data_6Q3
#
_chem_comp.id 6Q3
_chem_comp.name 3-(2-AMINO-6-METHYL-PYRIMIDIN-4-YL)OXYPROPAN-1-OL
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C8 H13 N3 O2"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2016-01-06
_chem_comp.pdbx_modified_date 2016-07-15
_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 183.208
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code 6Q3
_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 5FSN
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site EBI
#
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
6Q3 N3 N3 N 0 1 Y N N N N N 15.879 21.655 4.783 -0.773 -0.854 -0.001 N3 6Q3 1
6Q3 C2 C2 C 0 1 Y N N N N N 17.184 21.342 4.634 -2.023 -1.291 -0.000 C2 6Q3 2
6Q3 N2 N2 N 0 1 N N N N N N 17.691 20.423 5.454 -2.261 -2.655 0.000 N2 6Q3 3
6Q3 N1 N1 N 0 1 Y N N N N N 18.016 21.876 3.716 -3.052 -0.456 0.000 N1 6Q3 4
6Q3 C6 C6 C 0 1 Y N N N N N 17.503 22.802 2.892 -2.863 0.855 0.000 C6 6Q3 5
6Q3 C7 C7 C 0 1 N N N N N N 18.435 23.388 1.877 -4.041 1.794 0.001 C7 6Q3 6
6Q3 C4 C4 C 0 1 Y N N N N N 15.414 22.583 3.957 -0.512 0.447 -0.001 C4 6Q3 7
6Q3 C5 C5 C 0 1 Y N N N N N 16.180 23.195 2.981 -1.573 1.352 -0.000 C5 6Q3 8
6Q3 "O1'" "O1'" O 0 1 N N N N N N 10.320 21.622 4.526 5.546 0.167 0.000 "O1'" 6Q3 9
6Q3 "C1'" "C1'" C 0 1 N N N N N N 10.880 22.354 5.585 4.269 -0.474 0.000 "C1'" 6Q3 10
6Q3 "C2'" "C2'" C 0 1 N N N N N N 11.963 23.158 4.978 3.166 0.586 -0.000 "C2'" 6Q3 11
6Q3 "C3'" "C3'" C 0 1 N N N N N N 13.268 22.399 5.010 1.799 -0.100 -0.000 "C3'" 6Q3 12
6Q3 "O3'" "O3'" O 0 1 N N N N N N 14.120 22.993 4.021 0.769 0.891 -0.000 "O3'" 6Q3 13
6Q3 H21N H21N H 0 0 N N N N N N 16.978 20.102 6.077 -1.517 -3.277 0.001 H21N 6Q3 14
6Q3 H22N H22N H 0 0 N N N N N N 18.037 19.653 4.918 -3.172 -2.988 0.001 H22N 6Q3 15
6Q3 H71C H71C H 0 0 N N N N N N 19.431 22.935 1.988 -4.324 2.021 1.029 H71C 6Q3 16
6Q3 H72C H72C H 0 0 N N N N N N 18.051 23.186 0.866 -3.770 2.717 -0.513 H72C 6Q3 17
6Q3 H73C H73C H 0 0 N N N N N N 18.508 24.475 2.031 -4.880 1.325 -0.513 H73C 6Q3 18
6Q3 H5 H5 H 0 1 N N N N N N 15.765 23.943 2.321 -1.391 2.416 -0.001 H5 6Q3 19
6Q3 "H1'" "H1'" H 0 1 N N N N N N 9.612 21.081 4.854 6.294 -0.447 0.001 "H1'" 6Q3 20
6Q3 "H1'1" "H1'1" H 0 0 N N N N N N 10.124 23.009 6.042 4.175 -1.096 -0.890 "H1'1" 6Q3 21
6Q3 "H1'2" "H1'2" H 0 0 N N N N N N 11.287 21.675 6.349 4.174 -1.096 0.890 "H1'2" 6Q3 22
6Q3 "H2'1" "H2'1" H 0 0 N N N N N N 11.703 23.386 3.934 3.261 1.209 0.890 "H2'1" 6Q3 23
6Q3 "H2'2" "H2'2" H 0 0 N N N N N N 12.076 24.096 5.541 3.261 1.209 -0.890 "H2'2" 6Q3 24
6Q3 "H3'1" "H3'1" H 0 0 N N N N N N 13.729 22.481 6.005 1.704 -0.722 -0.890 "H3'1" 6Q3 25
6Q3 "H3'2" "H3'2" H 0 0 N N N N N N 13.095 21.339 4.773 1.704 -0.722 0.890 "H3'2" 6Q3 26
#
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
6Q3 N3 C2 SING Y N 1
6Q3 N3 C4 DOUB Y N 2
6Q3 C2 N2 SING N N 3
6Q3 C2 N1 DOUB Y N 4
6Q3 N1 C6 SING Y N 5
6Q3 C6 C7 SING N N 6
6Q3 C6 C5 DOUB Y N 7
6Q3 C4 C5 SING Y N 8
6Q3 C4 "O3'" SING N N 9
6Q3 "O1'" "C1'" SING N N 10
6Q3 "C1'" "C2'" SING N N 11
6Q3 "C2'" "C3'" SING N N 12
6Q3 "C3'" "O3'" SING N N 13
6Q3 N2 H21N SING N N 14
6Q3 N2 H22N SING N N 15
6Q3 C7 H71C SING N N 16
6Q3 C7 H72C SING N N 17
6Q3 C7 H73C SING N N 18
6Q3 C5 H5 SING N N 19
6Q3 "O1'" "H1'" SING N N 20
6Q3 "C1'" "H1'1" SING N N 21
6Q3 "C1'" "H1'2" SING N N 22
6Q3 "C2'" "H2'1" SING N N 23
6Q3 "C2'" "H2'2" SING N N 24
6Q3 "C3'" "H3'1" SING N N 25
6Q3 "C3'" "H3'2" SING N N 26
#
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
6Q3 InChI InChI 1.03 InChI=1S/C8H13N3O2/c1-6-5-7(11-8(9)10-6)13-4-2-3-12/h5,12H,2-4H2,1H3,(H2,9,10,11)
6Q3 InChIKey InChI 1.03 IGISMMDITOHCMM-UHFFFAOYSA-N
6Q3 SMILES_CANONICAL CACTVS 3.385 Cc1cc(OCCCO)nc(N)n1
6Q3 SMILES CACTVS 3.385 Cc1cc(OCCCO)nc(N)n1
6Q3 SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 Cc1cc(nc(n1)N)OCCCO
6Q3 SMILES "OpenEye OEToolkits" 1.7.6 Cc1cc(nc(n1)N)OCCCO
#
_pdbx_chem_comp_identifier.comp_id 6Q3
_pdbx_chem_comp_identifier.type "SYSTEMATIC NAME"
_pdbx_chem_comp_identifier.program "OpenEye OEToolkits"
_pdbx_chem_comp_identifier.program_version 1.7.6
_pdbx_chem_comp_identifier.identifier 3-(2-azanyl-6-methyl-pyrimidin-4-yl)oxypropan-1-ol
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
6Q3 'Create component' 2016-01-06 EBI
6Q3 'Initial release' 2016-07-20 RCSB
#
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
6Q3 N3 N 11.600 -1.785 1
6Q3 C2 C 12.899 -1.035 2
6Q3 N2 N 14.198 -1.785 3
6Q3 N1 N 12.899 0.465 4
6Q3 C6 C 11.600 1.215 5
6Q3 C7 C 11.600 2.715 6
6Q3 C4 C 10.301 -1.035 7
6Q3 C5 C 10.301 0.465 8
6Q3 "O1'" O 3.805 -1.785 9
6Q3 "C1'" C 5.104 -1.035 10
6Q3 "C2'" C 6.404 -1.785 11
6Q3 "C3'" C 7.702 -1.035 12
6Q3 "O3'" O 9.002 -1.785 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
6Q3 N3 C2 DOUBLE NONE 1
6Q3 N3 C4 SINGLE NONE 2
6Q3 C2 N2 SINGLE NONE 3
6Q3 C2 N1 SINGLE NONE 4
6Q3 N1 C6 DOUBLE NONE 5
6Q3 C6 C7 SINGLE NONE 6
6Q3 C6 C5 SINGLE NONE 7
6Q3 C4 C5 DOUBLE NONE 8
6Q3 C4 "O3'" SINGLE NONE 9
6Q3 "O1'" "C1'" SINGLE NONE 10
6Q3 "C1'" "C2'" SINGLE NONE 11
6Q3 "C2'" "C3'" SINGLE NONE 12
6Q3 "C3'" "O3'" SINGLE NONE 13
#
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
6Q3 MurckoScaffold S1 scaffold c1cncnc1 InChI=1S/C4H4N2/c1-2-5-4-6-3-1/h1-4H CZPWVGJYEJSRLH-UHFFFAOYSA-N
6Q3 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
6Q3 N3 S1 1
6Q3 C2 S1 1
6Q3 N1 S1 1
6Q3 C6 S1 1
6Q3 C4 S1 1
6Q3 C5 S1 1
6Q3 C5 F1 1
6Q3 C6 F1 1
6Q3 N1 F1 1
6Q3 C2 F1 1
6Q3 N3 F1 1
6Q3 C4 F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id 6Q3
_pdbe_chem_comp_rdkit_properties.exactmw 183.101
_pdbe_chem_comp_rdkit_properties.amw 183.211
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 5
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 3
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 7
_pdbe_chem_comp_rdkit_properties.NumHBD 2
_pdbe_chem_comp_rdkit_properties.NumHBA 5
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 13
_pdbe_chem_comp_rdkit_properties.NumAtoms 26
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 5
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.500
_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 0
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 95.046
_pdbe_chem_comp_rdkit_properties.tpsa 81.260
_pdbe_chem_comp_rdkit_properties.CrippenClogP -0.769
_pdbe_chem_comp_rdkit_properties.CrippenMR 46.679
_pdbe_chem_comp_rdkit_properties.chi0v 6.158
_pdbe_chem_comp_rdkit_properties.chi1v 2.980
_pdbe_chem_comp_rdkit_properties.chi2v 0.888
_pdbe_chem_comp_rdkit_properties.chi3v 0.888
_pdbe_chem_comp_rdkit_properties.chi4v 0.516
_pdbe_chem_comp_rdkit_properties.chi0n 19.158
_pdbe_chem_comp_rdkit_properties.chi1n 9.283
_pdbe_chem_comp_rdkit_properties.chi2n 0.888
_pdbe_chem_comp_rdkit_properties.chi3n 0.888
_pdbe_chem_comp_rdkit_properties.chi4n 0.516
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.360
_pdbe_chem_comp_rdkit_properties.kappa1 2.170
_pdbe_chem_comp_rdkit_properties.kappa2 4.613
_pdbe_chem_comp_rdkit_properties.kappa3 3.247
_pdbe_chem_comp_rdkit_properties.Phi 0.770
#
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
6Q3 UniChem PDBe 6Q3
6Q3 UniChem PubChem 80866888
6Q3 UniChem BRENDA 243707
#
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
6Q3 N3 -0.971 0.814 -0.608 ETKDGv3 1
6Q3 C2 -2.199 1.089 -0.942 ETKDGv3 2
6Q3 N2 -2.487 2.256 -1.709 ETKDGv3 3
6Q3 N1 -3.266 0.217 -0.533 ETKDGv3 4
6Q3 C6 -3.025 -0.860 0.157 ETKDGv3 5
6Q3 C7 -4.154 -1.734 0.599 ETKDGv3 6
6Q3 C4 -0.656 -0.356 0.169 ETKDGv3 7
6Q3 C5 -1.637 -1.179 0.552 ETKDGv3 8
6Q3 "O1'" 4.468 0.488 -1.027 ETKDGv3 9
6Q3 "C1'" 4.265 0.472 0.359 ETKDGv3 10
6Q3 "C2'" 3.055 -0.397 0.704 ETKDGv3 11
6Q3 "C3'" 1.756 0.192 0.155 ETKDGv3 12
6Q3 "O3'" 0.664 -0.641 0.529 ETKDGv3 13
6Q3 H21N -1.719 2.896 -2.010 ETKDGv3 14
6Q3 H22N -3.471 2.479 -1.977 ETKDGv3 15
6Q3 H71C -4.390 -1.523 1.663 ETKDGv3 16
6Q3 H72C -5.059 -1.545 -0.017 ETKDGv3 17
6Q3 H73C -3.872 -2.803 0.492 ETKDGv3 18
6Q3 H5 -1.419 -2.062 1.140 ETKDGv3 19
6Q3 "H1'" 5.257 1.070 -1.182 ETKDGv3 20
6Q3 "H1'1" 5.164 0.049 0.861 ETKDGv3 21
6Q3 "H1'2" 4.106 1.508 0.735 ETKDGv3 22
6Q3 "H2'1" 2.976 -0.479 1.810 ETKDGv3 23
6Q3 "H2'2" 3.204 -1.419 0.291 ETKDGv3 24
6Q3 "H3'1" 1.602 1.212 0.571 ETKDGv3 25
6Q3 "H3'2" 1.809 0.254 -0.954 ETKDGv3 26
#