data_T28
#
_chem_comp.id T28
_chem_comp.name "11-bromo-5,6,7,8-tetrahydropyrimido[4',5':3,4]cyclohepta[1,2-b]indol-2-amine"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C15 H13 Br N4"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2013-01-11
_chem_comp.pdbx_modified_date 2013-04-12
_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 329.195
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code T28
_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 4IDT
_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
T28 BR1 BR1 BR 0 0 N N N N N N 95.056 51.190 118.523 -4.055 -0.966 0.289 BR1 T28 1
T28 C12 C12 C 0 1 Y N N N N N 96.079 50.164 119.754 -2.658 0.275 -0.000 C12 T28 2
T28 C6 C6 C 0 1 Y N N N N N 96.310 48.803 119.565 -1.348 -0.172 0.013 C6 T28 3
T28 C2 C2 C 0 1 Y N N N N N 97.074 48.100 120.504 -0.352 0.781 -0.207 C2 T28 4
T28 C5 C5 C 0 1 Y N N N N N 97.600 48.742 121.614 -0.677 2.144 -0.435 C5 T28 5
T28 C11 C11 C 0 1 Y N N N N N 97.371 50.099 121.799 -2.003 2.567 -0.442 C11 T28 6
T28 C17 C17 C 0 1 Y N N N N N 96.615 50.804 120.870 -2.974 1.605 -0.226 C17 T28 7
T28 C1 C1 C 0 1 Y N N N N N 97.443 46.755 120.569 1.093 0.712 -0.262 C1 T28 8
T28 C4 C4 C 0 1 Y N N N N N 98.199 46.625 121.728 1.555 1.967 -0.525 C4 T28 9
T28 N9 N9 N 0 1 Y N N N N N 98.282 47.830 122.337 0.497 2.822 -0.622 N9 T28 10
T28 C3 C3 C 0 1 Y N N N N N 97.097 45.724 119.540 2.030 -0.414 -0.077 C3 T28 11
T28 N8 N8 N 0 1 Y N N N N N 96.194 46.118 118.617 1.858 -1.599 -0.641 N8 T28 12
T28 C15 C15 C 0 1 Y N N N N N 95.797 45.325 117.609 2.775 -2.546 -0.482 C15 T28 13
T28 N20 N20 N 0 1 N N N N N N 94.880 45.777 116.726 2.576 -3.781 -1.074 N20 T28 14
T28 N19 N19 N 0 1 Y N N N N N 96.309 44.088 117.484 3.875 -2.341 0.229 N19 T28 15
T28 C13 C13 C 0 1 Y N N N N N 97.212 43.649 118.364 4.095 -1.185 0.842 C13 T28 16
T28 C7 C7 C 0 1 Y N N N N N 97.650 44.449 119.415 3.155 -0.186 0.730 C7 T28 17
T28 C14 C14 C 0 1 N N N N N N 98.674 43.801 120.331 3.240 1.086 1.512 C14 T28 18
T28 C16 C16 C 0 1 N N N N N N 99.573 44.775 121.055 3.723 2.285 0.685 C16 T28 19
T28 C10 C10 C 0 1 N N N N N N 98.845 45.366 122.237 3.014 2.290 -0.672 C10 T28 20
T28 H6 H6 H 0 1 N N N N N N 95.904 48.295 118.703 -1.107 -1.211 0.186 H6 T28 21
T28 H11 H11 H 0 1 N N N N N N 97.779 50.605 122.662 -2.264 3.601 -0.612 H11 T28 22
T28 H17 H17 H 0 1 N N N N N N 96.441 51.860 121.015 -4.013 1.901 -0.229 H17 T28 23
T28 H1 H1 H 0 1 N N N N N N 98.772 48.015 123.189 0.567 3.774 -0.798 H1 T28 24
T28 H201 H201 H 0 0 N N N N N N 94.695 45.068 116.045 1.776 -3.945 -1.597 H201 T28 25
T28 H202 H202 H 0 0 N N N N N N 94.035 46.004 117.210 3.237 -4.483 -0.966 H202 T28 26
T28 H13 H13 H 0 1 N N N N N N 97.611 42.651 118.258 4.996 -1.030 1.418 H13 T28 27
T28 H142 H142 H 0 0 N N N N N N 98.134 43.207 121.083 2.253 1.315 1.914 H142 T28 28
T28 H141 H141 H 0 0 N N N N N N 99.306 43.136 119.724 3.927 0.938 2.346 H141 T28 29
T28 H162 H162 H 0 0 N N N N N N 100.472 44.249 121.407 3.495 3.209 1.217 H162 T28 30
T28 H161 H161 H 0 0 N N N N N N 99.866 45.582 120.367 4.800 2.210 0.532 H161 T28 31
T28 H102 H102 H 0 0 N N N N N N 98.082 44.666 122.607 3.480 1.548 -1.322 H102 T28 32
T28 H101 H101 H 0 0 N N N N N N 99.553 45.598 123.047 3.118 3.276 -1.126 H101 T28 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
T28 N20 C15 SING N N 1
T28 N19 C15 DOUB Y N 2
T28 N19 C13 SING Y N 3
T28 C15 N8 SING Y N 4
T28 C13 C7 DOUB Y N 5
T28 BR1 C12 SING N N 6
T28 N8 C3 DOUB Y N 7
T28 C7 C3 SING Y N 8
T28 C7 C14 SING N N 9
T28 C3 C1 SING N N 10
T28 C6 C12 DOUB Y N 11
T28 C6 C2 SING Y N 12
T28 C12 C17 SING Y N 13
T28 C14 C16 SING N N 14
T28 C2 C1 SING Y N 15
T28 C2 C5 DOUB Y N 16
T28 C1 C4 DOUB Y N 17
T28 C17 C11 DOUB Y N 18
T28 C16 C10 SING N N 19
T28 C5 C11 SING Y N 20
T28 C5 N9 SING Y N 21
T28 C4 C10 SING N N 22
T28 C4 N9 SING Y N 23
T28 C6 H6 SING N N 24
T28 C11 H11 SING N N 25
T28 C17 H17 SING N N 26
T28 N9 H1 SING N N 27
T28 N20 H201 SING N N 28
T28 N20 H202 SING N N 29
T28 C13 H13 SING N N 30
T28 C14 H142 SING N N 31
T28 C14 H141 SING N N 32
T28 C16 H162 SING N N 33
T28 C16 H161 SING N N 34
T28 C10 H102 SING N N 35
T28 C10 H101 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
T28 SMILES ACDLabs 12.01 Brc3cc4c2c1nc(ncc1CCCc2nc4cc3)N
T28 InChI InChI 1.03 InChI=1S/C15H13BrN4/c16-9-4-5-11-10(6-9)13-12(19-11)3-1-2-8-7-18-15(17)20-14(8)13/h4-7,19H,1-3H2,(H2,17,18,20)
T28 InChIKey InChI 1.03 MEOWHQIIZUZBTO-UHFFFAOYSA-N
T28 SMILES_CANONICAL CACTVS 3.370 Nc1ncc2CCCc3[nH]c4ccc(Br)cc4c3c2n1
T28 SMILES CACTVS 3.370 Nc1ncc2CCCc3[nH]c4ccc(Br)cc4c3c2n1
T28 SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 c1cc2c(cc1Br)c-3c([nH]2)CCCc4c3nc(nc4)N
T28 SMILES "OpenEye OEToolkits" 1.7.6 c1cc2c(cc1Br)c-3c([nH]2)CCCc4c3nc(nc4)N
#
_pdbx_chem_comp_identifier.comp_id T28
_pdbx_chem_comp_identifier.type "SYSTEMATIC NAME"
_pdbx_chem_comp_identifier.program ACDLabs
_pdbx_chem_comp_identifier.program_version 12.01
_pdbx_chem_comp_identifier.identifier "11-bromo-5,6,7,8-tetrahydropyrimido[4',5':3,4]cyclohepta[1,2-b]indol-2-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
T28 'Create component' 2013-01-11 RCSB
T28 'Initial release' 2013-04-17 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
T28 BR1 Br 7.685 -4.270 1
T28 C12 C 8.659 -3.129 2
T28 C6 C 8.145 -1.663 3
T28 C2 C 9.166 -0.493 4
T28 C5 C 10.633 -0.758 5
T28 C11 C 11.181 -2.211 6
T28 C17 C 10.187 -3.405 7
T28 C1 C 8.962 0.984 8
T28 C4 C 10.314 1.635 9
T28 N9 N 11.341 0.554 10
T28 C3 C 7.611 1.635 11
T28 N8 N 6.482 0.555 12
T28 C15 C 4.985 1.004 13
T28 N20 N 3.890 -0.021 14
T28 N19 N 4.638 2.527 15
T28 C13 C 5.791 3.581 16
T28 C7 C 7.277 3.097 17
T28 C14 C 8.212 4.270 18
T28 C16 C 9.712 4.270 19
T28 C10 C 10.647 3.097 20
#
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
T28 N20 C15 SINGLE NONE 1
T28 N19 C15 DOUBLE NONE 2
T28 N19 C13 SINGLE NONE 3
T28 C15 N8 SINGLE NONE 4
T28 C13 C7 DOUBLE NONE 5
T28 BR1 C12 SINGLE NONE 6
T28 N8 C3 DOUBLE NONE 7
T28 C7 C3 SINGLE NONE 8
T28 C7 C14 SINGLE NONE 9
T28 C3 C1 SINGLE NONE 10
T28 C6 C12 DOUBLE NONE 11
T28 C6 C2 SINGLE NONE 12
T28 C12 C17 SINGLE NONE 13
T28 C14 C16 SINGLE NONE 14
T28 C2 C1 SINGLE NONE 15
T28 C2 C5 DOUBLE NONE 16
T28 C1 C4 DOUBLE NONE 17
T28 C17 C11 DOUBLE NONE 18
T28 C16 C10 SINGLE NONE 19
T28 C5 C11 SINGLE NONE 20
T28 C5 N9 SINGLE NONE 21
T28 C4 C10 SINGLE NONE 22
T28 C4 N9 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
T28 MurckoScaffold S1 scaffold 'c1ccc2c3c([nH]c2c1)CCCc1cncnc1-3' InChI=1S/C15H13N3/c1-2-6-12-11(5-1)14-13(18-12)7-3-4-10-8-16-9-17-15(10)14/h1-2,5-6,8-9,18H,3-4,7H2 KCWNBCREKOALOR-UHFFFAOYSA-N
T28 indole F1 fragment 'c1ccc2[nH]ccc2c1' InChI=1S/C8H7N/c1-2-4-8-7(3-1)5-6-9-8/h1-6,9H SIKJAQJRHWYJAI-UHFFFAOYSA-N
T28 phenyl F2 fragment c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-UHFFFAOYSA-N
T28 pyrimidine F3 fragment c1cncnc1 InChI=1S/C4H4N2/c1-2-5-4-6-3-1/h1-4H CZPWVGJYEJSRLH-UHFFFAOYSA-N
T28 pyrrole F4 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
T28 C12 S1 1
T28 C6 S1 1
T28 C2 S1 1
T28 C5 S1 1
T28 C11 S1 1
T28 C17 S1 1
T28 C1 S1 1
T28 C4 S1 1
T28 N9 S1 1
T28 C3 S1 1
T28 N8 S1 1
T28 C15 S1 1
T28 N19 S1 1
T28 C13 S1 1
T28 C7 S1 1
T28 C14 S1 1
T28 C16 S1 1
T28 C10 S1 1
T28 C5 F1 1
T28 C2 F1 1
T28 C1 F1 1
T28 C4 F1 1
T28 N9 F1 1
T28 C6 F1 1
T28 C12 F1 1
T28 C17 F1 1
T28 C11 F1 1
T28 C12 F2 1
T28 C6 F2 1
T28 C2 F2 1
T28 C5 F2 1
T28 C11 F2 1
T28 C17 F2 1
T28 C7 F3 1
T28 C13 F3 1
T28 N19 F3 1
T28 C15 F3 1
T28 N8 F3 1
T28 C3 F3 1
T28 C5 F4 1
T28 C2 F4 1
T28 C1 F4 1
T28 C4 F4 1
T28 N9 F4 1
#
_pdbe_chem_comp_rdkit_properties.comp_id T28
_pdbe_chem_comp_rdkit_properties.exactmw 328.032
_pdbe_chem_comp_rdkit_properties.amw 329.201
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 4
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 3
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 1
_pdbe_chem_comp_rdkit_properties.NumHBD 2
_pdbe_chem_comp_rdkit_properties.NumHBA 3
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 20
_pdbe_chem_comp_rdkit_properties.NumAtoms 33
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 5
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.200
_pdbe_chem_comp_rdkit_properties.NumRings 4
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 3
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 1
_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 142.554
_pdbe_chem_comp_rdkit_properties.tpsa 67.590
_pdbe_chem_comp_rdkit_properties.CrippenClogP 2.160
_pdbe_chem_comp_rdkit_properties.CrippenMR 78.578
_pdbe_chem_comp_rdkit_properties.chi0v 11.253
_pdbe_chem_comp_rdkit_properties.chi1v 6.297
_pdbe_chem_comp_rdkit_properties.chi2v 3.191
_pdbe_chem_comp_rdkit_properties.chi3v 3.191
_pdbe_chem_comp_rdkit_properties.chi4v 2.307
_pdbe_chem_comp_rdkit_properties.chi0n 22.667
_pdbe_chem_comp_rdkit_properties.chi1n 11.846
_pdbe_chem_comp_rdkit_properties.chi2n 2.794
_pdbe_chem_comp_rdkit_properties.chi3n 2.794
_pdbe_chem_comp_rdkit_properties.chi4n 2.009
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.880
_pdbe_chem_comp_rdkit_properties.kappa1 4.562
_pdbe_chem_comp_rdkit_properties.kappa2 4.312
_pdbe_chem_comp_rdkit_properties.kappa3 1.733
_pdbe_chem_comp_rdkit_properties.Phi 0.984
#
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
T28 UniChem ChEMBL CHEMBL2334583
T28 UniChem PDBe T28
T28 UniChem ZINC ZINC000095592824
T28 UniChem SureChEMBL SCHEMBL12714288
T28 UniChem 'PubChem TPHARMA' 163561044
T28 UniChem BindingDb 50429616
T28 UniChem PubChem 58221397
#
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
T28 BR1 4.885 2.395 0.662 ETKDGv3 1
T28 C12 3.754 0.857 0.657 ETKDGv3 2
T28 C6 2.442 0.986 0.388 ETKDGv3 3
T28 C2 1.595 -0.229 0.390 ETKDGv3 4
T28 C5 2.126 -1.412 0.624 ETKDGv3 5
T28 C11 3.558 -1.581 0.919 ETKDGv3 6
T28 C17 4.337 -0.486 0.939 ETKDGv3 7
T28 C1 0.164 -0.422 0.085 ETKDGv3 8
T28 C4 -0.050 -1.758 0.163 ETKDGv3 9
T28 N9 1.161 -2.435 0.501 ETKDGv3 10
T28 C3 -0.790 0.691 -0.184 ETKDGv3 11
T28 N8 -0.475 1.879 0.247 ETKDGv3 12
T28 C15 -1.301 3.027 0.008 ETKDGv3 13
T28 N20 -0.905 4.305 0.500 ETKDGv3 14
T28 N19 -2.404 2.900 -0.666 ETKDGv3 15
T28 C13 -2.815 1.622 -1.166 ETKDGv3 16
T28 C7 -2.064 0.528 -0.943 ETKDGv3 17
T28 C14 -2.533 -0.813 -1.420 ETKDGv3 18
T28 C16 -2.600 -1.787 -0.244 ETKDGv3 19
T28 C10 -1.299 -2.566 -0.087 ETKDGv3 20
T28 H6 2.031 1.959 0.160 ETKDGv3 21
T28 H11 3.972 -2.562 1.112 ETKDGv3 22
T28 H17 5.393 -0.581 1.153 ETKDGv3 23
T28 H1 1.310 -3.463 0.605 ETKDGv3 24
T28 H201 -1.497 5.148 0.328 ETKDGv3 25
T28 H202 -0.015 4.408 1.036 ETKDGv3 26
T28 H13 -3.750 1.554 -1.709 ETKDGv3 27
T28 H142 -1.855 -1.182 -2.220 ETKDGv3 28
T28 H141 -3.548 -0.739 -1.870 ETKDGv3 29
T28 H162 -3.412 -2.521 -0.437 ETKDGv3 30
T28 H161 -2.855 -1.267 0.707 ETKDGv3 31
T28 H102 -1.135 -3.183 -0.997 ETKDGv3 32
T28 H101 -1.424 -3.273 0.761 ETKDGv3 33
#