data_RYQ
#
_chem_comp.id RYQ
_chem_comp.name 9-[(2-methyl-1,3-thiazol-4-yl)methyl]-9H-purine-2,6-diamine
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C10 H11 N7 S"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2022-06-23
_chem_comp.pdbx_modified_date 2022-07-08
_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 261.306
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code RYQ
_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 5SPF
_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
RYQ C16 C1 C 0 1 Y N N N N N -45.765 -29.418 3.833 -1.202 -0.366 -0.513 C16 RYQ 1
RYQ C17 C2 C 0 1 Y N N N N N -43.148 -27.611 0.967 3.261 -1.103 -0.530 C17 RYQ 2
RYQ C13 C3 C 0 1 Y N N N N N -44.851 -29.621 5.891 -2.447 1.571 -0.578 C13 RYQ 3
RYQ C10 C4 C 0 1 Y N N N N N -47.110 -29.331 5.784 -3.280 -0.169 0.697 C10 RYQ 4
RYQ C01 C5 C 0 1 N N N N N N -45.377 -25.515 -1.440 2.917 2.367 1.339 C01 RYQ 5
RYQ C02 C6 C 0 1 Y N N N N N -44.651 -26.409 -0.460 2.904 1.065 0.580 C02 RYQ 6
RYQ C04 C7 C 0 1 Y N N N N N -44.408 -28.239 0.895 2.057 -0.547 -0.700 C04 RYQ 7
RYQ C05 C8 C 0 1 N N N N N N -44.844 -29.512 1.552 0.969 -1.193 -1.518 C05 RYQ 8
RYQ C07 C9 C 0 1 Y N N N N N -47.235 -29.175 2.239 -0.618 -2.428 0.007 C07 RYQ 9
RYQ C09 C10 C 0 1 Y N N N N N -47.016 -29.280 4.382 -2.162 -0.941 0.335 C09 RYQ 10
RYQ N03 N1 N 0 1 Y N N N N N -45.297 -27.522 0.032 1.900 0.612 -0.093 N03 RYQ 11
RYQ N06 N2 N 0 1 Y N N N N N -45.917 -29.350 2.503 -0.241 -1.326 -0.703 N06 RYQ 12
RYQ N08 N3 N 0 1 Y N N N N N -47.917 -29.129 3.385 -1.742 -2.198 0.619 N08 RYQ 13
RYQ N11 N4 N 0 1 N N N N N N -48.354 -29.183 6.478 -4.255 -0.685 1.531 N11 RYQ 14
RYQ N12 N5 N 0 1 Y N N N N N -46.018 -29.510 6.482 -3.378 1.068 0.222 N12 RYQ 15
RYQ N14 N6 N 0 1 N N N N N N -43.716 -29.826 6.716 -2.596 2.866 -1.047 N14 RYQ 16
RYQ N15 N7 N 0 1 Y N N N N N -44.653 -29.583 4.602 -1.380 0.879 -0.943 N15 RYQ 17
RYQ S18 S1 S 0 1 Y N N N N N -43.081 -26.246 0.086 4.215 -0.029 0.491 S18 RYQ 18
RYQ H171 H1 H 0 0 N N N N N N -42.319 -27.994 1.543 3.589 -2.046 -0.942 H171 RYQ 19
RYQ H011 H2 H 0 0 N N N N N N -46.384 -25.916 -1.626 2.578 2.195 2.360 H011 RYQ 20
RYQ H012 H3 H 0 0 N N N N N N -45.458 -24.501 -1.021 3.931 2.768 1.355 H012 RYQ 21
RYQ H013 H4 H 0 0 N N N N N N -44.817 -25.477 -2.386 2.253 3.079 0.850 H013 RYQ 22
RYQ H052 H5 H 0 0 N N N N N N -45.180 -30.207 0.768 0.754 -0.574 -2.389 H052 RYQ 23
RYQ H051 H6 H 0 0 N N N N N N -43.979 -29.942 2.078 1.298 -2.179 -1.846 H051 RYQ 24
RYQ H071 H7 H 0 0 N N N N N N -47.667 -29.086 1.253 -0.063 -3.354 0.057 H071 RYQ 25
RYQ H111 H8 H 0 0 N N N N N N -48.196 -29.242 7.464 -5.022 -0.143 1.774 H111 RYQ 26
RYQ H112 H9 H 0 0 N N N N N N -48.755 -28.294 6.258 -4.173 -1.589 1.872 H112 RYQ 27
RYQ H142 H10 H 0 0 N N N N N N -42.900 -29.913 6.145 -3.372 3.389 -0.789 H142 RYQ 28
RYQ H141 H11 H 0 0 N N N N N N -43.608 -29.047 7.334 -1.925 3.251 -1.632 H141 RYQ 29
#
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
RYQ C01 C02 SING N N 1
RYQ C02 N03 DOUB Y N 2
RYQ C02 S18 SING Y N 3
RYQ N03 C04 SING Y N 4
RYQ S18 C17 SING Y N 5
RYQ C04 C17 DOUB Y N 6
RYQ C04 C05 SING N N 7
RYQ C05 N06 SING N N 8
RYQ C07 N06 SING Y N 9
RYQ C07 N08 DOUB Y N 10
RYQ N06 C16 SING Y N 11
RYQ N08 C09 SING Y N 12
RYQ C16 C09 DOUB Y N 13
RYQ C16 N15 SING Y N 14
RYQ C09 C10 SING Y N 15
RYQ N15 C13 DOUB Y N 16
RYQ C10 N11 SING N N 17
RYQ C10 N12 DOUB Y N 18
RYQ C13 N12 SING Y N 19
RYQ C13 N14 SING N N 20
RYQ C17 H171 SING N N 21
RYQ C01 H011 SING N N 22
RYQ C01 H012 SING N N 23
RYQ C01 H013 SING N N 24
RYQ C05 H052 SING N N 25
RYQ C05 H051 SING N N 26
RYQ C07 H071 SING N N 27
RYQ N11 H111 SING N N 28
RYQ N11 H112 SING N N 29
RYQ N14 H142 SING N N 30
RYQ N14 H141 SING N N 31
#
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
RYQ SMILES ACDLabs 12.01 Cc1nc(Cn2cnc3c(N)nc(N)nc23)cs1
RYQ InChI InChI 1.06 InChI=1S/C10H11N7S/c1-5-14-6(3-18-5)2-17-4-13-7-8(11)15-10(12)16-9(7)17/h3-4H,2H2,1H3,(H4,11,12,15,16)
RYQ InChIKey InChI 1.06 INTFUQJSFGYBOV-UHFFFAOYSA-N
RYQ SMILES_CANONICAL CACTVS 3.385 Cc1scc(Cn2cnc3c(N)nc(N)nc23)n1
RYQ SMILES CACTVS 3.385 Cc1scc(Cn2cnc3c(N)nc(N)nc23)n1
RYQ SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 Cc1nc(cs1)Cn2cnc3c2nc(nc3N)N
RYQ SMILES "OpenEye OEToolkits" 2.0.7 Cc1nc(cs1)Cn2cnc3c2nc(nc3N)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
RYQ "SYSTEMATIC NAME" ACDLabs 12.01 9-[(2-methyl-1,3-thiazol-4-yl)methyl]-9H-purine-2,6-diamine
RYQ "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 9-[(2-methyl-1,3-thiazol-4-yl)methyl]purine-2,6-diamine
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
RYQ 'Create component' 2022-06-23 RCSB
RYQ 'Initial release' 2022-07-13 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
RYQ C16 C 7.702 -0.150 1
RYQ C17 C 12.169 1.036 2
RYQ C13 C 5.104 -0.150 3
RYQ C10 C 6.404 -2.400 4
RYQ C01 C 14.165 4.365 5
RYQ C02 C 13.160 3.252 6
RYQ C04 C 11.056 2.042 7
RYQ C05 C 9.588 1.733 8
RYQ C07 C 9.997 -0.900 9
RYQ C09 C 7.702 -1.650 10
RYQ N03 N 11.668 3.412 11
RYQ N06 N 9.122 0.307 12
RYQ N08 N 9.122 -2.107 13
RYQ N11 N 6.404 -3.900 14
RYQ N12 N 5.104 -1.650 15
RYQ N14 N 3.805 0.600 16
RYQ N15 N 6.404 0.600 17
RYQ S18 S 13.469 1.784 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
RYQ C01 C02 SINGLE NONE 1
RYQ C02 N03 DOUBLE NONE 2
RYQ C02 S18 SINGLE NONE 3
RYQ N03 C04 SINGLE NONE 4
RYQ S18 C17 SINGLE NONE 5
RYQ C04 C17 DOUBLE NONE 6
RYQ C04 C05 SINGLE NONE 7
RYQ C05 N06 SINGLE NONE 8
RYQ C07 N06 SINGLE NONE 9
RYQ C07 N08 DOUBLE NONE 10
RYQ N06 C16 SINGLE NONE 11
RYQ N08 C09 SINGLE NONE 12
RYQ C16 C09 DOUBLE NONE 13
RYQ C16 N15 SINGLE NONE 14
RYQ C09 C10 SINGLE NONE 15
RYQ N15 C13 DOUBLE NONE 16
RYQ C10 N11 SINGLE NONE 17
RYQ C10 N12 DOUBLE NONE 18
RYQ C13 N12 SINGLE NONE 19
RYQ C13 N14 SINGLE NONE 20
#
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
RYQ MurckoScaffold S1 scaffold c1ncc2ncn(Cc3cscn3)c2n1 InChI=1S/C9H7N5S/c1-8-9(11-4-10-1)14(5-12-8)2-7-3-15-6-13-7/h1,3-6H,2H2 XTFGEMFEHPAGSH-UHFFFAOYSA-N
RYQ 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
RYQ imidazole F2 fragment 'c1c[nH]cn1' InChI=1S/C3H4N2/c1-2-5-3-4-1/h1-3H,(H,4,5) RAXXELZNTBOGNW-UHFFFAOYSA-N
RYQ 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
RYQ pyrimidine F4 fragment c1cncnc1 InChI=1S/C4H4N2/c1-2-5-4-6-3-1/h1-4H CZPWVGJYEJSRLH-UHFFFAOYSA-N
RYQ thiazole F5 fragment c1cscn1 InChI=1S/C3H3NS/c1-2-5-3-4-1/h1-3H FZWLAAWBMGSTSO-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
RYQ C16 S1 1
RYQ C17 S1 1
RYQ C13 S1 1
RYQ C10 S1 1
RYQ C02 S1 1
RYQ C04 S1 1
RYQ C05 S1 1
RYQ C07 S1 1
RYQ C09 S1 1
RYQ N03 S1 1
RYQ N06 S1 1
RYQ N08 S1 1
RYQ N12 S1 1
RYQ N15 S1 1
RYQ S18 S1 1
RYQ N12 F1 1
RYQ C10 F1 1
RYQ C09 F1 1
RYQ C16 F1 1
RYQ N15 F1 1
RYQ C13 F1 1
RYQ N06 F1 1
RYQ C07 F1 1
RYQ N08 F1 1
RYQ N11 F1 1
RYQ C16 F2 1
RYQ C09 F2 1
RYQ N08 F2 1
RYQ C07 F2 1
RYQ N06 F2 1
RYQ N08 F3 1
RYQ C07 F3 1
RYQ N06 F3 1
RYQ C16 F3 1
RYQ C09 F3 1
RYQ C10 F3 1
RYQ N12 F3 1
RYQ C13 F3 1
RYQ N15 F3 1
RYQ C09 F4 1
RYQ C16 F4 1
RYQ N15 F4 1
RYQ C13 F4 1
RYQ N12 F4 1
RYQ C10 F4 1
RYQ C17 F5 1
RYQ C04 F5 1
RYQ N03 F5 1
RYQ C02 F5 1
RYQ S18 F5 1
#
_pdbe_chem_comp_rdkit_properties.comp_id RYQ
_pdbe_chem_comp_rdkit_properties.exactmw 261.080
_pdbe_chem_comp_rdkit_properties.amw 261.314
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 7
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 4
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 5
_pdbe_chem_comp_rdkit_properties.NumHBD 2
_pdbe_chem_comp_rdkit_properties.NumHBA 8
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 18
_pdbe_chem_comp_rdkit_properties.NumAtoms 29
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 8
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.200
_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 122.205
_pdbe_chem_comp_rdkit_properties.tpsa 108.530
_pdbe_chem_comp_rdkit_properties.CrippenClogP -0.495
_pdbe_chem_comp_rdkit_properties.CrippenMR 65.715
_pdbe_chem_comp_rdkit_properties.chi0v 9.355
_pdbe_chem_comp_rdkit_properties.chi1v 5.382
_pdbe_chem_comp_rdkit_properties.chi2v 2.564
_pdbe_chem_comp_rdkit_properties.chi3v 2.564
_pdbe_chem_comp_rdkit_properties.chi4v 1.721
_pdbe_chem_comp_rdkit_properties.chi0n 19.539
_pdbe_chem_comp_rdkit_properties.chi1n 9.854
_pdbe_chem_comp_rdkit_properties.chi2n 1.984
_pdbe_chem_comp_rdkit_properties.chi3n 1.984
_pdbe_chem_comp_rdkit_properties.chi4n 1.299
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -2.220
_pdbe_chem_comp_rdkit_properties.kappa1 4.162
_pdbe_chem_comp_rdkit_properties.kappa2 3.913
_pdbe_chem_comp_rdkit_properties.kappa3 1.758
_pdbe_chem_comp_rdkit_properties.Phi 0.905
#
_pdbe_chem_comp_external_mappings.comp_id RYQ
_pdbe_chem_comp_external_mappings.source UniChem
_pdbe_chem_comp_external_mappings.resource PDBe
_pdbe_chem_comp_external_mappings.resource_id RYQ
#
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
RYQ C16 1.294 -0.767 -0.555 ETKDGv3 1
RYQ C17 -1.981 -0.939 0.827 ETKDGv3 2
RYQ C13 2.325 -1.396 1.470 ETKDGv3 3
RYQ C10 3.066 0.586 0.327 ETKDGv3 4
RYQ C01 -4.236 2.206 -0.137 ETKDGv3 5
RYQ C02 -3.319 1.049 0.065 ETKDGv3 6
RYQ C04 -1.913 -0.657 -0.477 ETKDGv3 7
RYQ C05 -1.032 -1.409 -1.428 ETKDGv3 8
RYQ C07 0.540 0.478 -2.210 ETKDGv3 9
RYQ C09 2.048 0.290 -0.688 ETKDGv3 10
RYQ N03 -2.682 0.478 -0.907 ETKDGv3 11
RYQ N06 0.269 -0.757 -1.531 ETKDGv3 12
RYQ N08 1.578 1.115 -1.749 ETKDGv3 13
RYQ N11 3.903 1.737 0.227 ETKDGv3 14
RYQ N12 3.181 -0.233 1.339 ETKDGv3 15
RYQ N14 2.469 -2.259 2.596 ETKDGv3 16
RYQ N15 1.411 -1.648 0.568 ETKDGv3 17
RYQ S18 -3.064 0.227 1.622 ETKDGv3 18
RYQ H171 -1.448 -1.741 1.320 ETKDGv3 19
RYQ H011 -3.853 2.859 -0.949 ETKDGv3 20
RYQ H012 -5.245 1.834 -0.410 ETKDGv3 21
RYQ H013 -4.306 2.799 0.798 ETKDGv3 22
RYQ H052 -0.897 -2.459 -1.088 ETKDGv3 23
RYQ H051 -1.511 -1.436 -2.430 ETKDGv3 24
RYQ H071 -0.076 0.867 -3.009 ETKDGv3 25
RYQ H111 3.813 2.393 -0.581 ETKDGv3 26
RYQ H112 4.619 1.935 0.961 ETKDGv3 27
RYQ H142 3.193 -2.059 3.321 ETKDGv3 28
RYQ H141 1.854 -3.095 2.707 ETKDGv3 29
#