data_J0C
#
_chem_comp.id J0C
_chem_comp.name
2-azanyl-5-[[2-(3-but-3-ynyl-1,2-diazirin-3-yl)ethylamino]methyl]-1,7-dihydropyrrolo[2,3-d]pyrimidin-4-one
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C14 H17 N7 O"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2021-03-09
_chem_comp.pdbx_modified_date 2021-11-12
_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 299.331
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code J0C
_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 7E9E
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site PDBJ
#
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
J0C C10 C1 C 0 1 N N N N N N -1.385 -16.186 -2.918 -0.751 -1.482 -0.755 C10 J0C 1
J0C C13 C2 C 0 1 N N N N N N 1.788 -14.238 -3.396 2.546 -0.138 0.480 C13 J0C 2
J0C C17 C3 C 0 1 N N N N N N 2.019 -14.522 -6.060 5.055 0.501 0.689 C17 J0C 3
J0C C20 C4 C 0 1 N N N N N N 4.243 -16.893 -4.478 8.299 1.536 1.358 C20 J0C 4
J0C C21 C5 C 0 1 Y N N N N N -3.818 -16.029 -2.013 -2.723 -2.426 0.557 C21 J0C 5
J0C C2 C6 C 0 1 N N N N N N -3.038 -14.458 -5.353 -3.016 1.052 -0.666 C2 J0C 6
J0C C4 C7 C 0 1 N N N N N N -5.376 -13.645 -5.746 -5.136 1.412 0.195 C4 J0C 7
J0C C7 C8 C 0 1 Y N N N N N -4.830 -14.915 -3.639 -4.173 -0.724 0.575 C7 J0C 8
J0C C8 C9 C 0 1 Y N N N N N -3.502 -15.056 -4.021 -3.043 -0.307 -0.123 C8 J0C 9
J0C C9 C10 C 0 1 Y N N N N N -2.864 -15.755 -2.989 -2.117 -1.436 -0.121 C9 J0C 10
J0C C12 C11 C 0 1 N N N N N N 0.910 -15.507 -3.237 1.566 -0.840 -0.462 C12 J0C 11
J0C C14 C12 C 0 1 N N N N N N 1.747 -13.633 -4.821 3.948 -0.164 -0.131 C14 J0C 12
J0C C18 C13 C 0 1 N N N N N N 3.517 -14.885 -6.184 6.384 0.386 -0.060 C18 J0C 13
J0C C19 C14 C 0 1 N N N N N N 3.928 -16.017 -5.226 7.450 1.026 0.729 C19 J0C 14
J0C N3 N1 N 0 1 N N N N N N -4.000 -13.778 -6.158 -4.085 1.842 -0.469 N3 J0C 15
J0C N5 N2 N 0 1 N N N N N N -6.350 -12.950 -6.565 -6.198 2.261 0.363 N5 J0C 16
J0C N6 N3 N 0 1 N N N N N N -5.812 -14.208 -4.485 -5.214 0.162 0.720 N6 J0C 17
J0C N11 N4 N 0 1 N N N N N N -0.500 -15.169 -3.505 0.219 -0.814 0.124 N11 J0C 18
J0C N15 N5 N 0 1 N N N N N N 0.855 -12.520 -5.006 4.304 -1.272 -1.021 N15 J0C 19
J0C N16 N6 N 0 1 N N N N N N 2.275 -12.298 -4.922 4.077 -0.192 -1.590 N16 J0C 20
J0C N22 N7 N 0 1 Y N N N N N -4.997 -15.506 -2.414 -3.959 -2.003 0.973 N22 J0C 21
J0C O1 O1 O 0 1 N N N N N N -1.915 -14.544 -5.741 -2.045 1.458 -1.285 O1 J0C 22
J0C H1 H1 H 0 1 N N N N N N -1.261 -17.130 -3.469 -0.453 -2.520 -0.902 H1 J0C 23
J0C H2 H2 H 0 1 N N N N N N -1.107 -16.337 -1.865 -0.779 -0.971 -1.717 H2 J0C 24
J0C H3 H3 H 0 1 N N N N N N 2.829 -14.503 -3.160 2.232 0.896 0.625 H3 J0C 25
J0C H4 H4 H 0 1 N N N N N N 1.433 -13.478 -2.685 2.558 -0.652 1.441 H4 J0C 26
J0C H5 H5 H 0 1 N N N N N N 1.708 -13.979 -6.964 4.813 1.553 0.840 H5 J0C 27
J0C H6 H6 H 0 1 N N N N N N 1.434 -15.449 -5.969 5.139 0.005 1.656 H6 J0C 28
J0C H7 H7 H 0 1 N N N N N N 4.523 -17.671 -3.814 9.059 1.993 1.921 H7 J0C 29
J0C H8 H8 H 0 1 N N N N N N -3.645 -16.567 -1.093 -2.304 -3.404 0.741 H8 J0C 30
J0C H9 H9 H 0 1 N N N N N N 1.006 -15.892 -2.211 1.553 -0.325 -1.423 H9 J0C 31
J0C H10 H10 H 0 1 N N N N N N 1.244 -16.275 -3.950 1.879 -1.874 -0.608 H10 J0C 32
J0C H11 H11 H 0 1 N N N N N N 3.718 -15.206 -7.217 6.626 -0.666 -0.212 H11 J0C 33
J0C H12 H12 H 0 1 N N N N N N 4.117 -13.992 -5.954 6.300 0.882 -1.027 H12 J0C 34
J0C H13 H13 H 0 1 N N N N N N -6.074 -12.549 -7.438 -6.984 1.964 0.848 H13 J0C 35
J0C H14 H14 H 0 1 N N N N N N -7.298 -12.872 -6.256 -6.163 3.158 -0.003 H14 J0C 36
J0C H15 H15 H 0 1 N N N N N N -6.764 -14.119 -4.192 -6.012 -0.109 1.200 H15 J0C 37
J0C H16 H16 H 0 1 N N N N N N -0.708 -14.278 -3.103 0.218 -1.228 1.045 H16 J0C 38
J0C H20 H20 H 0 1 N N N N N N -5.854 -15.544 -1.900 -4.588 -2.539 1.480 H20 J0C 39
#
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
J0C N5 C4 SING N N 1
J0C C18 C17 SING N N 2
J0C C18 C19 SING N N 3
J0C N3 C4 DOUB N N 4
J0C N3 C2 SING N N 5
J0C C17 C14 SING N N 6
J0C C4 N6 SING N N 7
J0C O1 C2 DOUB N N 8
J0C C2 C8 SING N N 9
J0C C19 C20 TRIP N N 10
J0C N15 N16 DOUB N N 11
J0C N15 C14 SING N N 12
J0C N16 C14 SING N N 13
J0C C14 C13 SING N N 14
J0C N6 C7 SING N N 15
J0C C8 C7 DOUB Y N 16
J0C C8 C9 SING Y N 17
J0C C7 N22 SING Y N 18
J0C N11 C12 SING N N 19
J0C N11 C10 SING N N 20
J0C C13 C12 SING N N 21
J0C C9 C10 SING N N 22
J0C C9 C21 DOUB Y N 23
J0C N22 C21 SING Y N 24
J0C C10 H1 SING N N 25
J0C C10 H2 SING N N 26
J0C C13 H3 SING N N 27
J0C C13 H4 SING N N 28
J0C C17 H5 SING N N 29
J0C C17 H6 SING N N 30
J0C C20 H7 SING N N 31
J0C C21 H8 SING N N 32
J0C C12 H9 SING N N 33
J0C C12 H10 SING N N 34
J0C C18 H11 SING N N 35
J0C C18 H12 SING N N 36
J0C N5 H13 SING N N 37
J0C N5 H14 SING N N 38
J0C N6 H15 SING N N 39
J0C N11 H16 SING N N 40
J0C N22 H20 SING N N 41
#
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
J0C InChI InChI 1.03 InChI=1S/C14H17N7O/c1-2-3-4-14(20-21-14)5-6-16-7-9-8-17-11-10(9)12(22)19-13(15)18-11/h1,8,16H,3-7H2,(H4,15,17,18,19,22)
J0C InChIKey InChI 1.03 XAJHFEIBEFHTRZ-UHFFFAOYSA-N
J0C SMILES_CANONICAL CACTVS 3.385 "NC1=NC(=O)c2c(CNCCC3(CCC#C)N=N3)c[nH]c2N1"
J0C SMILES CACTVS 3.385 "NC1=NC(=O)c2c(CNCCC3(CCC#C)N=N3)c[nH]c2N1"
J0C SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C#CCCC1(N=N1)CCNCc2c[nH]c3c2C(=O)N=C(N3)N"
J0C SMILES "OpenEye OEToolkits" 2.0.7 "C#CCCC1(N=N1)CCNCc2c[nH]c3c2C(=O)N=C(N3)N"
#
_pdbx_chem_comp_identifier.comp_id J0C
_pdbx_chem_comp_identifier.type "SYSTEMATIC NAME"
_pdbx_chem_comp_identifier.program "OpenEye OEToolkits"
_pdbx_chem_comp_identifier.program_version 2.0.7
_pdbx_chem_comp_identifier.identifier
2-azanyl-5-[[2-(3-but-3-ynyl-1,2-diazirin-3-yl)ethylamino]methyl]-1,7-dihydropyrrolo[2,3-d]pyrimidin-4-one
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
J0C 'Create component' 2021-03-09 PDBJ
J0C 'Initial release' 2021-11-17 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
J0C C10 C 9.588 0.062 1
J0C C13 C 12.989 2.107 2
J0C C17 C 14.923 3.842 3
J0C C20 C 18.860 3.344 4
J0C C21 C 9.997 -2.570 5
J0C C2 C 6.404 -1.070 6
J0C C4 C 5.104 -3.320 7
J0C C7 C 7.702 -3.320 8
J0C C8 C 7.702 -1.820 9
J0C C9 C 9.122 -1.363 10
J0C C12 C 11.522 1.798 11
J0C C14 C 13.455 3.533 12
J0C C18 C 15.925 2.725 13
J0C C19 C 17.393 3.035 14
J0C N3 N 5.104 -1.820 15
J0C N5 N 3.805 -4.070 16
J0C N6 N 6.404 -4.070 17
J0C N11 N 11.056 0.372 18
J0C N15 N 13.146 5.000 19
J0C N16 N 12.030 3.999 20
J0C N22 N 9.122 -3.778 21
J0C O1 O 6.404 0.430 22
#
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
J0C N5 C4 SINGLE NONE 1
J0C C18 C17 SINGLE NONE 2
J0C C18 C19 SINGLE NONE 3
J0C N3 C4 DOUBLE NONE 4
J0C N3 C2 SINGLE NONE 5
J0C C17 C14 SINGLE NONE 6
J0C C4 N6 SINGLE NONE 7
J0C O1 C2 DOUBLE NONE 8
J0C C2 C8 SINGLE NONE 9
J0C C19 C20 TRIPLE NONE 10
J0C N15 N16 DOUBLE NONE 11
J0C N15 C14 SINGLE NONE 12
J0C N16 C14 SINGLE NONE 13
J0C C14 C13 SINGLE NONE 14
J0C N6 C7 SINGLE NONE 15
J0C C8 C7 DOUBLE NONE 16
J0C C8 C9 SINGLE NONE 17
J0C C7 N22 SINGLE NONE 18
J0C N11 C12 SINGLE NONE 19
J0C N11 C10 SINGLE NONE 20
J0C C13 C12 SINGLE NONE 21
J0C C9 C10 SINGLE NONE 22
J0C C9 C21 DOUBLE NONE 23
J0C N22 C21 SINGLE NONE 24
#
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
J0C MurckoScaffold S1 scaffold 'O=c1nc[nH]c2[nH]cc(CNCCC3N=N3)c12' InChI=1S/C10H12N6O/c17-10-8-6(3-11-2-1-7-15-16-7)4-12-9(8)13-5-14-10/h4-5,7,11H,1-3H2,(H2,12,13,14,17) FJLJPUFJRLVDSX-UHFFFAOYSA-N
J0C pyrimidine F1 fragment c1cncnc1 InChI=1S/C4H4N2/c1-2-5-4-6-3-1/h1-4H CZPWVGJYEJSRLH-UHFFFAOYSA-N
J0C 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
J0C C10 S1 1
J0C C13 S1 1
J0C C21 S1 1
J0C C2 S1 1
J0C C4 S1 1
J0C C7 S1 1
J0C C8 S1 1
J0C C9 S1 1
J0C C12 S1 1
J0C C14 S1 1
J0C N3 S1 1
J0C N6 S1 1
J0C N11 S1 1
J0C N15 S1 1
J0C N16 S1 1
J0C N22 S1 1
J0C O1 S1 1
J0C C8 F1 1
J0C C2 F1 1
J0C N3 F1 1
J0C C4 F1 1
J0C N6 F1 1
J0C C7 F1 1
J0C C21 F2 1
J0C C9 F2 1
J0C C8 F2 1
J0C C7 F2 1
J0C N22 F2 1
#
_pdbe_chem_comp_rdkit_properties.comp_id J0C
_pdbe_chem_comp_rdkit_properties.exactmw 299.149
_pdbe_chem_comp_rdkit_properties.amw 299.338
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 8
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 5
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 8
_pdbe_chem_comp_rdkit_properties.NumHBD 4
_pdbe_chem_comp_rdkit_properties.NumHBA 6
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 22
_pdbe_chem_comp_rdkit_properties.NumAtoms 39
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 8
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.429
_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 3
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 2
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 0
_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 150.347
_pdbe_chem_comp_rdkit_properties.tpsa 124.310
_pdbe_chem_comp_rdkit_properties.CrippenClogP 0.925
_pdbe_chem_comp_rdkit_properties.CrippenMR 79.916
_pdbe_chem_comp_rdkit_properties.chi0v 10.539
_pdbe_chem_comp_rdkit_properties.chi1v 5.614
_pdbe_chem_comp_rdkit_properties.chi2v 2.422
_pdbe_chem_comp_rdkit_properties.chi3v 2.422
_pdbe_chem_comp_rdkit_properties.chi4v 1.453
_pdbe_chem_comp_rdkit_properties.chi0n 27.539
_pdbe_chem_comp_rdkit_properties.chi1n 13.850
_pdbe_chem_comp_rdkit_properties.chi2n 2.422
_pdbe_chem_comp_rdkit_properties.chi3n 2.422
_pdbe_chem_comp_rdkit_properties.chi4n 1.453
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -2.660
_pdbe_chem_comp_rdkit_properties.kappa1 4.425
_pdbe_chem_comp_rdkit_properties.kappa2 5.614
_pdbe_chem_comp_rdkit_properties.kappa3 2.845
_pdbe_chem_comp_rdkit_properties.Phi 1.129
#
_pdbe_chem_comp_external_mappings.comp_id J0C
_pdbe_chem_comp_external_mappings.source UniChem
_pdbe_chem_comp_external_mappings.resource PDBe
_pdbe_chem_comp_external_mappings.resource_id J0C
#
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
J0C C10 -1.504 0.229 -1.200 ETKDGv3 1
J0C C13 2.147 -0.524 -1.718 ETKDGv3 2
J0C C17 3.709 1.666 -2.011 ETKDGv3 3
J0C C20 4.902 4.220 0.086 ETKDGv3 4
J0C C21 -3.546 -1.238 -0.953 ETKDGv3 5
J0C C2 -1.774 -0.220 2.117 ETKDGv3 6
J0C C4 -3.135 -1.421 3.687 ETKDGv3 7
J0C C7 -3.637 -1.476 1.269 ETKDGv3 8
J0C C8 -2.619 -0.691 1.017 ETKDGv3 9
J0C C9 -2.551 -0.515 -0.431 ETKDGv3 10
J0C C12 0.821 0.236 -1.829 ETKDGv3 11
J0C C14 3.295 0.237 -2.405 ETKDGv3 12
J0C C18 4.089 1.750 -0.530 ETKDGv3 13
J0C C19 4.536 3.106 -0.192 ETKDGv3 14
J0C N3 -2.113 -0.638 3.452 ETKDGv3 15
J0C N5 -3.433 -1.811 5.027 ETKDGv3 16
J0C N6 -3.959 -1.894 2.599 ETKDGv3 17
J0C N11 -0.252 -0.535 -1.191 ETKDGv3 18
J0C N15 3.414 -0.018 -3.683 ETKDGv3 19
J0C N16 4.293 -0.527 -2.770 ETKDGv3 20
J0C N22 -4.299 -1.877 0.080 ETKDGv3 21
J0C O1 -0.780 0.523 1.911 ETKDGv3 22
J0C H1 -1.357 1.218 -0.715 ETKDGv3 23
J0C H2 -1.848 0.399 -2.246 ETKDGv3 24
J0C H3 2.023 -1.536 -2.167 ETKDGv3 25
J0C H4 2.397 -0.669 -0.645 ETKDGv3 26
J0C H5 4.573 2.006 -2.629 ETKDGv3 27
J0C H6 2.863 2.356 -2.218 ETKDGv3 28
J0C H7 5.224 5.198 0.331 ETKDGv3 29
J0C H8 -3.748 -1.352 -2.010 ETKDGv3 30
J0C H9 0.929 1.219 -1.318 ETKDGv3 31
J0C H10 0.582 0.412 -2.903 ETKDGv3 32
J0C H11 3.213 1.501 0.105 ETKDGv3 33
J0C H12 4.911 1.037 -0.307 ETKDGv3 34
J0C H13 -4.245 -2.436 5.227 ETKDGv3 35
J0C H14 -2.843 -1.476 5.820 ETKDGv3 36
J0C H15 -4.770 -2.528 2.773 ETKDGv3 37
J0C H16 -0.405 -1.404 -1.757 ETKDGv3 38
J0C H20 -5.107 -2.529 -0.021 ETKDGv3 39
#