 'Create component' 2009-04-23 RCSB
B61 'Modify descriptor' 2011-06-04 RCSB
#
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
B61 O2 O 6.404 3.026 1
B61 C1 C 6.404 1.526 2
B61 C4 C 7.702 0.776 3
B61 C7 C 7.702 -0.724 4
B61 N6 N 6.404 -1.474 5
B61 C5 C 5.104 -0.724 6
B61 N8 N 3.805 -1.474 7
B61 N3 N 5.104 0.776 8
B61 N9 N 9.043 1.578 9
B61 C10 C 10.402 0.807 10
B61 C17 C 11.699 1.562 11
B61 C23 C 13.001 0.817 12
B61 O24 O 14.303 0.072 13
B61 C25 C 13.746 2.119 14
B61 C26 C 12.256 -0.485 15
B61 C11 C 10.402 -0.755 16
B61 N12 N 9.043 -1.526 17
B61 C13 C 9.026 -3.026 18
#
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
B61 C1 O2 DOUBLE NONE 1
B61 C1 N3 SINGLE NONE 2
B61 C4 C1 SINGLE NONE 3
B61 C7 C4 DOUBLE NONE 4
B61 C7 N6 SINGLE NONE 5
B61 N6 C5 DOUBLE NONE 6
B61 C5 N3 SINGLE NONE 7
B61 C5 N8 SINGLE NONE 8
B61 N9 C4 SINGLE NONE 9
B61 C10 N9 DOUBLE NONE 10
B61 C17 C10 SINGLE NONE 11
B61 C23 C17 SINGLE NONE 12
B61 O24 C23 SINGLE NONE 13
B61 C25 C23 SINGLE NONE 14
B61 C26 C23 SINGLE NONE 15
B61 C11 C10 SINGLE NONE 16
B61 C11 N12 SINGLE NONE 17
B61 N12 C7 SINGLE NONE 18
B61 C13 N12 SINGLE NONE 19
#
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
B61 MurckoScaffold S1 scaffold 'O=c1[nH]cnc2c1N=CCN2' InChI=1S/C6H6N4O/c11-6-4-5(9-3-10-6)8-2-1-7-4/h1,3H,2H2,(H2,8,9,10,11) RSPZIHWNURGJFC-UHFFFAOYSA-N
B61 pyrimidine F1 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
B61 O2 S1 1
B61 C1 S1 1
B61 C4 S1 1
B61 C7 S1 1
B61 N6 S1 1
B61 C5 S1 1
B61 N3 S1 1
B61 N9 S1 1
B61 C10 S1 1
B61 C11 S1 1
B61 N12 S1 1
B61 C4 F1 1
B61 C1 F1 1
B61 N3 F1 1
B61 C5 F1 1
B61 N6 F1 1
B61 C7 F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id B61
_pdbe_chem_comp_rdkit_properties.exactmw 251.138
_pdbe_chem_comp_rdkit_properties.amw 251.290
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 7
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 4
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 7
_pdbe_chem_comp_rdkit_properties.NumHBD 3
_pdbe_chem_comp_rdkit_properties.NumHBA 6
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 18
_pdbe_chem_comp_rdkit_properties.NumAtoms 35
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 7
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.545
_pdbe_chem_comp_rdkit_properties.NumRings 2
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 1
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 1
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 0
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 2
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 0
_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 0
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 128.516
_pdbe_chem_comp_rdkit_properties.tpsa 107.600
_pdbe_chem_comp_rdkit_properties.CrippenClogP -0.207
_pdbe_chem_comp_rdkit_properties.CrippenMR 68.186
_pdbe_chem_comp_rdkit_properties.chi0v 8.553
_pdbe_chem_comp_rdkit_properties.chi1v 4.394
_pdbe_chem_comp_rdkit_properties.chi2v 1.769
_pdbe_chem_comp_rdkit_properties.chi3v 1.769
_pdbe_chem_comp_rdkit_properties.chi4v 1.184
_pdbe_chem_comp_rdkit_properties.chi0n 25.553
_pdbe_chem_comp_rdkit_properties.chi1n 12.644
_pdbe_chem_comp_rdkit_properties.chi2n 1.769
_pdbe_chem_comp_rdkit_properties.chi3n 1.769
_pdbe_chem_comp_rdkit_properties.chi4n 1.184
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.890
_pdbe_chem_comp_rdkit_properties.kappa1 3.161
_pdbe_chem_comp_rdkit_properties.kappa2 4.093
_pdbe_chem_comp_rdkit_properties.kappa3 2.506
_pdbe_chem_comp_rdkit_properties.Phi 0.719
#
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
B61 UniChem ZINC ZINC000045300674
B61 UniChem PubChem 136180738
B61 UniChem BindingDb 50378558
#
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
B61 O2 1.609 1.714 -3.014 ETKDGv3 1
B61 C1 2.129 1.265 -1.958 ETKDGv3 2
B61 C4 1.367 0.395 -1.053 ETKDGv3 3
B61 C7 1.958 -0.058 0.062 ETKDGv3 4
B61 N6 3.320 0.307 0.366 ETKDGv3 5
B61 C5 4.037 1.074 -0.406 ETKDGv3 6
B61 N8 5.379 1.392 -0.041 ETKDGv3 7
B61 N3 3.477 1.596 -1.618 ETKDGv3 8
B61 N9 0.008 0.060 -1.345 ETKDGv3 9
B61 C10 -0.710 -0.724 -0.596 ETKDGv3 10
B61 C17 -2.126 -1.037 -1.004 ETKDGv3 11
B61 C23 -3.117 0.134 -0.766 ETKDGv3 12
B61 O24 -2.759 1.246 -1.555 ETKDGv3 13
B61 C25 -3.177 0.522 0.730 ETKDGv3 14
B61 C26 -4.520 -0.311 -1.210 ETKDGv3 15
B61 C11 -0.114 -1.418 0.608 ETKDGv3 16
B61 N12 1.218 -0.903 0.963 ETKDGv3 17
B61 C13 1.842 -1.354 2.208 ETKDGv3 18
B61 HN8 5.962 2.006 -0.652 ETKDGv3 19
B61 HN8A 5.792 1.015 0.841 ETKDGv3 20
B61 H17 -2.478 -1.932 -0.443 ETKDGv3 21
B61 H17A -2.127 -1.315 -2.081 ETKDGv3 22
B61 HO24 -1.993 1.708 -1.124 ETKDGv3 23
B61 H25 -3.914 1.338 0.887 ETKDGv3 24
B61 H25A -2.189 0.882 1.088 ETKDGv3 25
B61 H25B -3.475 -0.351 1.349 ETKDGv3 26
B61 H26 -5.250 0.515 -1.072 ETKDGv3 27
B61 H26A -4.515 -0.588 -2.287 ETKDGv3 28
B61 H26B -4.863 -1.189 -0.621 ETKDGv3 29
B61 H11 -0.800 -1.283 1.471 ETKDGv3 30
B61 H13 1.164 -2.028 2.775 ETKDGv3 31
B61 H13A 2.079 -0.476 2.846 ETKDGv3 32
B61 H13B 2.777 -1.909 1.981 ETKDGv3 33
B61 H16 4.044 2.212 -2.244 ETKDGv3 34
B61 H171 -0.035 -2.504 0.390 ETKDGv3 35
#