data_W5D
#
_chem_comp.id W5D
_chem_comp.name 4-(1,4-oxazonan-4-yl)-7H-pyrrolo[2,3-d]pyrimidine
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C13 H18 N4 O"
_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 246.308
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code W5D
_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 5RSI
_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
W5D C10 C1 C 0 1 Y N N N N N -45.123 -29.429 4.184 -0.853 0.586 0.138 C10 W5D 1
W5D C17 C2 C 0 1 Y N N N N N -47.736 -29.128 4.386 -1.791 -1.832 -0.399 C17 W5D 2
W5D C01 C3 C 0 1 N N N N N N -46.649 -30.829 -0.141 3.934 -1.125 -0.311 C01 W5D 3
W5D C03 C4 C 0 1 N N N N N N -46.813 -29.228 1.524 2.222 -1.263 1.315 C03 W5D 4
W5D C04 C5 C 0 1 N N N N N N -45.601 -29.376 1.448 0.762 -0.814 1.144 C04 W5D 5
W5D C05 C6 C 0 1 N N N N N N -45.401 -30.532 0.217 3.990 0.415 -0.302 C05 W5D 6
W5D C06 C7 C 0 1 N N N N N N -44.513 -31.703 0.528 2.941 0.884 -1.365 C06 W5D 7
W5D C07 C8 C 0 1 N N N N N N -45.006 -32.105 1.771 2.057 1.932 -0.657 C07 W5D 8
W5D C08 C9 C 0 1 N N N N N N -44.158 -31.030 2.732 1.321 1.450 0.611 C08 W5D 9
W5D C12 C10 C 0 1 Y N N N N N -44.156 -29.415 6.239 -2.546 2.143 0.318 C12 W5D 10
W5D C14 C11 C 0 1 Y N N N N N -46.382 -29.151 6.123 -3.177 -0.022 -0.137 C14 W5D 11
W5D C16 C12 C 0 1 Y N N N N N -48.440 -28.975 5.500 -3.066 -2.223 -0.561 C16 W5D 12
W5D C18 C13 C 0 1 Y N N N N N -46.387 -29.294 4.769 -1.821 -0.398 -0.120 C18 W5D 13
W5D N09 N1 N 0 1 N N N N N N -44.869 -29.645 2.796 0.492 0.266 0.165 N09 W5D 14
W5D N11 N2 N 0 1 Y N N N N N -44.055 -29.483 4.959 -1.262 1.833 0.349 N11 W5D 15
W5D N13 N3 N 0 1 Y N N N N N -45.265 -29.205 6.826 -3.487 1.255 0.082 N13 W5D 16
W5D N15 N4 N 0 1 Y N N N N N -47.630 -29.020 6.529 -3.904 -1.149 -0.407 N15 W5D 17
W5D O02 O1 O 0 1 N N N N N N -47.234 -29.461 -0.018 2.662 -1.735 -0.004 O02 W5D 18
W5D H171 H1 H 0 0 N N N N N N -48.122 -29.126 3.377 -0.913 -2.458 -0.462 H171 W5D 19
W5D H011 H2 H 0 0 N N N N N N -46.706 -31.215 -1.169 4.240 -1.466 -1.300 H011 W5D 20
W5D H012 H3 H 0 0 N N N N N N -47.120 -31.547 0.547 4.666 -1.492 0.408 H012 W5D 21
W5D H031 H4 H 0 0 N N N N N N -47.273 -29.975 2.188 2.837 -0.423 1.637 H031 W5D 22
W5D H032 H5 H 0 0 N N N N N N -47.078 -28.218 1.869 2.282 -2.073 2.042 H032 W5D 23
W5D H041 H6 H 0 0 N N N N N N -45.406 -30.229 0.781 0.177 -1.686 0.851 H041 W5D 24
W5D H1 H7 H 0 1 N N N N N N -45.176 -28.462 1.009 0.398 -0.483 2.116 H1 W5D 25
W5D H2 H8 H 0 1 N N N N N N -44.939 -29.968 -0.607 3.722 0.796 0.683 H2 W5D 26
W5D H051 H9 H 0 0 N N N N N N -45.449 -29.898 1.114 4.987 0.757 -0.581 H051 W5D 27
W5D H061 H10 H 0 0 N N N N N N -44.620 -32.499 -0.223 3.448 1.336 -2.218 H061 W5D 28
W5D H062 H11 H 0 0 N N N N N N -43.457 -31.400 0.593 2.334 0.040 -1.691 H062 W5D 29
W5D H071 H12 H 0 0 N N N N N N -46.094 -31.964 1.851 2.687 2.779 -0.383 H071 W5D 30
W5D H072 H13 H 0 0 N N N N N N -44.755 -33.152 1.998 1.312 2.285 -1.369 H072 W5D 31
W5D H081 H14 H 0 0 N N N N N N -44.083 -31.441 3.749 2.040 1.143 1.371 H081 W5D 32
W5D H082 H15 H 0 0 N N N N N N -43.149 -30.896 2.315 0.676 2.240 0.996 H082 W5D 33
W5D H121 H16 H 0 0 N N N N N N -43.266 -29.541 6.838 -2.835 3.169 0.495 H121 W5D 34
W5D H161 H17 H 0 0 N N N N N N -49.510 -28.836 5.551 -3.383 -3.231 -0.780 H161 W5D 35
W5D H151 H18 H 0 0 N N N N N N -47.917 -28.963 7.485 -4.871 -1.183 -0.479 H151 W5D 36
#
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
W5D C10 C18 DOUB Y N 1
W5D C10 N09 SING N N 2
W5D C10 N11 SING Y N 3
W5D C17 C16 DOUB Y N 4
W5D C17 C18 SING Y N 5
W5D C01 C05 SING N N 6
W5D C01 O02 SING N N 7
W5D C03 C04 SING N N 8
W5D C03 O02 SING N N 9
W5D C04 N09 SING N N 10
W5D C05 C06 SING N N 11
W5D C06 C07 SING N N 12
W5D C07 C08 SING N N 13
W5D C08 N09 SING N N 14
W5D C12 N11 DOUB Y N 15
W5D C12 N13 SING Y N 16
W5D C14 C18 SING Y N 17
W5D C14 N13 DOUB Y N 18
W5D C14 N15 SING Y N 19
W5D C16 N15 SING Y N 20
W5D C17 H171 SING N N 21
W5D C01 H011 SING N N 22
W5D C01 H012 SING N N 23
W5D C03 H031 SING N N 24
W5D C03 H032 SING N N 25
W5D C04 H041 SING N N 26
W5D C04 H1 SING N N 27
W5D C05 H2 SING N N 28
W5D C05 H051 SING N N 29
W5D C06 H061 SING N N 30
W5D C06 H062 SING N N 31
W5D C07 H071 SING N N 32
W5D C07 H072 SING N N 33
W5D C08 H081 SING N N 34
W5D C08 H082 SING N N 35
W5D C12 H121 SING N N 36
W5D C16 H161 SING N N 37
W5D N15 H151 SING N N 38
#
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
W5D SMILES ACDLabs 12.01 c2(c1ccnc1ncn2)N3CCOCCCCC3
W5D InChI InChI 1.03 InChI=1S/C13H18N4O/c1-2-6-17(7-9-18-8-3-1)13-11-4-5-14-12(11)15-10-16-13/h4-5,10H,1-3,6-9H2,(H,14,15,16)
W5D InChIKey InChI 1.03 UZDOXWRWKJXTPZ-UHFFFAOYSA-N
W5D SMILES_CANONICAL CACTVS 3.385 C1CCOCCN(CC1)c2ncnc3[nH]ccc23
W5D SMILES CACTVS 3.385 C1CCOCCN(CC1)c2ncnc3[nH]ccc23
W5D SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 c1c[nH]c2c1c(ncn2)N3CCCCCOCC3
W5D SMILES "OpenEye OEToolkits" 2.0.7 c1c[nH]c2c1c(ncn2)N3CCCCCOCC3
#
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
W5D "SYSTEMATIC NAME" ACDLabs 12.01 4-(1,4-oxazonan-4-yl)-7H-pyrrolo[2,3-d]pyrimidine
W5D "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 4-(7~{H}-pyrrolo[2,3-d]pyrimidin-4-yl)-1,4-oxazonane
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
W5D 'Create component' 2020-09-29 RCSB
W5D '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
W5D C10 C 5.160 -1.081 1
W5D C17 C 7.878 -1.374 2
W5D C01 C 4.410 4.672 3
W5D C03 C 3.000 2.231 4
W5D C04 C 3.750 0.932 5
W5D C05 C 5.910 4.672 6
W5D C06 C 7.059 3.708 7
W5D C07 C 7.319 2.231 8
W5D C08 C 6.569 0.932 9
W5D C12 C 3.861 -3.331 10
W5D C14 C 6.458 -3.331 11
W5D C16 C 8.753 -2.581 12
W5D C18 C 6.458 -1.831 13
W5D N09 N 5.160 0.419 14
W5D N11 N 3.861 -1.831 15
W5D N13 N 5.160 -4.081 16
W5D N15 N 7.878 -3.788 17
W5D O02 O 3.260 3.708 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
W5D C10 C18 DOUBLE NONE 1
W5D C10 N09 SINGLE NONE 2
W5D C10 N11 SINGLE NONE 3
W5D C17 C16 DOUBLE NONE 4
W5D C17 C18 SINGLE NONE 5
W5D C01 C05 SINGLE NONE 6
W5D C01 O02 SINGLE NONE 7
W5D C03 C04 SINGLE NONE 8
W5D C03 O02 SINGLE NONE 9
W5D C04 N09 SINGLE NONE 10
W5D C05 C06 SINGLE NONE 11
W5D C06 C07 SINGLE NONE 12
W5D C07 C08 SINGLE NONE 13
W5D C08 N09 SINGLE NONE 14
W5D C12 N11 DOUBLE NONE 15
W5D C12 N13 SINGLE NONE 16
W5D C14 C18 SINGLE NONE 17
W5D C14 N13 DOUBLE NONE 18
W5D C14 N15 SINGLE NONE 19
W5D C16 N15 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
W5D MurckoScaffold S1 scaffold 'c1nc(N2CCCCCOCC2)c2cc[nH]c2n1' InChI=1S/C13H18N4O/c1-2-6-17(7-9-18-8-3-1)13-11-4-5-14-12(11)15-10-16-13/h4-5,10H,1-3,6-9H2,(H,14,15,16) UZDOXWRWKJXTPZ-UHFFFAOYSA-N
W5D pyrimidine F1 fragment c1cncnc1 InChI=1S/C4H4N2/c1-2-5-4-6-3-1/h1-4H CZPWVGJYEJSRLH-UHFFFAOYSA-N
W5D pyrrole F2 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
W5D C10 S1 1
W5D C17 S1 1
W5D C01 S1 1
W5D C03 S1 1
W5D C04 S1 1
W5D C05 S1 1
W5D C06 S1 1
W5D C07 S1 1
W5D C08 S1 1
W5D C12 S1 1
W5D C14 S1 1
W5D C16 S1 1
W5D C18 S1 1
W5D N09 S1 1
W5D N11 S1 1
W5D N13 S1 1
W5D N15 S1 1
W5D O02 S1 1
W5D C18 F1 1
W5D C10 F1 1
W5D N11 F1 1
W5D C12 F1 1
W5D N13 F1 1
W5D C14 F1 1
W5D C14 F2 1
W5D C18 F2 1
W5D C17 F2 1
W5D C16 F2 1
W5D N15 F2 1
#
_pdbe_chem_comp_rdkit_properties.comp_id W5D
_pdbe_chem_comp_rdkit_properties.exactmw 246.148
_pdbe_chem_comp_rdkit_properties.amw 246.314
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 5
_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 4
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 18
_pdbe_chem_comp_rdkit_properties.NumAtoms 36
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 5
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.538
_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 1
_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 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 131.531
_pdbe_chem_comp_rdkit_properties.tpsa 54.040
_pdbe_chem_comp_rdkit_properties.CrippenClogP 1.156
_pdbe_chem_comp_rdkit_properties.CrippenMR 67.742
_pdbe_chem_comp_rdkit_properties.chi0v 8.697
_pdbe_chem_comp_rdkit_properties.chi1v 4.671
_pdbe_chem_comp_rdkit_properties.chi2v 1.917
_pdbe_chem_comp_rdkit_properties.chi3v 1.917
_pdbe_chem_comp_rdkit_properties.chi4v 1.217
_pdbe_chem_comp_rdkit_properties.chi0n 26.697
_pdbe_chem_comp_rdkit_properties.chi1n 13.618
_pdbe_chem_comp_rdkit_properties.chi2n 1.917
_pdbe_chem_comp_rdkit_properties.chi3n 1.917
_pdbe_chem_comp_rdkit_properties.chi4n 1.217
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.620
_pdbe_chem_comp_rdkit_properties.kappa1 2.928
_pdbe_chem_comp_rdkit_properties.kappa2 5.351
_pdbe_chem_comp_rdkit_properties.kappa3 2.310
_pdbe_chem_comp_rdkit_properties.Phi 0.870
#
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
W5D UniChem PDBe W5D
W5D UniChem PubChem 155804583
#
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
W5D C10 1.475 -0.690 -1.040 ETKDGv3 1
W5D C17 2.534 1.016 0.586 ETKDGv3 2
W5D C01 -2.986 1.403 0.391 ETKDGv3 3
W5D C03 -0.895 2.053 -0.520 ETKDGv3 4
W5D C04 -0.001 1.314 -1.527 ETKDGv3 5
W5D C05 -3.712 0.065 0.170 ETKDGv3 6
W5D C06 -2.936 -1.193 0.625 ETKDGv3 7
W5D C07 -1.417 -1.192 0.376 ETKDGv3 8
W5D C08 -1.014 -0.981 -1.095 ETKDGv3 9
W5D C12 2.945 -2.524 -1.579 ETKDGv3 10
W5D C14 3.715 -0.799 -0.182 ETKDGv3 11
W5D C16 3.757 1.015 1.137 ETKDGv3 12
W5D C18 2.446 -0.146 -0.296 ETKDGv3 13
W5D N09 0.164 -0.104 -1.164 ETKDGv3 14
W5D N11 1.776 -1.943 -1.700 ETKDGv3 15
W5D N13 3.978 -1.928 -0.763 ETKDGv3 16
W5D N15 4.559 -0.091 0.703 ETKDGv3 17
W5D O02 -2.250 1.732 -0.775 ETKDGv3 18
W5D H171 1.767 1.747 0.790 ETKDGv3 19
W5D H011 -3.756 2.193 0.527 ETKDGv3 20
W5D H012 -2.414 1.375 1.345 ETKDGv3 21
W5D H031 -0.768 3.146 -0.675 ETKDGv3 22
W5D H032 -0.538 1.831 0.508 ETKDGv3 23
W5D H041 -0.444 1.385 -2.544 ETKDGv3 24
W5D H1 0.985 1.823 -1.577 ETKDGv3 25
W5D H2 -4.672 0.088 0.731 ETKDGv3 26
W5D H051 -3.990 -0.034 -0.903 ETKDGv3 27
W5D H061 -3.096 -1.322 1.718 ETKDGv3 28
W5D H062 -3.381 -2.083 0.129 ETKDGv3 29
W5D H071 -1.006 -2.167 0.716 ETKDGv3 30
W5D H072 -0.946 -0.430 1.030 ETKDGv3 31
W5D H081 -1.841 -0.551 -1.694 ETKDGv3 32
W5D H082 -0.801 -1.964 -1.569 ETKDGv3 33
W5D H121 3.135 -3.460 -2.086 ETKDGv3 34
W5D H161 4.101 1.758 1.844 ETKDGv3 35
W5D H151 5.524 -0.341 1.011 ETKDGv3 36
#