data_RQR
#
_chem_comp.id RQR
_chem_comp.name "(1S,4R)-4-[(thieno[2,3-d]pyrimidine-4-carbonyl)amino]cyclopent-2-ene-1-carboxylic acid"
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C13 H11 N3 O3 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 2022-07-01
_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 289.310
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code RQR
_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 5SSK
_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
RQR N1 N1 N 0 1 N N N N N N -44.245 -29.467 2.161 0.885 0.085 0.325 N1 RQR 1
RQR S1 S1 S 0 1 Y N N N N N -48.246 -28.761 6.952 -5.417 -0.203 -0.181 S1 RQR 2
RQR C13 C1 C 0 1 Y N N N N N -44.535 -29.349 6.138 -2.453 2.492 -0.192 C13 RQR 3
RQR O2 O1 O 0 1 N N N N N N -43.876 -33.731 2.264 5.308 1.604 0.337 O2 RQR 4
RQR C12 C2 C 0 1 Y N N N N N -46.720 -28.991 6.205 -3.917 0.712 -0.143 C12 RQR 5
RQR C11 C3 C 0 1 Y N N N N N -49.023 -28.588 5.407 -4.573 -1.724 0.039 C11 RQR 6
RQR O3 O2 O 0 1 N N N N N N -42.760 -32.011 3.075 6.561 0.123 -0.722 O3 RQR 7
RQR C10 C4 C 0 1 Y N N N N N -48.102 -28.701 4.349 -3.267 -1.544 0.132 C10 RQR 8
RQR C9 C5 C 0 1 Y N N N N N -46.803 -28.937 4.832 -2.834 -0.168 0.035 C9 RQR 9
RQR C8 C6 C 0 1 Y N N N N N -45.579 -29.088 4.165 -1.535 0.398 0.090 C8 RQR 10
RQR C7 C7 C 0 1 N N N N N N -45.524 -29.106 2.659 -0.345 -0.465 0.275 C7 RQR 11
RQR C6 C8 C 0 1 N N N N N N -42.049 -31.063 0.510 3.848 -1.177 -0.931 C6 RQR 12
RQR C5 C9 C 0 1 N N N N N N -42.449 -29.715 0.528 2.549 -1.276 -0.835 C5 RQR 13
RQR C4 C10 C 0 1 N N R N N N -43.988 -29.688 0.764 2.062 -0.768 0.502 C4 RQR 14
RQR C3 C11 C 0 1 N N N N N N -44.468 -31.071 0.538 3.244 0.054 1.065 C3 RQR 15
RQR C2 C12 C 0 1 N N S N N N -43.306 -31.966 0.705 4.442 -0.588 0.327 C2 RQR 16
RQR C1 C13 C 0 1 N N N N N N -43.305 -32.614 2.105 5.468 0.460 -0.019 C1 RQR 17
RQR O1 O3 O 0 1 N N N N N N -46.468 -28.905 1.948 -0.477 -1.668 0.380 O1 RQR 18
RQR N2 N2 N 0 1 Y N N N N N -45.594 -29.198 6.894 -3.679 2.019 -0.250 N2 RQR 19
RQR N3 N3 N 0 1 Y N N N N N -44.456 -29.322 4.835 -1.404 1.713 -0.027 N3 RQR 20
RQR H7 H1 H 0 1 N N N N N N -43.491 -29.572 2.809 0.990 1.046 0.241 H7 RQR 21
RQR H10 H2 H 0 1 N N N N N N -43.605 -29.518 6.661 -2.301 3.558 -0.283 H10 RQR 22
RQR H9 H3 H 0 1 N N N N N N -50.081 -28.415 5.275 -5.060 -2.687 0.092 H9 RQR 23
RQR H11 H4 H 0 1 N N N N N N -42.862 -32.526 3.867 7.191 0.830 -0.920 H11 RQR 24
RQR H8 H5 H 0 1 N N N N N N -48.359 -28.617 3.303 -2.576 -2.363 0.270 H8 RQR 25
RQR H6 H6 H 0 1 N N N N N N -41.036 -31.416 0.382 4.422 -1.481 -1.793 H6 RQR 26
RQR H5 H7 H 0 1 N N N N N N -41.807 -28.856 0.401 1.908 -1.668 -1.611 H5 RQR 27
RQR H2 H8 H 0 1 N N N N N N -44.483 -28.956 0.109 1.829 -1.603 1.163 H2 RQR 28
RQR H3 H9 H 0 1 N N N N N N -44.876 -31.168 -0.479 3.145 1.108 0.807 H3 RQR 29
RQR H4 H10 H 0 1 N N N N N N -45.248 -31.324 1.271 3.333 -0.077 2.143 H4 RQR 30
RQR H1 H11 H 0 1 N N N N N N -43.312 -32.752 -0.064 4.890 -1.371 0.939 H1 RQR 31
#
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
RQR C6 C5 DOUB N N 1
RQR C6 C2 SING N N 2
RQR C5 C4 SING N N 3
RQR C3 C2 SING N N 4
RQR C3 C4 SING N N 5
RQR C2 C1 SING N N 6
RQR C4 N1 SING N N 7
RQR O1 C7 DOUB N N 8
RQR C1 O2 DOUB N N 9
RQR C1 O3 SING N N 10
RQR N1 C7 SING N N 11
RQR C7 C8 SING N N 12
RQR C8 C9 DOUB Y N 13
RQR C8 N3 SING Y N 14
RQR C10 C9 SING Y N 15
RQR C10 C11 DOUB Y N 16
RQR C9 C12 SING Y N 17
RQR N3 C13 DOUB Y N 18
RQR C11 S1 SING Y N 19
RQR C13 N2 SING Y N 20
RQR C12 N2 DOUB Y N 21
RQR C12 S1 SING Y N 22
RQR N1 H7 SING N N 23
RQR C13 H10 SING N N 24
RQR C11 H9 SING N N 25
RQR O3 H11 SING N N 26
RQR C10 H8 SING N N 27
RQR C6 H6 SING N N 28
RQR C5 H5 SING N N 29
RQR C4 H2 SING N N 30
RQR C3 H3 SING N N 31
RQR C3 H4 SING N N 32
RQR C2 H1 SING N N 33
#
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
RQR SMILES ACDLabs 12.01 O=C(O)C1C=CC(C1)NC(=O)c1ncnc2sccc12
RQR InChI InChI 1.06 InChI=1S/C13H11N3O3S/c17-11(16-8-2-1-7(5-8)13(18)19)10-9-3-4-20-12(9)15-6-14-10/h1-4,6-8H,5H2,(H,16,17)(H,18,19)/t7-,8+/m1/s1
RQR InChIKey InChI 1.06 QXCOOMUNLBGYCR-SFYZADRCSA-N
RQR SMILES_CANONICAL CACTVS 3.385 OC(=O)[C@H]1C[C@@H](NC(=O)c2ncnc3sccc23)C=C1
RQR SMILES CACTVS 3.385 OC(=O)[CH]1C[CH](NC(=O)c2ncnc3sccc23)C=C1
RQR SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 c1csc2c1c(ncn2)C(=O)N[C@@H]3C[C@@H](C=C3)C(=O)O
RQR SMILES "OpenEye OEToolkits" 2.0.7 c1csc2c1c(ncn2)C(=O)NC3CC(C=C3)C(=O)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
RQR "SYSTEMATIC NAME" ACDLabs 12.01 "(1S,4R)-4-[(thieno[2,3-d]pyrimidine-4-carbonyl)amino]cyclopent-2-ene-1-carboxylic acid"
RQR "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "(1~{S},4~{R})-4-(thieno[2,3-d]pyrimidin-4-ylcarbonylamino)cyclopent-2-ene-1-carboxylic acid"
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
RQR 'Create component' 2022-06-23 RCSB
RQR 'Initial release' 2022-07-06 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
RQR N1 N 6.123 -0.947 1
RQR S1 S 10.141 -5.904 2
RQR C13 C 6.123 -5.447 3
RQR O2 O 5.102 5.445 4
RQR C12 C 8.722 -5.447 5
RQR C11 C 11.016 -4.697 6
RQR O3 O 3.000 3.918 7
RQR C10 C 10.141 -3.490 8
RQR C9 C 8.722 -3.947 9
RQR C8 C 7.422 -3.197 10
RQR C7 C 7.422 -1.697 11
RQR C6 C 6.873 2.861 12
RQR C5 C 7.337 1.435 13
RQR C4 C 6.123 0.553 14
RQR C3 C 4.910 1.435 15
RQR C2 C 5.373 2.861 16
RQR C1 C 4.492 4.075 17
RQR O1 O 8.722 -0.947 18
RQR N2 N 7.422 -6.197 19
RQR N3 N 6.123 -3.947 20
#
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
RQR C6 C5 DOUBLE NONE 1
RQR C6 C2 SINGLE NONE 2
RQR C5 C4 SINGLE NONE 3
RQR C3 C2 SINGLE NONE 4
RQR C3 C4 SINGLE NONE 5
RQR C2 C1 SINGLE BEGINDASH 6
RQR C4 N1 SINGLE BEGINDASH 7
RQR O1 C7 DOUBLE NONE 8
RQR C1 O2 DOUBLE NONE 9
RQR C1 O3 SINGLE NONE 10
RQR N1 C7 SINGLE NONE 11
RQR C7 C8 SINGLE NONE 12
RQR C8 C9 SINGLE NONE 13
RQR C8 N3 DOUBLE NONE 14
RQR C10 C9 SINGLE NONE 15
RQR C10 C11 DOUBLE NONE 16
RQR C9 C12 DOUBLE NONE 17
RQR N3 C13 SINGLE NONE 18
RQR C11 S1 SINGLE NONE 19
RQR C13 N2 DOUBLE NONE 20
RQR C12 N2 SINGLE NONE 21
RQR C12 S1 SINGLE NONE 22
#
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
RQR MurckoScaffold S1 scaffold 'O=C(N[C@H]1C=CCC1)c1ncnc2sccc12' InChI=1S/C12H11N3OS/c16-11(15-8-3-1-2-4-8)10-9-5-6-17-12(9)14-7-13-10/h1,3,5-8H,2,4H2,(H,15,16)/t8-/m0/s1 XYXFSBCSHOEBRU-QMMMGPOBSA-N
RQR amide F1 fragment CC(N)=O InChI=1S/C2H5NO/c1-2(3)4/h1H3,(H2,3,4) DLFVBJFMPXGRIB-UHFFFAOYSA-N
RQR pyrimidine F2 fragment c1cncnc1 InChI=1S/C4H4N2/c1-2-5-4-6-3-1/h1-4H CZPWVGJYEJSRLH-UHFFFAOYSA-N
RQR thiophen F3 fragment c1ccsc1 InChI=1S/C4H4S/c1-2-4-5-3-1/h1-4H YTPLMLYBLZKORZ-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
RQR N1 S1 1
RQR S1 S1 1
RQR C13 S1 1
RQR C12 S1 1
RQR C11 S1 1
RQR C10 S1 1
RQR C9 S1 1
RQR C8 S1 1
RQR C7 S1 1
RQR C6 S1 1
RQR C5 S1 1
RQR C4 S1 1
RQR C3 S1 1
RQR C2 S1 1
RQR O1 S1 1
RQR N2 S1 1
RQR N3 S1 1
RQR N1 F1 1
RQR C7 F1 1
RQR O1 F1 1
RQR C8 F1 1
RQR C9 F2 1
RQR C8 F2 1
RQR N3 F2 1
RQR C13 F2 1
RQR N2 F2 1
RQR C12 F2 1
RQR C12 F3 1
RQR C9 F3 1
RQR C10 F3 1
RQR C11 F3 1
RQR S1 F3 1
#
_pdbe_chem_comp_rdkit_properties.comp_id RQR
_pdbe_chem_comp_rdkit_properties.exactmw 289.052
_pdbe_chem_comp_rdkit_properties.amw 289.316
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 6
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 2
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 3
_pdbe_chem_comp_rdkit_properties.NumHBD 2
_pdbe_chem_comp_rdkit_properties.NumHBA 6
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 20
_pdbe_chem_comp_rdkit_properties.NumAtoms 31
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 7
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 1
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.231
_pdbe_chem_comp_rdkit_properties.NumRings 3
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 2
_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 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 2
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 133.318
_pdbe_chem_comp_rdkit_properties.tpsa 92.180
_pdbe_chem_comp_rdkit_properties.CrippenClogP 0.967
_pdbe_chem_comp_rdkit_properties.CrippenMR 71.080
_pdbe_chem_comp_rdkit_properties.chi0v 10.291
_pdbe_chem_comp_rdkit_properties.chi1v 5.929
_pdbe_chem_comp_rdkit_properties.chi2v 2.950
_pdbe_chem_comp_rdkit_properties.chi3v 2.950
_pdbe_chem_comp_rdkit_properties.chi4v 2.001
_pdbe_chem_comp_rdkit_properties.chi0n 20.475
_pdbe_chem_comp_rdkit_properties.chi1n 10.468
_pdbe_chem_comp_rdkit_properties.chi2n 2.257
_pdbe_chem_comp_rdkit_properties.chi3n 2.257
_pdbe_chem_comp_rdkit_properties.chi4n 1.415
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -2.280
_pdbe_chem_comp_rdkit_properties.kappa1 5.249
_pdbe_chem_comp_rdkit_properties.kappa2 5.009
_pdbe_chem_comp_rdkit_properties.kappa3 2.272
_pdbe_chem_comp_rdkit_properties.Phi 1.315
#
_pdbe_chem_comp_external_mappings.comp_id RQR
_pdbe_chem_comp_external_mappings.source UniChem
_pdbe_chem_comp_external_mappings.resource PDBe
_pdbe_chem_comp_external_mappings.resource_id RQR
#
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
RQR N1 -0.015 0.069 0.407 ETKDGv3 1
RQR S1 -4.614 -1.136 -2.259 ETKDGv3 2
RQR C13 -3.727 2.692 -1.340 ETKDGv3 3
RQR O2 2.644 -0.233 -1.898 ETKDGv3 4
RQR C12 -3.864 0.360 -1.675 ETKDGv3 5
RQR C11 -3.473 -2.124 -1.299 ETKDGv3 6
RQR O3 4.865 0.228 -1.546 ETKDGv3 7
RQR C10 -2.632 -1.340 -0.622 ETKDGv3 8
RQR C9 -2.850 0.107 -0.856 ETKDGv3 9
RQR C8 -2.159 1.255 -0.219 ETKDGv3 10
RQR C7 -0.992 1.088 0.665 ETKDGv3 11
RQR C6 2.801 -1.647 0.660 ETKDGv3 12
RQR C5 1.580 -1.586 1.165 ETKDGv3 13
RQR C4 1.100 -0.185 1.321 ETKDGv3 14
RQR C3 2.318 0.676 0.952 ETKDGv3 15
RQR C2 3.371 -0.297 0.391 ETKDGv3 16
RQR C1 3.597 -0.104 -1.082 ETKDGv3 17
RQR O1 -0.828 1.889 1.625 ETKDGv3 18
RQR N2 -4.323 1.693 -1.926 ETKDGv3 19
RQR N3 -2.608 2.458 -0.458 ETKDGv3 20
RQR H7 0.002 -0.374 -0.540 ETKDGv3 21
RQR H10 -4.067 3.702 -1.520 ETKDGv3 22
RQR H9 -3.474 -3.205 -1.247 ETKDGv3 23
RQR H11 5.037 0.365 -2.535 ETKDGv3 24
RQR H8 -1.890 -1.742 0.054 ETKDGv3 25
RQR H6 3.316 -2.580 0.453 ETKDGv3 26
RQR H5 0.990 -2.464 1.408 ETKDGv3 27
RQR H2 0.791 -0.018 2.376 ETKDGv3 28
RQR H3 2.056 1.484 0.233 ETKDGv3 29
RQR H4 2.717 1.159 1.872 ETKDGv3 30
RQR H1 4.332 -0.186 0.940 ETKDGv3 31
#