data_2N6
#
_chem_comp.id 2N6
_chem_comp.name 4-(2,4-dimethylphenyl)-2-(methylsulfanyl)-7H-pyrrolo[2,3-d]pyrimidine-5-carbonitrile
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C16 H14 N4 S"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2012-06-06
_chem_comp.pdbx_modified_date 2012-10-19
_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 294.374
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code 2N6
_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 4FCQ
_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
2N6 C19 C19 C 0 1 N N N N N N 32.804 13.470 24.361 -0.896 2.133 1.718 C19 2N6 1
2N6 C17 C17 C 0 1 Y N N N N N 33.556 12.120 24.183 -1.796 1.461 0.714 C17 2N6 2
2N6 C16 C16 C 0 1 Y N N N N N 34.905 12.222 23.869 -3.136 1.787 0.659 C16 2N6 3
2N6 C15 C15 C 0 1 Y N N N N N 35.692 11.088 23.676 -3.963 1.175 -0.266 C15 2N6 4
2N6 C18 C18 C 0 1 N N N N N N 37.184 11.222 23.285 -5.425 1.536 -0.320 C18 2N6 5
2N6 C14 C14 C 0 1 Y N N N N N 35.126 9.834 23.815 -3.453 0.232 -1.141 C14 2N6 6
2N6 C13 C13 C 0 1 Y N N N N N 33.809 9.708 24.166 -2.114 -0.102 -1.095 C13 2N6 7
2N6 C5 C5 C 0 1 Y N N N N N 32.998 10.835 24.319 -1.276 0.511 -0.165 C5 2N6 8
2N6 C4 C4 C 0 1 Y N N N N N 31.689 10.605 24.747 0.162 0.160 -0.115 C4 2N6 9
2N6 C8 C8 C 0 1 Y N N N N N 30.521 10.943 24.076 0.571 -1.172 0.038 C8 2N6 10
2N6 N1 N1 N 0 1 Y N N N N N 31.550 10.050 25.975 1.098 1.102 -0.220 N1 2N6 11
2N6 C2 C2 C 0 1 Y N N N N N 30.325 9.816 26.552 2.386 0.790 -0.176 C2 2N6 12
2N6 S6 S6 S 0 1 N N N N N N 30.177 9.014 28.120 3.576 2.082 -0.319 S6 2N6 13
2N6 C7 C7 C 0 1 N N N N N N 31.304 7.596 27.984 5.103 1.117 -0.197 C7 2N6 14
2N6 N3 N3 N 0 1 Y N N N N N 29.209 10.146 25.914 2.812 -0.454 -0.027 N3 2N6 15
2N6 C9 C9 C 0 1 Y N N N N N 29.295 10.675 24.681 1.948 -1.460 0.080 C9 2N6 16
2N6 N10 N10 N 0 1 Y N N N N N 28.360 11.071 23.855 2.079 -2.816 0.234 N10 2N6 17
2N6 C11 C11 C 0 1 Y N N N N N 28.914 11.582 22.750 0.856 -3.409 0.292 C11 2N6 18
2N6 C12 C12 C 0 1 Y N N N N N 30.234 11.533 22.849 -0.119 -2.463 0.178 C12 2N6 19
2N6 C20 C20 C 0 1 N N N N N N 31.231 11.969 21.906 -1.534 -2.682 0.193 C20 2N6 20
2N6 N21 N21 N 0 1 N N N N N N 32.050 12.270 21.185 -2.657 -2.856 0.205 N21 2N6 21
2N6 H1 H1 H 0 1 N N N N N N 32.389 13.789 23.394 -0.400 2.984 1.249 H1 2N6 22
2N6 H2 H2 H 0 1 N N N N N N 31.987 13.342 25.086 -1.490 2.480 2.564 H2 2N6 23
2N6 H3 H3 H 0 1 N N N N N N 33.505 14.234 24.729 -0.146 1.423 2.067 H3 2N6 24
2N6 H4 H4 H 0 1 N N N N N N 35.353 13.200 23.772 -3.539 2.523 1.339 H4 2N6 25
2N6 H5 H5 H 0 1 N N N N N N 37.275 11.252 22.189 -5.986 0.880 0.345 H5 2N6 26
2N6 H6 H6 H 0 1 N N N N N N 37.593 12.149 23.713 -5.555 2.571 -0.005 H6 2N6 27
2N6 H7 H7 H 0 1 N N N N N N 37.744 10.360 23.676 -5.790 1.417 -1.340 H7 2N6 28
2N6 H8 H8 H 0 1 N N N N N N 35.725 8.951 23.646 -4.103 -0.243 -1.860 H8 2N6 29
2N6 H9 H9 H 0 1 N N N N N N 33.392 8.725 24.327 -1.717 -0.838 -1.779 H9 2N6 30
2N6 H10 H10 H 0 1 N N N N N N 31.286 7.022 28.922 5.128 0.596 0.760 H10 2N6 31
2N6 H11 H11 H 0 1 N N N N N N 30.983 6.951 27.153 5.139 0.389 -1.008 H11 2N6 32
2N6 H12 H12 H 0 1 N N N N N N 32.326 7.957 27.794 5.961 1.785 -0.270 H12 2N6 33
2N6 H13 H13 H 0 1 N N N N N N 27.377 11.002 24.025 2.925 -3.286 0.293 H13 2N6 34
2N6 H14 H14 H 0 1 N N N N N N 28.368 11.975 21.905 0.683 -4.469 0.409 H14 2N6 35
#
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
2N6 N21 C20 TRIP N N 1
2N6 C20 C12 SING N N 2
2N6 C11 C12 DOUB Y N 3
2N6 C11 N10 SING Y N 4
2N6 C12 C8 SING Y N 5
2N6 C18 C15 SING N N 6
2N6 C15 C14 DOUB Y N 7
2N6 C15 C16 SING Y N 8
2N6 C14 C13 SING Y N 9
2N6 N10 C9 SING Y N 10
2N6 C16 C17 DOUB Y N 11
2N6 C8 C9 DOUB Y N 12
2N6 C8 C4 SING Y N 13
2N6 C13 C5 DOUB Y N 14
2N6 C17 C5 SING Y N 15
2N6 C17 C19 SING N N 16
2N6 C5 C4 SING N N 17
2N6 C9 N3 SING Y N 18
2N6 C4 N1 DOUB Y N 19
2N6 N3 C2 DOUB Y N 20
2N6 N1 C2 SING Y N 21
2N6 C2 S6 SING N N 22
2N6 C7 S6 SING N N 23
2N6 C19 H1 SING N N 24
2N6 C19 H2 SING N N 25
2N6 C19 H3 SING N N 26
2N6 C16 H4 SING N N 27
2N6 C18 H5 SING N N 28
2N6 C18 H6 SING N N 29
2N6 C18 H7 SING N N 30
2N6 C14 H8 SING N N 31
2N6 C13 H9 SING N N 32
2N6 C7 H10 SING N N 33
2N6 C7 H11 SING N N 34
2N6 C7 H12 SING N N 35
2N6 N10 H13 SING N N 36
2N6 C11 H14 SING N N 37
#
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
2N6 SMILES ACDLabs 12.01 "N#Cc2c1c(nc(nc1nc2)SC)c3ccc(cc3C)C"
2N6 InChI InChI 1.03 InChI=1S/C16H14N4S/c1-9-4-5-12(10(2)6-9)14-13-11(7-17)8-18-15(13)20-16(19-14)21-3/h4-6,8H,1-3H3,(H,18,19,20)
2N6 InChIKey InChI 1.03 LXUVFEGNZXPXCA-UHFFFAOYSA-N
2N6 SMILES_CANONICAL CACTVS 3.370 "CSc1nc2[nH]cc(C#N)c2c(n1)c3ccc(C)cc3C"
2N6 SMILES CACTVS 3.370 "CSc1nc2[nH]cc(C#N)c2c(n1)c3ccc(C)cc3C"
2N6 SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "Cc1ccc(c(c1)C)c2c3c(c[nH]c3nc(n2)SC)C#N"
2N6 SMILES "OpenEye OEToolkits" 1.7.6 "Cc1ccc(c(c1)C)c2c3c(c[nH]c3nc(n2)SC)C#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
2N6 "SYSTEMATIC NAME" ACDLabs 12.01 4-(2,4-dimethylphenyl)-2-(methylsulfanyl)-7H-pyrrolo[2,3-d]pyrimidine-5-carbonitrile
2N6 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 4-(2,4-dimethylphenyl)-2-methylsulfanyl-7H-pyrrolo[2,3-d]pyrimidine-5-carbonitrile
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
2N6 'Create component' 2012-06-06 RCSB
2N6 'Initial release' 2012-10-19 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
2N6 C19 C 3.000 0.750 1
2N6 C17 C 4.299 1.500 2
2N6 C16 C 4.299 3.000 3
2N6 C15 C 5.598 3.750 4
2N6 C18 C 5.598 5.250 5
2N6 C14 C 6.897 3.000 6
2N6 C13 C 6.897 1.500 7
2N6 C5 C 5.598 0.750 8
2N6 C4 C 5.598 -0.750 9
2N6 C8 C 6.897 -1.500 10
2N6 N1 N 4.299 -1.500 11
2N6 C2 C 4.299 -3.000 12
2N6 S6 S 3.000 -3.750 13
2N6 C7 C 3.000 -5.250 14
2N6 N3 N 5.598 -3.750 15
2N6 C9 C 6.897 -3.000 16
2N6 N10 N 8.316 -3.457 17
2N6 C11 C 9.192 -2.250 18
2N6 C12 C 8.316 -1.043 19
2N6 C20 C 8.783 0.383 20
2N6 N21 N 9.248 1.809 21
#
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
2N6 N21 C20 TRIPLE NONE 1
2N6 C20 C12 SINGLE NONE 2
2N6 C11 C12 DOUBLE NONE 3
2N6 C11 N10 SINGLE NONE 4
2N6 C12 C8 SINGLE NONE 5
2N6 C18 C15 SINGLE NONE 6
2N6 C15 C14 DOUBLE NONE 7
2N6 C15 C16 SINGLE NONE 8
2N6 C14 C13 SINGLE NONE 9
2N6 N10 C9 SINGLE NONE 10
2N6 C16 C17 DOUBLE NONE 11
2N6 C8 C9 DOUBLE NONE 12
2N6 C8 C4 SINGLE NONE 13
2N6 C13 C5 DOUBLE NONE 14
2N6 C17 C5 SINGLE NONE 15
2N6 C17 C19 SINGLE NONE 16
2N6 C5 C4 SINGLE NONE 17
2N6 C9 N3 SINGLE NONE 18
2N6 C4 N1 DOUBLE NONE 19
2N6 N3 C2 DOUBLE NONE 20
2N6 N1 C2 SINGLE NONE 21
2N6 C2 S6 SINGLE NONE 22
2N6 C7 S6 SINGLE NONE 23
#
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
2N6 MurckoScaffold S1 scaffold 'c1ccc(-c2ncnc3[nH]ccc23)cc1' InChI=1S/C12H9N3/c1-2-4-9(5-3-1)11-10-6-7-13-12(10)15-8-14-11/h1-8H,(H,13,14,15) XWMVYDXYOLGHBU-UHFFFAOYSA-N
2N6 phenyl F1 fragment c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-UHFFFAOYSA-N
2N6 pyrimidine F2 fragment c1cncnc1 InChI=1S/C4H4N2/c1-2-5-4-6-3-1/h1-4H CZPWVGJYEJSRLH-UHFFFAOYSA-N
2N6 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
2N6 C17 S1 1
2N6 C16 S1 1
2N6 C15 S1 1
2N6 C14 S1 1
2N6 C13 S1 1
2N6 C5 S1 1
2N6 C4 S1 1
2N6 C8 S1 1
2N6 N1 S1 1
2N6 C2 S1 1
2N6 N3 S1 1
2N6 C9 S1 1
2N6 N10 S1 1
2N6 C11 S1 1
2N6 C12 S1 1
2N6 C17 F1 1
2N6 C16 F1 1
2N6 C15 F1 1
2N6 C14 F1 1
2N6 C13 F1 1
2N6 C5 F1 1
2N6 C8 F2 1
2N6 C9 F2 1
2N6 N3 F2 1
2N6 C2 F2 1
2N6 N1 F2 1
2N6 C4 F2 1
2N6 C9 F3 1
2N6 C8 F3 1
2N6 C12 F3 1
2N6 C11 F3 1
2N6 N10 F3 1
#
_pdbe_chem_comp_rdkit_properties.comp_id 2N6
_pdbe_chem_comp_rdkit_properties.exactmw 294.094
_pdbe_chem_comp_rdkit_properties.amw 294.383
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 4
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 1
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 5
_pdbe_chem_comp_rdkit_properties.NumHBD 1
_pdbe_chem_comp_rdkit_properties.NumHBA 4
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 21
_pdbe_chem_comp_rdkit_properties.NumAtoms 35
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 5
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.188
_pdbe_chem_comp_rdkit_properties.NumRings 3
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 3
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 0
_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 0
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 146.522
_pdbe_chem_comp_rdkit_properties.tpsa 65.360
_pdbe_chem_comp_rdkit_properties.CrippenClogP 2.755
_pdbe_chem_comp_rdkit_properties.CrippenMR 81.539
_pdbe_chem_comp_rdkit_properties.chi0v 11.014
_pdbe_chem_comp_rdkit_properties.chi1v 6.290
_pdbe_chem_comp_rdkit_properties.chi2v 3.011
_pdbe_chem_comp_rdkit_properties.chi3v 3.011
_pdbe_chem_comp_rdkit_properties.chi4v 2.065
_pdbe_chem_comp_rdkit_properties.chi0n 24.197
_pdbe_chem_comp_rdkit_properties.chi1n 12.421
_pdbe_chem_comp_rdkit_properties.chi2n 2.645
_pdbe_chem_comp_rdkit_properties.chi3n 2.645
_pdbe_chem_comp_rdkit_properties.chi4n 1.796
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -2.320
_pdbe_chem_comp_rdkit_properties.kappa1 4.855
_pdbe_chem_comp_rdkit_properties.kappa2 5.226
_pdbe_chem_comp_rdkit_properties.kappa3 2.278
_pdbe_chem_comp_rdkit_properties.Phi 1.208
#
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
2N6 UniChem ZINC ZINC000095572554
2N6 UniChem SureChEMBL SCHEMBL2563404
2N6 UniChem 'PubChem TPHARMA' 26697553
2N6 UniChem PubChem 16738716
2N6 UniChem BindingDb 50394079
#
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
2N6 C19 -1.040 -0.581 -2.484 ETKDGv3 1
2N6 C17 -1.593 -0.081 -1.176 ETKDGv3 2
2N6 C16 -2.907 0.189 -1.065 ETKDGv3 3
2N6 C15 -3.475 0.678 0.213 ETKDGv3 4
2N6 C18 -4.952 0.912 0.337 ETKDGv3 5
2N6 C14 -2.670 0.843 1.273 ETKDGv3 6
2N6 C13 -1.224 0.583 1.156 ETKDGv3 7
2N6 C5 -0.698 0.142 0.000 ETKDGv3 8
2N6 C4 0.760 -0.070 -0.099 ETKDGv3 9
2N6 C8 1.496 -0.952 0.829 ETKDGv3 10
2N6 N1 1.447 0.559 -1.015 ETKDGv3 11
2N6 C2 2.881 0.407 -1.129 ETKDGv3 12
2N6 S6 3.768 1.286 -2.410 ETKDGv3 13
2N6 C7 4.039 2.755 -1.370 ETKDGv3 14
2N6 N3 3.531 -0.372 -0.307 ETKDGv3 15
2N6 C9 2.801 -1.065 0.711 ETKDGv3 16
2N6 N10 3.326 -2.055 1.581 ETKDGv3 17
2N6 C11 2.170 -2.567 2.245 ETKDGv3 18
2N6 C12 1.074 -1.938 1.825 ETKDGv3 19
2N6 C20 -0.271 -2.277 2.205 ETKDGv3 20
2N6 N21 -1.353 -2.550 2.510 ETKDGv3 21
2N6 H1 -0.543 0.255 -3.019 ETKDGv3 22
2N6 H2 -1.840 -0.995 -3.135 ETKDGv3 23
2N6 H3 -0.303 -1.391 -2.303 ETKDGv3 24
2N6 H4 -3.568 0.042 -1.912 ETKDGv3 25
2N6 H5 -5.154 1.794 0.982 ETKDGv3 26
2N6 H6 -5.402 1.105 -0.660 ETKDGv3 27
2N6 H7 -5.432 0.016 0.782 ETKDGv3 28
2N6 H8 -3.070 1.175 2.223 ETKDGv3 29
2N6 H9 -0.591 0.766 2.017 ETKDGv3 30
2N6 H10 4.602 3.512 -1.953 ETKDGv3 31
2N6 H11 3.065 3.188 -1.062 ETKDGv3 32
2N6 H12 4.629 2.481 -0.471 ETKDGv3 33
2N6 H13 4.307 -2.407 1.637 ETKDGv3 34
2N6 H14 2.190 -3.387 2.952 ETKDGv3 35
#