data_J9H
#
_chem_comp.id J9H
_chem_comp.name "pentacoordinate Pt(II) compound"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C17 H18 N3 Pt"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 1
_chem_comp.pdbx_initial_date 2019-02-12
_chem_comp.pdbx_modified_date 2019-02-22
_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 459.423
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code J9H
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag Y
_chem_comp.pdbx_ideal_coordinates_details ?
_chem_comp.pdbx_ideal_coordinates_missing_flag Y
_chem_comp.pdbx_model_coordinates_db_code 6QE9
_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
J9H C9A C1 C 0 1 N N N N N N 43.119 11.505 65.194 ? ? ? C9A J9H 1
J9H C9 C2 C 0 1 Y N N N N N 43.539 12.047 63.857 ? ? ? C9 J9H 2
J9H C8 C3 C 0 1 Y N N N N N 44.096 13.319 63.756 ? ? ? C8 J9H 3
J9H C7 C4 C 0 1 Y N N N N N 44.489 13.820 62.519 ? ? ? C7 J9H 4
J9H N10 N1 N 1 1 Y N N N N N 43.374 11.283 62.759 ? ? ? N10 J9H 5
J9H C10 C5 C 0 1 Y N N N N N 43.763 11.761 61.512 ? ? ? C10 J9H 6
J9H C6A C6 C 0 1 Y N N N N N 44.319 13.032 61.391 ? ? ? C6A J9H 7
J9H C1A C7 C 0 1 Y N N N N N 43.586 10.956 60.387 ? ? ? C1A J9H 8
J9H C4A C8 C 0 1 Y N N N N N 43.974 11.445 59.145 ? ? ? C4A J9H 9
J9H C5 C9 C 0 1 Y N N N N N 44.529 12.711 59.023 ? ? ? C5 J9H 10
J9H C6 C10 C 0 1 Y N N N N N 44.704 13.506 60.148 ? ? ? C6 J9H 11
J9H N1 N2 N 0 1 N N N N N N 43.035 9.713 60.512 ? ? ? N1 J9H 12
J9H C2 C11 C 0 1 N N N N N N 42.867 8.934 59.411 ? ? ? C2 J9H 13
J9H C2A C12 C 0 1 N N N N N N 42.270 7.556 59.513 ? ? ? C2A J9H 14
J9H C3 C13 C 0 1 N N N N N N 43.244 9.398 58.160 ? ? ? C3 J9H 15
J9H C4 C14 C 0 1 N N N N N N 43.802 10.660 58.022 ? ? ? C4 J9H 16
J9H PT PT1 PT 0 0 N N N N N N 42.261 9.550 61.979 ? ? ? PT J9H 17
J9H CP C15 C 0 1 N N N N N N 44.939 8.085 62.232 ? ? ? CP J9H 18
J9H C21 C16 C 0 1 N N N N N N 39.439 10.816 61.751 ? ? ? C21 J9H 19
J9H C22 C17 C 0 1 N N N N N N 40.025 10.410 60.434 ? ? ? C22 J9H 20
J9H H1 H1 H 0 1 N N N N N N 43.963 10.971 65.655 ? ? ? H1 J9H 21
J9H H2 H2 H 0 1 N N N N N N 42.810 12.336 65.846 ? ? ? H2 J9H 22
J9H H3 H3 H 0 1 N N N N N N 42.276 10.811 65.060 ? ? ? H3 J9H 23
J9H H4 H4 H 0 1 N N N N N N 44.224 13.921 64.644 ? ? ? H4 J9H 24
J9H H5 H5 H 0 1 N N N N N N 44.920 14.807 62.439 ? ? ? H5 J9H 25
J9H H6 H6 H 0 1 N N N N N N 44.825 13.079 58.052 ? ? ? H6 J9H 26
J9H H7 H7 H 0 1 N N N N N N 45.139 14.490 60.054 ? ? ? H7 J9H 27
J9H H8 H8 H 0 1 N N N N N N 42.026 7.338 60.563 ? ? ? H8 J9H 28
J9H H9 H9 H 0 1 N N N N N N 41.354 7.508 58.906 ? ? ? H9 J9H 29
J9H H10 H10 H 0 1 N N N N N N 42.994 6.815 59.144 ? ? ? H10 J9H 30
J9H H11 H11 H 0 1 N N N N N N 43.103 8.774 57.290 ? ? ? H11 J9H 31
J9H H12 H12 H 0 1 N N N N N N 44.795 10.525 57.569 ? ? ? H12 J9H 32
J9H H13 H13 H 0 1 N N N N N N 43.157 11.223 57.331 ? ? ? H13 J9H 33
J9H H14 H14 H 0 1 N N N N N N 45.029 7.655 63.241 ? ? ? H14 J9H 34
J9H H15 H15 H 0 1 N N N N N N 44.988 7.279 61.485 ? ? ? H15 J9H 35
J9H H16 H16 H 0 1 N N N N N N 45.762 8.794 62.061 ? ? ? H16 J9H 36
J9H N2 N3 N 0 1 N Y N N N N ? ? ? ? ? ? N2 J9H 37
J9H H17 H17 H 0 1 N N N N N N ? ? ? ? ? ? H17 J9H 38
J9H H18 H18 H 0 1 N N N N N N ? ? ? ? ? ? H18 J9H 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
J9H C4 C3 SING N N 1
J9H C4 C4A SING N N 2
J9H C3 C2 DOUB N N 3
J9H C5 C4A DOUB Y N 4
J9H C5 C6 SING Y N 5
J9H C4A C1A SING Y N 6
J9H C2 C2A SING N N 7
J9H C2 N1 SING N N 8
J9H C6 C6A DOUB Y N 9
J9H C1A N1 SING N N 10
J9H C1A C10 DOUB Y N 11
J9H C22 C21 DOUB N N 12
J9H N1 PT SING N N 13
J9H C6A C10 SING Y N 14
J9H C6A C7 SING Y N 15
J9H C10 N10 SING Y N 16
J9H PT N10 SING N N 17
J9H C7 C8 DOUB Y N 18
J9H N10 C9 DOUB Y N 19
J9H C8 C9 SING Y N 20
J9H C9 C9A SING N N 21
J9H PT C22 SING N N 22
J9H C9A H1 SING N N 23
J9H C9A H2 SING N N 24
J9H C9A H3 SING N N 25
J9H C8 H4 SING N N 26
J9H C7 H5 SING N N 27
J9H C5 H6 SING N N 28
J9H C6 H7 SING N N 29
J9H C2A H8 SING N N 30
J9H C2A H9 SING N N 31
J9H C2A H10 SING N N 32
J9H C3 H11 SING N N 33
J9H C4 H12 SING N N 34
J9H C4 H13 SING N N 35
J9H CP H14 SING N N 36
J9H CP H15 SING N N 37
J9H CP H16 SING N N 38
J9H C21 PT SING N N 39
J9H CP PT SING N N 40
J9H PT N2 SING N N 41
J9H N2 H17 SING N N 42
J9H N2 H18 SING N N 43
#
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
J9H InChI InChI 1.03 InChI=1S/C14H13N2.C2H2.CH3.H2N.Pt/c1-9-3-5-11-7-8-12-6-4-10(2)16-14(12)13(11)15-9;1-2;;;/h3-5,7-8H,6H2,1-2H3;1-2H;1H3;1H2;/q-1;;;-1;+3
J9H InChIKey InChI 1.03 LXADSRPTCIXTGZ-UHFFFAOYSA-N
J9H SMILES_CANONICAL CACTVS 3.385 CC1=CCc2ccc3ccc(C)[n+]4c3c2N1[Pt]4(C)N.C=C
J9H SMILES CACTVS 3.385 CC1=CCc2ccc3ccc(C)[n+]4c3c2N1[Pt]4(C)N.C=C
J9H SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 Cc1ccc2ccc3c4c2[n+]1[Pt]5(N4C(=CC3)C)([C]=[C]5)(C)N
J9H SMILES "OpenEye OEToolkits" 2.0.7 Cc1ccc2ccc3c4c2[n+]1[Pt]5(N4C(=CC3)C)([C]=[C]5)(C)N
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
J9H 'Create component' 2019-02-12 RCSB
J9H 'Initial release' 2019-02-27 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
J9H C9A C -1.652 3.605 1
J9H C9 C -1.921 2.127 2
J9H C8 C -3.358 1.606 3
J9H C7 C -3.611 0.099 4
J9H N10 N -0.782 1.148 5
J9H C10 C -1.094 -0.282 6
J9H C6A C -2.437 -0.846 7
J9H C1A C 0.093 -1.071 8
J9H C4A C 0.093 -2.527 9
J9H C5 C -1.269 -3.232 10
J9H C6 C -2.562 -2.369 11
J9H N1 N 1.290 -0.236 12
J9H C2 C 2.641 -0.910 13
J9H C2A C 3.898 -0.093 14
J9H C3 C 2.710 -2.439 15
J9H C4 C 1.417 -3.255 16
J9H PT Pt 0.770 1.224 17
J9H CP C 2.178 1.745 18
J9H C21 C 1.459 2.556 19
J9H C22 C -0.037 2.486 20
J9H N2 N 2.173 0.665 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
J9H C4 C3 SINGLE NONE 1
J9H C4 C4A SINGLE NONE 2
J9H C3 C2 DOUBLE NONE 3
J9H C5 C4A DOUBLE NONE 4
J9H C5 C6 SINGLE NONE 5
J9H C4A C1A SINGLE NONE 6
J9H C2 C2A SINGLE NONE 7
J9H C2 N1 SINGLE NONE 8
J9H C6 C6A DOUBLE NONE 9
J9H C1A N1 SINGLE NONE 10
J9H C1A C10 DOUBLE NONE 11
J9H C22 C21 DOUBLE NONE 12
J9H N1 PT SINGLE NONE 13
J9H C6A C10 SINGLE NONE 14
J9H C6A C7 SINGLE NONE 15
J9H C10 N10 SINGLE NONE 16
J9H PT N10 SINGLE NONE 17
J9H C7 C8 DOUBLE NONE 18
J9H N10 C9 DOUBLE NONE 19
J9H C8 C9 SINGLE NONE 20
J9H C9 C9A SINGLE NONE 21
J9H PT C22 SINGLE NONE 22
J9H C21 PT SINGLE NONE 23
J9H CP PT SINGLE NONE 24
J9H PT N2 SINGLE NONE 25
#
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
J9H MurckoScaffold S1 scaffold '[C]1=[C][Pt]12N1C=CCc3ccc4ccc[n+]2c4c31' 'InChI=1S/C12H9N2.C2.Pt/c1-3-9-5-6-10-4-2-8-14-12(10)11(9)13-7-1;1-2;/h1-3,5-8H,4H2;;/q-1;;+2' XIFCVSKAWUYOEK-UHFFFAOYSA-N
J9H phenyl F1 fragment c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-UHFFFAOYSA-N
J9H pyridine F2 fragment c1ccncc1 InChI=1S/C5H5N/c1-2-4-6-5-3-1/h1-5H JUJWROOIHBZHMG-UHFFFAOYSA-N
J9H quinoline F3 fragment c1ccc2ncccc2c1 InChI=1S/C9H7N/c1-2-6-9-8(4-1)5-3-7-10-9/h1-7H SMWDFEZZVXVKRB-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
J9H C9 S1 1
J9H C8 S1 1
J9H C7 S1 1
J9H N10 S1 1
J9H C10 S1 1
J9H C6A S1 1
J9H C1A S1 1
J9H C4A S1 1
J9H C5 S1 1
J9H C6 S1 1
J9H N1 S1 1
J9H C2 S1 1
J9H C3 S1 1
J9H C4 S1 1
J9H PT S1 1
J9H C21 S1 1
J9H C22 S1 1
J9H C10 F1 1
J9H C1A F1 1
J9H C4A F1 1
J9H C5 F1 1
J9H C6 F1 1
J9H C6A F1 1
J9H C9 F2 1
J9H C8 F2 1
J9H C7 F2 1
J9H C6A F2 1
J9H C10 F2 1
J9H N10 F2 1
J9H C5 F3 1
J9H C6 F3 1
J9H C6A F3 1
J9H C10 F3 1
J9H C1A F3 1
J9H C4A F3 1
J9H N10 F3 1
J9H C9 F3 1
J9H C8 F3 1
J9H C7 F3 1
#
_pdbe_chem_comp_rdkit_properties.comp_id J9H
_pdbe_chem_comp_rdkit_properties.exactmw 459.114
_pdbe_chem_comp_rdkit_properties.amw 459.430
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 3
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 2
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 4
_pdbe_chem_comp_rdkit_properties.NumHBD 1
_pdbe_chem_comp_rdkit_properties.NumHBA 2
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 21
_pdbe_chem_comp_rdkit_properties.NumAtoms 39
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 4
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.235
_pdbe_chem_comp_rdkit_properties.NumRings 5
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 2
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 3
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 0
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 4
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 3
_pdbe_chem_comp_rdkit_properties.NumSpiroAtoms 1
_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 148.687
_pdbe_chem_comp_rdkit_properties.tpsa 33.140
_pdbe_chem_comp_rdkit_properties.CrippenClogP 1.714
_pdbe_chem_comp_rdkit_properties.CrippenMR 77.193
_pdbe_chem_comp_rdkit_properties.chi0v 12.430
_pdbe_chem_comp_rdkit_properties.chi1v 12.000
_pdbe_chem_comp_rdkit_properties.chi2v 12.959
_pdbe_chem_comp_rdkit_properties.chi3v 12.959
_pdbe_chem_comp_rdkit_properties.chi4v 13.122
_pdbe_chem_comp_rdkit_properties.chi0n 28.158
_pdbe_chem_comp_rdkit_properties.chi1n 14.437
_pdbe_chem_comp_rdkit_properties.chi2n 3.400
_pdbe_chem_comp_rdkit_properties.chi3n 3.400
_pdbe_chem_comp_rdkit_properties.chi4n 2.503
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.442
_pdbe_chem_comp_rdkit_properties.kappa1 3.900
_pdbe_chem_comp_rdkit_properties.kappa2 2.757
_pdbe_chem_comp_rdkit_properties.kappa3 1.022
_pdbe_chem_comp_rdkit_properties.Phi 0.512
#
_pdbe_chem_comp_external_mappings.comp_id J9H
_pdbe_chem_comp_external_mappings.source UniChem
_pdbe_chem_comp_external_mappings.resource PDBe
_pdbe_chem_comp_external_mappings.resource_id J9H
#
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
J9H C9A -3.952 0.397 1.248 ETKDGv3 1
J9H C9 -2.739 1.089 0.716 ETKDGv3 2
J9H C8 -2.881 2.405 0.037 ETKDGv3 3
J9H C7 -1.821 3.031 -0.489 ETKDGv3 4
J9H N10 -1.578 0.500 0.800 ETKDGv3 5
J9H C10 -0.391 1.097 0.267 ETKDGv3 6
J9H C6A -0.489 2.409 -0.408 ETKDGv3 7
J9H C1A 0.785 0.471 0.350 ETKDGv3 8
J9H C4A 1.999 1.086 -0.230 ETKDGv3 9
J9H C5 1.911 2.284 -0.836 ETKDGv3 10
J9H C6 0.606 2.977 -0.934 ETKDGv3 11
J9H N1 0.877 -0.807 0.969 ETKDGv3 12
J9H C2 2.108 -1.537 0.988 ETKDGv3 13
J9H C2A 2.113 -2.927 1.544 ETKDGv3 14
J9H C3 3.231 -1.017 0.462 ETKDGv3 15
J9H C4 3.324 0.378 -0.111 ETKDGv3 16
J9H PT -0.146 -1.174 1.384 ETKDGv3 17
J9H CP -1.503 -2.334 0.393 ETKDGv3 18
J9H C21 -1.840 -0.507 -2.539 ETKDGv3 19
J9H C22 -1.159 0.379 -3.258 ETKDGv3 20
J9H H1 -3.666 -0.376 1.993 ETKDGv3 21
J9H H2 -4.495 -0.091 0.411 ETKDGv3 22
J9H H3 -4.624 1.130 1.742 ETKDGv3 23
J9H H4 -3.858 2.866 -0.035 ETKDGv3 24
J9H H5 -1.950 3.989 -0.979 ETKDGv3 25
J9H H6 2.791 2.753 -1.259 ETKDGv3 26
J9H H7 0.548 3.935 -1.436 ETKDGv3 27
J9H H8 1.172 -3.122 2.100 ETKDGv3 28
J9H H9 2.967 -3.059 2.242 ETKDGv3 29
J9H H10 2.198 -3.660 0.715 ETKDGv3 30
J9H H11 4.141 -1.605 0.477 ETKDGv3 31
J9H H12 3.995 0.979 0.539 ETKDGv3 32
J9H H13 3.789 0.308 -1.118 ETKDGv3 33
J9H H14 -2.522 -2.351 -0.046 ETKDGv3 34
J9H H15 -1.565 -2.549 1.479 ETKDGv3 35
J9H H16 -0.872 -3.100 -0.102 ETKDGv3 36
J9H N2 0.824 -1.356 -2.588 ETKDGv3 37
J9H H17 0.956 -2.075 -1.843 ETKDGv3 38
J9H H18 1.716 -0.815 -2.644 ETKDGv3 39
#