data_W8D
#
_chem_comp.id W8D
_chem_comp.name 3-{[(2R)-oxolan-2-yl]methyl}-3H-purin-6-amine
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C10 H13 N5 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 219.243
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code W8D
_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 5RVF
_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
W8D C10 C1 C 0 1 N N R N N N -44.521 -28.102 1.663 -2.137 -0.491 -0.109 C10 W8D 1
W8D C13 C2 C 0 1 N N N N N N -43.695 -26.746 0.010 -4.506 0.079 -0.045 C13 W8D 2
W8D C15 C3 C 0 1 Y N N N N N -47.287 -29.101 3.183 0.332 1.407 0.757 C15 W8D 3
W8D C02 C4 C 0 1 Y N N N N N -47.680 -28.984 5.403 2.491 1.194 -0.045 C02 W8D 4
W8D C03 C5 C 0 1 Y N N N N N -46.259 -29.124 5.612 2.329 -0.198 -0.144 C03 W8D 5
W8D C05 C6 C 0 1 Y N N N N N -44.262 -29.362 6.325 2.409 -2.334 -0.412 C05 W8D 6
W8D C07 C7 C 0 1 Y N N N N N -45.489 -29.282 4.583 1.090 -0.759 0.240 C07 W8D 7
W8D C09 C8 C 0 1 N N N N N N -45.110 -29.422 2.091 -1.198 -0.455 1.098 C09 W8D 8
W8D C12 C9 C 0 1 N N N N N N -45.188 -26.395 0.177 -3.705 0.898 -1.095 C12 W8D 9
W8D C14 C10 C 0 1 N N N N N N -43.584 -28.097 0.655 -3.509 -1.052 0.311 C14 W8D 10
W8D N01 N1 N 0 1 N N N N N N -48.546 -28.818 6.531 3.676 1.783 -0.406 N01 W8D 11
W8D N04 N2 N 0 1 Y N N N N N -45.494 -29.149 6.759 3.103 -1.223 -0.538 N04 W8D 12
W8D N06 N3 N 0 1 Y N N N N N -44.229 -29.418 5.011 1.195 -2.066 0.055 N06 W8D 13
W8D N08 N4 N 0 1 Y N N N N N -45.987 -29.265 3.323 0.101 0.086 0.691 N08 W8D 14
W8D N16 N5 N 0 1 Y N N N N N -48.140 -28.967 4.218 1.475 1.937 0.405 N16 W8D 15
W8D O11 O1 O 0 1 N N N N N N -45.691 -27.287 1.016 -2.349 0.842 -0.604 O11 W8D 16
W8D H101 H1 H 0 0 N N N N N N -44.160 -27.558 2.548 -1.707 -1.113 -0.895 H101 W8D 17
W8D H132 H2 H 0 0 N N N N N N -43.418 -26.793 -1.053 -4.733 0.686 0.831 H132 W8D 18
W8D H131 H3 H 0 0 N N N N N N -43.058 -26.011 0.523 -5.418 -0.328 -0.482 H131 W8D 19
W8D H151 H4 H 0 0 N N N N N N -47.692 -29.072 2.182 -0.456 2.056 1.109 H151 W8D 20
W8D H051 H5 H 0 0 N N N N N N -43.399 -29.475 6.964 2.774 -3.321 -0.655 H051 W8D 21
W8D H092 H6 H 0 0 N N N N N N -45.718 -29.826 1.268 -1.628 0.178 1.874 H092 W8D 22
W8D H091 H7 H 0 0 N N N N N N -44.292 -30.121 2.321 -1.066 -1.465 1.486 H091 W8D 23
W8D H121 H8 H 0 0 N N N N N N -45.296 -25.381 0.590 -3.775 0.434 -2.079 H121 W8D 24
W8D H122 H9 H 0 0 N N N N N N -45.703 -26.453 -0.793 -4.060 1.928 -1.130 H122 W8D 25
W8D H141 H10 H 0 0 N N N N N N -43.801 -28.891 -0.075 -3.741 -1.956 -0.253 H141 W8D 26
W8D H142 H11 H 0 0 N N N N N N -42.575 -28.244 1.068 -3.527 -1.253 1.382 H142 W8D 27
W8D H011 H12 H 0 0 N N N N N N -49.487 -28.699 6.215 4.409 1.238 -0.732 H011 W8D 28
W8D H012 H13 H 0 0 N N N N N N -48.491 -29.627 7.116 3.781 2.745 -0.336 H012 W8D 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
W8D C13 C12 SING N N 1
W8D C13 C14 SING N N 2
W8D C12 O11 SING N N 3
W8D C14 C10 SING N N 4
W8D O11 C10 SING N N 5
W8D C10 C09 SING N N 6
W8D C09 N08 SING N N 7
W8D C15 N08 SING Y N 8
W8D C15 N16 DOUB Y N 9
W8D N08 C07 SING Y N 10
W8D N16 C02 SING Y N 11
W8D C07 N06 DOUB Y N 12
W8D C07 C03 SING Y N 13
W8D N06 C05 SING Y N 14
W8D C02 C03 DOUB Y N 15
W8D C02 N01 SING N N 16
W8D C03 N04 SING Y N 17
W8D C05 N04 DOUB Y N 18
W8D C10 H101 SING N N 19
W8D C13 H132 SING N N 20
W8D C13 H131 SING N N 21
W8D C15 H151 SING N N 22
W8D C05 H051 SING N N 23
W8D C09 H092 SING N N 24
W8D C09 H091 SING N N 25
W8D C12 H121 SING N N 26
W8D C12 H122 SING N N 27
W8D C14 H141 SING N N 28
W8D C14 H142 SING N N 29
W8D N01 H011 SING N N 30
W8D N01 H012 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
W8D SMILES ACDLabs 12.01 C3(CN2C=NC(=C1N=CN=C12)N)CCCO3
W8D InChI InChI 1.03 InChI=1S/C10H13N5O/c11-9-8-10(13-5-12-8)15(6-14-9)4-7-2-1-3-16-7/h5-7H,1-4,11H2/t7-/m1/s1
W8D InChIKey InChI 1.03 GVRQWFFFCDLKPP-SSDOTTSWSA-N
W8D SMILES_CANONICAL CACTVS 3.385 Nc1ncn(C[C@H]2CCCO2)c3ncnc13
W8D SMILES CACTVS 3.385 Nc1ncn(C[CH]2CCCO2)c3ncnc13
W8D SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 c1nc-2c(ncn(c2n1)C[C@H]3CCCO3)N
W8D SMILES "OpenEye OEToolkits" 2.0.7 c1nc-2c(ncn(c2n1)CC3CCCO3)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
W8D "SYSTEMATIC NAME" ACDLabs 12.01 3-{[(2R)-oxolan-2-yl]methyl}-3H-purin-6-amine
W8D "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 3-[[(2~{R})-oxolan-2-yl]methyl]purin-6-amine
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
W8D 'Create component' 2020-09-29 RCSB
W8D 'Initial release' 2020-12-16 RCSB
#
loop_
_software.name
_software.version
_software.description
rdkit 2025.03.3 'Core functionality.'
pdbeccdutils 1.0.0 '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
W8D C10 C -0.016 -2.379 1
W8D C13 C 2.358 -2.882 2
W8D C15 C -2.617 0.619 3
W8D C02 C -1.320 2.870 4
W8D C03 C -0.020 2.121 5
W8D C05 C 2.289 1.373 6
W8D C07 C -0.019 0.621 7
W8D C09 C -1.316 -1.630 8
W8D C12 C 1.609 -4.181 9
W8D C14 C 1.353 -1.767 10
W8D N01 N -1.321 4.370 11
W8D N04 N 1.406 2.586 12
W8D N06 N 1.408 0.159 13
W8D N08 N -1.317 -0.130 14
W8D N16 N -2.618 2.119 15
W8D O11 O 0.142 -3.871 16
#
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
W8D C13 C12 SINGLE NONE 1
W8D C13 C14 SINGLE NONE 2
W8D C12 O11 SINGLE NONE 3
W8D C14 C10 SINGLE NONE 4
W8D O11 C10 SINGLE NONE 5
W8D C10 C09 SINGLE BEGINWEDGE 6
W8D C09 N08 SINGLE NONE 7
W8D C15 N08 SINGLE NONE 8
W8D C15 N16 DOUBLE NONE 9
W8D N08 C07 SINGLE NONE 10
W8D N16 C02 SINGLE NONE 11
W8D C07 N06 DOUBLE NONE 12
W8D C07 C03 SINGLE NONE 13
W8D N06 C05 SINGLE NONE 14
W8D C02 C03 DOUBLE NONE 15
W8D C02 N01 SINGLE NONE 16
W8D C03 N04 SINGLE NONE 17
W8D C05 N04 DOUBLE NONE 18
#
_pdbe_chem_comp_substructure.comp_id W8D
_pdbe_chem_comp_substructure.substructure_name MurckoScaffold
_pdbe_chem_comp_substructure.id S1
_pdbe_chem_comp_substructure.substructure_type scaffold
_pdbe_chem_comp_substructure.substructure_smiles 'c1nc2cncn(C[C@H]3CCCO3)c-2n1'
_pdbe_chem_comp_substructure.substructure_inchis
InChI=1S/C10H12N4O/c1-2-8(15-3-1)5-14-7-11-4-9-10(14)13-6-12-9/h4,6-8H,1-3,5H2/t8-/m1/s1
_pdbe_chem_comp_substructure.substructure_inchikeys DDHLNJRWRNYFHG-MRVPVSSYSA-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
W8D C10 S1 1
W8D C13 S1 1
W8D C15 S1 1
W8D C02 S1 1
W8D C03 S1 1
W8D C05 S1 1
W8D C07 S1 1
W8D C09 S1 1
W8D C12 S1 1
W8D C14 S1 1
W8D N04 S1 1
W8D N06 S1 1
W8D N08 S1 1
W8D N16 S1 1
W8D O11 S1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id W8D
_pdbe_chem_comp_rdkit_properties.exactmw 219.112
_pdbe_chem_comp_rdkit_properties.amw 219.248
_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 1
_pdbe_chem_comp_rdkit_properties.NumHBA 6
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 16
_pdbe_chem_comp_rdkit_properties.NumAtoms 29
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 6
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.500
_pdbe_chem_comp_rdkit_properties.NumRings 3
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 0
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 3
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 1
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 3
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 3
_pdbe_chem_comp_rdkit_properties.NumSpiroAtoms 0
_pdbe_chem_comp_rdkit_properties.NumBridgeheadAtoms 0
_pdbe_chem_comp_rdkit_properties.NumAtomStereoCenters 1
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 111.199
_pdbe_chem_comp_rdkit_properties.tpsa 78.850
_pdbe_chem_comp_rdkit_properties.CrippenClogP -0.222
_pdbe_chem_comp_rdkit_properties.CrippenMR 55.679
_pdbe_chem_comp_rdkit_properties.chi0v 7.644
_pdbe_chem_comp_rdkit_properties.chi1v 4.144
_pdbe_chem_comp_rdkit_properties.chi2v 1.803
_pdbe_chem_comp_rdkit_properties.chi3v 1.803
_pdbe_chem_comp_rdkit_properties.chi4v 1.143
_pdbe_chem_comp_rdkit_properties.chi0n 20.644
_pdbe_chem_comp_rdkit_properties.chi1n 10.539
_pdbe_chem_comp_rdkit_properties.chi2n 1.803
_pdbe_chem_comp_rdkit_properties.chi3n 1.803
_pdbe_chem_comp_rdkit_properties.chi4n 1.143
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.690
_pdbe_chem_comp_rdkit_properties.kappa1 2.951
_pdbe_chem_comp_rdkit_properties.kappa2 3.712
_pdbe_chem_comp_rdkit_properties.kappa3 1.508
_pdbe_chem_comp_rdkit_properties.Phi 0.685
#
#
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
W8D C10 -1.683 0.243 0.666 ETKDGv3 1
W8D C13 -3.494 -0.432 -0.700 ETKDGv3 2
W8D C15 1.288 1.400 1.451 ETKDGv3 3
W8D C02 3.314 0.208 0.849 ETKDGv3 4
W8D C03 2.753 -0.230 -0.276 ETKDGv3 5
W8D C05 2.257 -1.168 -2.113 ETKDGv3 6
W8D C07 1.427 0.113 -0.612 ETKDGv3 7
W8D C09 -0.765 1.255 -0.039 ETKDGv3 8
W8D C12 -2.504 -1.556 -0.478 ETKDGv3 9
W8D C14 -3.154 0.534 0.391 ETKDGv3 10
W8D N01 4.652 -0.143 1.203 ETKDGv3 11
W8D N04 3.265 -1.074 -1.289 ETKDGv3 12
W8D N06 1.076 -0.437 -1.722 ETKDGv3 13
W8D N08 0.640 0.952 0.236 ETKDGv3 14
W8D N16 2.524 1.051 1.722 ETKDGv3 15
W8D O11 -1.382 -1.063 0.219 ETKDGv3 16
W8D H101 -1.499 0.300 1.761 ETKDGv3 17
W8D H132 -4.545 -0.785 -0.628 ETKDGv3 18
W8D H131 -3.318 0.039 -1.693 ETKDGv3 19
W8D H151 0.750 2.027 2.151 ETKDGv3 20
W8D H051 2.307 -1.755 -3.020 ETKDGv3 21
W8D H092 -0.997 2.282 0.320 ETKDGv3 22
W8D H091 -0.950 1.239 -1.135 ETKDGv3 23
W8D H121 -2.181 -1.985 -1.450 ETKDGv3 24
W8D H122 -2.976 -2.361 0.126 ETKDGv3 25
W8D H141 -3.758 0.301 1.296 ETKDGv3 26
W8D H142 -3.349 1.585 0.084 ETKDGv3 27
W8D H011 5.234 -0.752 0.586 ETKDGv3 28
W8D H012 5.066 0.212 2.094 ETKDGv3 29
#