data_W5G
#
_chem_comp.id W5G
_chem_comp.name 4-(5-azaspiro[2.5]octan-5-yl)-7H-pyrrolo[2,3-d]pyrimidine
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C13 H16 N4"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2020-09-29
_chem_comp.pdbx_modified_date 2020-12-11
_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 228.293
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code W5G
_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 5RSH
_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
W5G N12 N1 N 0 1 Y N N N N N -45.327 -29.095 6.925 -3.030 1.628 0.228 N12 W5G 1
W5G C13 C1 C 0 1 Y N N N N N -46.461 -29.012 6.195 -2.997 0.324 -0.042 C13 W5G 2
W5G C15 C2 C 0 1 Y N N N N N -48.533 -28.819 5.387 -3.356 -1.844 -0.494 C15 W5G 3
W5G C17 C3 C 0 1 Y N N N N N -46.399 -29.107 4.846 -1.744 -0.306 -0.158 C17 W5G 4
W5G C01 C4 C 0 1 N N N N N N -42.008 -30.938 0.979 3.730 0.265 -1.446 C01 W5G 5
W5G C02 C5 C 0 1 N N N N N N -42.565 -31.604 2.219 4.301 1.116 -0.310 C02 W5G 6
W5G C03 C6 C 0 1 N N N N N N -43.470 -30.649 1.391 3.091 0.218 -0.059 C03 W5G 7
W5G C04 C7 C 0 1 N N N N N N -44.516 -31.184 0.497 3.301 -1.046 0.781 C04 W5G 8
W5G C05 C8 C 0 1 N N N N N N -45.914 -31.126 0.922 2.114 -1.988 0.549 C05 W5G 9
W5G C06 C9 C 0 1 N N N N N N -46.285 -30.041 1.970 0.812 -1.237 0.837 C06 W5G 10
W5G C08 C10 C 0 1 N N N N N N -43.853 -29.291 1.986 1.727 0.891 0.121 C08 W5G 11
W5G C09 C11 C 0 1 Y N N N N N -45.141 -29.278 4.224 -0.584 0.464 0.014 C09 W5G 12
W5G C11 C12 C 0 1 Y N N N N N -44.163 -29.250 6.327 -1.916 2.312 0.382 C11 W5G 13
W5G C16 C13 C 0 1 Y N N N N N -47.695 -28.991 4.321 -2.020 -1.711 -0.452 C16 W5G 14
W5G N07 N2 N 0 1 N N N N N N -45.137 -29.379 2.766 0.670 -0.110 -0.091 N07 W5G 15
W5G N10 N3 N 0 1 Y N N N N N -44.064 -29.325 5.005 -0.721 1.760 0.280 N10 W5G 16
W5G N14 N4 N 0 1 Y N N N N N -47.784 -28.839 6.486 -3.951 -0.633 -0.250 N14 W5G 17
W5G H151 H1 H 0 0 N N N N N N -49.605 -28.691 5.345 -3.883 -2.766 -0.692 H151 W5G 18
W5G H011 H2 H 0 0 N N N N N N -41.801 -31.539 0.081 3.183 0.780 -2.235 H011 W5G 19
W5G H012 H3 H 0 0 N N N N N N -41.246 -30.150 1.076 4.307 -0.604 -1.764 H012 W5G 20
W5G H021 H4 H 0 0 N N N N N N -42.764 -32.686 2.218 5.254 0.808 0.120 H021 W5G 21
W5G H022 H5 H 0 0 N N N N N N -42.209 -31.297 3.213 4.130 2.192 -0.352 H022 W5G 22
W5G H042 H6 H 0 0 N N N N N N -44.277 -32.243 0.320 4.225 -1.539 0.476 H042 W5G 23
W5G H041 H7 H 0 0 N N N N N N -44.444 -30.629 -0.450 3.357 -0.780 1.836 H041 W5G 24
W5G H052 H8 H 0 0 N N N N N N -46.527 -30.946 0.026 2.116 -2.329 -0.486 H052 W5G 25
W5G H051 H9 H 0 0 N N N N N N -46.172 -32.105 1.352 2.195 -2.847 1.216 H051 W5G 26
W5G H061 H10 H 0 0 N N N N N N -46.818 -29.240 1.437 -0.032 -1.916 0.715 H061 W5G 27
W5G H062 H11 H 0 0 N N N N N N -46.962 -30.509 2.700 0.829 -0.863 1.861 H062 W5G 28
W5G H082 H12 H 0 0 N N N N N N -43.049 -28.954 2.656 1.650 1.294 1.131 H082 W5G 29
W5G H081 H13 H 0 0 N N N N N N -43.979 -28.565 1.170 1.618 1.696 -0.605 H081 W5G 30
W5G H111 H14 H 0 0 N N N N N N -43.268 -29.318 6.927 -1.983 3.367 0.600 H111 W5G 31
W5G H161 H15 H 0 0 N N N N N N -47.975 -29.030 3.279 -1.291 -2.492 -0.605 H161 W5G 32
W5G H141 H16 H 0 0 N N N N N N -48.146 -28.739 7.413 -4.908 -0.478 -0.229 H141 W5G 33
#
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
W5G C04 C05 SING N N 1
W5G C04 C03 SING N N 2
W5G C05 C06 SING N N 3
W5G C01 C03 SING N N 4
W5G C01 C02 SING N N 5
W5G C03 C08 SING N N 6
W5G C03 C02 SING N N 7
W5G C06 N07 SING N N 8
W5G C08 N07 SING N N 9
W5G N07 C09 SING N N 10
W5G C09 C17 DOUB Y N 11
W5G C09 N10 SING Y N 12
W5G C16 C17 SING Y N 13
W5G C16 C15 DOUB Y N 14
W5G C17 C13 SING Y N 15
W5G N10 C11 DOUB Y N 16
W5G C15 N14 SING Y N 17
W5G C13 N14 SING Y N 18
W5G C13 N12 DOUB Y N 19
W5G C11 N12 SING Y N 20
W5G C15 H151 SING N N 21
W5G C01 H011 SING N N 22
W5G C01 H012 SING N N 23
W5G C02 H021 SING N N 24
W5G C02 H022 SING N N 25
W5G C04 H042 SING N N 26
W5G C04 H041 SING N N 27
W5G C05 H052 SING N N 28
W5G C05 H051 SING N N 29
W5G C06 H061 SING N N 30
W5G C06 H062 SING N N 31
W5G C08 H082 SING N N 32
W5G C08 H081 SING N N 33
W5G C11 H111 SING N N 34
W5G C16 H161 SING N N 35
W5G N14 H141 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
W5G SMILES ACDLabs 12.01 n2c1nccc1c(nc2)N4CCCC3(CC3)C4
W5G InChI InChI 1.03 InChI=1S/C13H16N4/c1-3-13(4-5-13)8-17(7-1)12-10-2-6-14-11(10)15-9-16-12/h2,6,9H,1,3-5,7-8H2,(H,14,15,16)
W5G InChIKey InChI 1.03 GGTHBUVHAUVHID-UHFFFAOYSA-N
W5G SMILES_CANONICAL CACTVS 3.385 C1CN(CC2(C1)CC2)c3ncnc4[nH]ccc34
W5G SMILES CACTVS 3.385 C1CN(CC2(C1)CC2)c3ncnc4[nH]ccc34
W5G SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 c1c[nH]c2c1c(ncn2)N3CCCC4(C3)CC4
W5G SMILES "OpenEye OEToolkits" 2.0.7 c1c[nH]c2c1c(ncn2)N3CCCC4(C3)CC4
#
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
W5G "SYSTEMATIC NAME" ACDLabs 12.01 4-(5-azaspiro[2.5]octan-5-yl)-7H-pyrrolo[2,3-d]pyrimidine
W5G "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 4-(5-azaspiro[2.5]octan-5-yl)-7~{H}-pyrrolo[2,3-d]pyrimidine
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
W5G 'Create component' 2020-09-29 RCSB
W5G 'Initial release' 2020-12-16 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
W5G N12 N 3.000 1.450 1
W5G C13 C 4.299 2.200 2
W5G C15 C 6.096 3.812 3
W5G C17 C 5.598 1.450 4
W5G C01 C 8.946 -4.349 5
W5G C02 C 7.446 -4.349 6
W5G C03 C 8.196 -3.050 7
W5G C04 C 9.495 -2.300 8
W5G C05 C 9.495 -0.800 9
W5G C06 C 8.196 -0.050 10
W5G C08 C 6.897 -2.300 11
W5G C09 C 5.598 -0.050 12
W5G C11 C 3.000 -0.050 13
W5G C16 C 6.704 2.450 14
W5G N07 N 6.897 -0.800 15
W5G N10 N 4.299 -0.800 16
W5G N14 N 4.613 3.657 17
#
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
W5G C04 C05 SINGLE NONE 1
W5G C04 C03 SINGLE NONE 2
W5G C05 C06 SINGLE NONE 3
W5G C01 C03 SINGLE NONE 4
W5G C01 C02 SINGLE NONE 5
W5G C03 C08 SINGLE NONE 6
W5G C03 C02 SINGLE NONE 7
W5G C06 N07 SINGLE NONE 8
W5G C08 N07 SINGLE NONE 9
W5G N07 C09 SINGLE NONE 10
W5G C09 C17 DOUBLE NONE 11
W5G C09 N10 SINGLE NONE 12
W5G C16 C17 SINGLE NONE 13
W5G C16 C15 DOUBLE NONE 14
W5G C17 C13 SINGLE NONE 15
W5G N10 C11 DOUBLE NONE 16
W5G C15 N14 SINGLE NONE 17
W5G C13 N14 SINGLE NONE 18
W5G C13 N12 DOUBLE NONE 19
W5G C11 N12 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
W5G MurckoScaffold S1 scaffold 'c1nc(N2CCCC3(CC3)C2)c2cc[nH]c2n1' InChI=1S/C13H16N4/c1-3-13(4-5-13)8-17(7-1)12-10-2-6-14-11(10)15-9-16-12/h2,6,9H,1,3-5,7-8H2,(H,14,15,16) GGTHBUVHAUVHID-UHFFFAOYSA-N
W5G cyclopropane F1 fragment C1CC1 InChI=1S/C3H6/c1-2-3-1/h1-3H2 LVZWSLJZHVFIQJ-UHFFFAOYSA-N
W5G pyrimidine F2 fragment c1cncnc1 InChI=1S/C4H4N2/c1-2-5-4-6-3-1/h1-4H CZPWVGJYEJSRLH-UHFFFAOYSA-N
W5G pyrrole F3 fragment 'c1cc[nH]c1' InChI=1S/C4H5N/c1-2-4-5-3-1/h1-5H KAESVJOAVNADME-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
W5G N12 S1 1
W5G C13 S1 1
W5G C15 S1 1
W5G C17 S1 1
W5G C01 S1 1
W5G C02 S1 1
W5G C03 S1 1
W5G C04 S1 1
W5G C05 S1 1
W5G C06 S1 1
W5G C08 S1 1
W5G C09 S1 1
W5G C11 S1 1
W5G C16 S1 1
W5G N07 S1 1
W5G N10 S1 1
W5G N14 S1 1
W5G C01 F1 1
W5G C03 F1 1
W5G C02 F1 1
W5G C17 F2 1
W5G C09 F2 1
W5G N10 F2 1
W5G C11 F2 1
W5G N12 F2 1
W5G C13 F2 1
W5G C13 F3 1
W5G C17 F3 1
W5G C16 F3 1
W5G C15 F3 1
W5G N14 F3 1
#
_pdbe_chem_comp_rdkit_properties.comp_id W5G
_pdbe_chem_comp_rdkit_properties.exactmw 228.137
_pdbe_chem_comp_rdkit_properties.amw 228.299
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 4
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 1
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 1
_pdbe_chem_comp_rdkit_properties.NumHBD 1
_pdbe_chem_comp_rdkit_properties.NumHBA 3
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 17
_pdbe_chem_comp_rdkit_properties.NumAtoms 33
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 4
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.538
_pdbe_chem_comp_rdkit_properties.NumRings 4
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 2
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 2
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 2
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 3
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 2
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumSpiroAtoms 1
_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 122.602
_pdbe_chem_comp_rdkit_properties.tpsa 44.810
_pdbe_chem_comp_rdkit_properties.CrippenClogP 1.529
_pdbe_chem_comp_rdkit_properties.CrippenMR 63.973
_pdbe_chem_comp_rdkit_properties.chi0v 8.289
_pdbe_chem_comp_rdkit_properties.chi1v 4.762
_pdbe_chem_comp_rdkit_properties.chi2v 2.386
_pdbe_chem_comp_rdkit_properties.chi3v 2.386
_pdbe_chem_comp_rdkit_properties.chi4v 1.511
_pdbe_chem_comp_rdkit_properties.chi0n 24.289
_pdbe_chem_comp_rdkit_properties.chi1n 12.710
_pdbe_chem_comp_rdkit_properties.chi2n 2.386
_pdbe_chem_comp_rdkit_properties.chi3n 2.386
_pdbe_chem_comp_rdkit_properties.chi4n 1.511
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.580
_pdbe_chem_comp_rdkit_properties.kappa1 2.706
_pdbe_chem_comp_rdkit_properties.kappa2 3.215
_pdbe_chem_comp_rdkit_properties.kappa3 1.431
_pdbe_chem_comp_rdkit_properties.Phi 0.512
#
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
W5G UniChem PDBe W5G
W5G UniChem SureChEMBL SCHEMBL20470386
W5G UniChem PubChem 127896820
#
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
W5G N12 4.075 1.112 0.556 ETKDGv3 1
W5G C13 3.698 0.113 -0.178 ETKDGv3 2
W5G C15 3.600 -1.546 -1.685 ETKDGv3 3
W5G C17 2.330 -0.296 -0.289 ETKDGv3 4
W5G C01 -2.909 1.187 -1.284 ETKDGv3 5
W5G C02 -3.474 1.727 0.022 ETKDGv3 6
W5G C03 -2.408 0.638 0.051 ETKDGv3 7
W5G C04 -2.891 -0.776 0.431 ETKDGv3 8
W5G C05 -1.764 -1.589 1.075 ETKDGv3 9
W5G C06 -0.448 -1.403 0.312 ETKDGv3 10
W5G C08 -1.005 1.089 0.498 ETKDGv3 11
W5G C09 1.378 0.351 0.399 ETKDGv3 12
W5G C11 3.064 1.815 1.310 ETKDGv3 13
W5G C16 2.333 -1.366 -1.286 ETKDGv3 14
W5G N07 -0.021 0.008 0.324 ETKDGv3 15
W5G N10 1.806 1.457 1.229 ETKDGv3 16
W5G N14 4.517 -0.659 -1.033 ETKDGv3 17
W5G H151 3.901 -2.267 -2.434 ETKDGv3 18
W5G H011 -3.634 0.556 -1.842 ETKDGv3 19
W5G H012 -2.245 1.907 -1.807 ETKDGv3 20
W5G H021 -4.517 1.399 0.220 ETKDGv3 21
W5G H022 -3.125 2.754 0.264 ETKDGv3 22
W5G H042 -3.244 -1.318 -0.473 ETKDGv3 23
W5G H041 -3.739 -0.715 1.147 ETKDGv3 24
W5G H052 -2.042 -2.665 1.084 ETKDGv3 25
W5G H051 -1.624 -1.263 2.130 ETKDGv3 26
W5G H061 0.324 -2.041 0.794 ETKDGv3 27
W5G H062 -0.587 -1.739 -0.737 ETKDGv3 28
W5G H082 -1.047 1.368 1.572 ETKDGv3 29
W5G H081 -0.678 1.986 -0.073 ETKDGv3 30
W5G H111 3.347 2.648 1.940 ETKDGv3 31
W5G H161 1.485 -1.910 -1.676 ETKDGv3 32
W5G H141 5.544 -0.566 -1.197 ETKDGv3 33
#