data_PA2
#
_chem_comp.id PA2
_chem_comp.name "PAROMOMYCIN (RING 2)"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C6 H14 N2 O2"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 1999-07-08
_chem_comp.pdbx_modified_date 2011-06-04
_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 146.188
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code PA2
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag N
_chem_comp.pdbx_ideal_coordinates_details ?
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code 1PBR
_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
PA2 C1 C1 C 0 1 N N R N N N 0.234 -5.603 41.991 -1.273 -0.311 -0.416 C1 PA2 1
PA2 N1 N1 N 0 1 N N N N N N -0.524 -6.518 41.118 -2.482 0.191 -1.082 N1 PA2 2
PA2 C2 C2 C 0 1 N N S N N N 1.002 -4.515 41.181 -0.034 0.235 -1.127 C2 PA2 3
PA2 O2 O2 O 0 1 N N N N N N 1.915 -5.124 40.271 -0.039 -0.193 -2.490 O2 PA2 4
PA2 C3 C3 C 0 1 N N S N N N 1.804 -3.570 42.123 1.224 -0.287 -0.432 C3 PA2 5
PA2 O3 O3 O 0 1 N N N N N N 2.358 -2.480 41.328 2.382 0.223 -1.097 O3 PA2 6
PA2 C4 C4 C 0 1 N N N N N N 0.911 -2.980 43.263 1.230 0.171 1.026 C4 PA2 7
PA2 C5 C5 C 0 1 N N S N N N 0.105 -4.076 44.031 -0.009 -0.375 1.737 C5 PA2 8
PA2 N5 N5 N 0 1 N N N N N N -0.804 -3.480 45.035 -0.003 0.065 3.139 N5 PA2 9
PA2 C6 C6 C 0 1 N N N N N N -0.710 -4.949 43.042 -1.268 0.147 1.043 C6 PA2 10
PA2 H1 H1 H 0 1 N N N N N N 1.001 -6.211 42.524 -1.263 -1.400 -0.454 H1 PA2 11
PA2 HN11 1HN1 H 0 0 N N N N N N -1.026 -7.230 41.648 -3.270 -0.193 -0.582 HN11 PA2 12
PA2 HN12 2HN1 H 0 0 N N N N N N 0.080 -6.941 40.413 -2.502 1.188 -0.933 HN12 PA2 13
PA2 H2 H2 H 0 1 N N N N N N 0.241 -3.920 40.622 -0.044 1.324 -1.089 H2 PA2 14
PA2 HO2 HO2 H 0 1 N N N N N N 2.383 -4.460 39.777 0.756 0.172 -2.901 HO2 PA2 15
PA2 H3 H3 H 0 1 N N N N N N 2.614 -4.164 42.606 1.234 -1.376 -0.471 H3 PA2 16
PA2 HO3 HO3 H 0 1 N N N N N N 2.847 -1.903 41.902 3.151 -0.129 -0.629 HO3 PA2 17
PA2 H41 1H4 H 0 1 N N N N N N 1.517 -2.364 43.967 1.220 1.260 1.065 H41 PA2 18
PA2 H42 2H4 H 0 1 N N N N N N 0.232 -2.188 42.868 2.127 -0.201 1.521 H42 PA2 19
PA2 H5 H5 H 0 1 N N N N N N 0.844 -4.717 44.565 0.001 -1.464 1.699 H5 PA2 20
PA2 HN51 1HN5 H 0 0 N N N N N N -1.330 -4.195 45.536 0.839 -0.300 3.555 HN51 PA2 21
PA2 HN52 2HN5 H 0 0 N N N N N N -1.424 -2.788 44.612 0.091 1.069 3.126 HN52 PA2 22
PA2 H61 1H6 H 0 1 N N N N N N -1.532 -4.371 42.559 -2.151 -0.241 1.550 H61 PA2 23
PA2 H62 2H6 H 0 1 N N N N N N -1.330 -5.708 43.572 -1.278 1.237 1.081 H62 PA2 24
#
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
PA2 C1 N1 SING N N 1
PA2 C1 C2 SING N N 2
PA2 C1 C6 SING N N 3
PA2 C1 H1 SING N N 4
PA2 N1 HN11 SING N N 5
PA2 N1 HN12 SING N N 6
PA2 C2 O2 SING N N 7
PA2 C2 C3 SING N N 8
PA2 C2 H2 SING N N 9
PA2 O2 HO2 SING N N 10
PA2 C3 O3 SING N N 11
PA2 C3 C4 SING N N 12
PA2 C3 H3 SING N N 13
PA2 O3 HO3 SING N N 14
PA2 C4 C5 SING N N 15
PA2 C4 H41 SING N N 16
PA2 C4 H42 SING N N 17
PA2 C5 N5 SING N N 18
PA2 C5 C6 SING N N 19
PA2 C5 H5 SING N N 20
PA2 N5 HN51 SING N N 21
PA2 N5 HN52 SING N N 22
PA2 C6 H61 SING N N 23
PA2 C6 H62 SING N N 24
#
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
PA2 SMILES ACDLabs 10.04 OC1CC(N)CC(N)C1O
PA2 SMILES_CANONICAL CACTVS 3.341 N[C@H]1C[C@@H](N)[C@H](O)[C@@H](O)C1
PA2 SMILES CACTVS 3.341 N[CH]1C[CH](N)[CH](O)[CH](O)C1
PA2 SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 C1[C@@H](C[C@@H]([C@H]([C@@H]1N)O)O)N
PA2 SMILES "OpenEye OEToolkits" 1.5.0 C1C(CC(C(C1N)O)O)N
PA2 InChI InChI 1.03 InChI=1S/C6H14N2O2/c7-3-1-4(8)6(10)5(9)2-3/h3-6,9-10H,1-2,7-8H2/t3-,4+,5-,6-/m0/s1
PA2 InChIKey InChI 1.03 QOLDZWBHLDQIJR-FSIIMWSLSA-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
PA2 "SYSTEMATIC NAME" ACDLabs 10.04 (1S,2S,3R,5S)-3,5-diaminocyclohexane-1,2-diol
PA2 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 (1S,2S,3R,5S)-3,5-diaminocyclohexane-1,2-diol
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
PA2 'Create component' 1999-07-08 RCSB
PA2 'Modify descriptor' 2011-06-04 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
PA2 C1 C 6.404 0.983 1
PA2 N1 N 6.404 2.482 2
PA2 C2 C 5.104 0.233 3
PA2 O2 O 3.805 0.983 4
PA2 C3 C 5.104 -1.268 5
PA2 O3 O 3.805 -2.018 6
PA2 C4 C 6.404 -2.018 7
PA2 C5 C 7.702 -1.268 8
PA2 N5 N 9.002 -2.018 9
PA2 C6 C 7.702 0.233 10
#
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
PA2 C1 N1 SINGLE BEGINDASH 1
PA2 C1 C2 SINGLE NONE 2
PA2 C1 C6 SINGLE NONE 3
PA2 C2 O2 SINGLE BEGINWEDGE 4
PA2 C2 C3 SINGLE NONE 5
PA2 C3 O3 SINGLE BEGINDASH 6
PA2 C3 C4 SINGLE NONE 7
PA2 C4 C5 SINGLE NONE 8
PA2 C5 N5 SINGLE BEGINDASH 9
PA2 C5 C6 SINGLE NONE 10
#
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
PA2 MurckoScaffold S1 scaffold C1CCCCC1 InChI=1S/C6H12/c1-2-4-6-5-3-1/h1-6H2 XDTMQSROBMDMFD-UHFFFAOYSA-N
PA2 cyclohexane F1 fragment C1CCCCC1 InChI=1S/C6H12/c1-2-4-6-5-3-1/h1-6H2 XDTMQSROBMDMFD-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
PA2 C1 S1 1
PA2 C2 S1 1
PA2 C3 S1 1
PA2 C4 S1 1
PA2 C5 S1 1
PA2 C6 S1 1
PA2 C1 F1 1
PA2 C2 F1 1
PA2 C3 F1 1
PA2 C4 F1 1
PA2 C5 F1 1
PA2 C6 F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id PA2
_pdbe_chem_comp_rdkit_properties.exactmw 146.106
_pdbe_chem_comp_rdkit_properties.amw 146.190
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 4
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 6
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 4
_pdbe_chem_comp_rdkit_properties.NumHBD 4
_pdbe_chem_comp_rdkit_properties.NumHBA 4
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 10
_pdbe_chem_comp_rdkit_properties.NumAtoms 24
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 4
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 1
_pdbe_chem_comp_rdkit_properties.NumRings 1
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 0
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 1
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 1
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 0
_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 4
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 79.902
_pdbe_chem_comp_rdkit_properties.tpsa 92.500
_pdbe_chem_comp_rdkit_properties.CrippenClogP -1.843
_pdbe_chem_comp_rdkit_properties.CrippenMR 37.198
_pdbe_chem_comp_rdkit_properties.chi0v 4.711
_pdbe_chem_comp_rdkit_properties.chi1v 2.355
_pdbe_chem_comp_rdkit_properties.chi2v 0.890
_pdbe_chem_comp_rdkit_properties.chi3v 0.890
_pdbe_chem_comp_rdkit_properties.chi4v 0.472
_pdbe_chem_comp_rdkit_properties.chi0n 18.711
_pdbe_chem_comp_rdkit_properties.chi1n 8.961
_pdbe_chem_comp_rdkit_properties.chi2n 0.890
_pdbe_chem_comp_rdkit_properties.chi3n 0.890
_pdbe_chem_comp_rdkit_properties.chi4n 0.472
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.160
_pdbe_chem_comp_rdkit_properties.kappa1 1.353
_pdbe_chem_comp_rdkit_properties.kappa2 2.837
_pdbe_chem_comp_rdkit_properties.kappa3 1.462
_pdbe_chem_comp_rdkit_properties.Phi 0.384
#
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
PA2 UniChem ChEBI 72340
PA2 UniChem PubChem 5289102
#
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
PA2 C1 -0.979 -0.971 -0.023 ETKDGv3 1
PA2 N1 -1.863 -1.845 0.753 ETKDGv3 2
PA2 C2 -1.222 0.507 0.363 ETKDGv3 3
PA2 O2 -2.544 0.857 0.037 ETKDGv3 4
PA2 C3 -0.244 1.440 -0.387 ETKDGv3 5
PA2 O3 -0.424 2.767 0.038 ETKDGv3 6
PA2 C4 1.212 1.032 -0.120 ETKDGv3 7
PA2 C5 1.456 -0.437 -0.515 ETKDGv3 8
PA2 N5 2.838 -0.832 -0.238 ETKDGv3 9
PA2 C6 0.488 -1.363 0.238 ETKDGv3 10
PA2 H1 -1.197 -1.104 -1.108 ETKDGv3 11
PA2 HN11 -2.853 -1.641 0.483 ETKDGv3 12
PA2 HN12 -1.691 -2.834 0.460 ETKDGv3 13
PA2 H2 -1.058 0.615 1.463 ETKDGv3 14
PA2 HO2 -2.812 1.589 0.652 ETKDGv3 15
PA2 H3 -0.431 1.364 -1.486 ETKDGv3 16
PA2 HO3 -1.174 3.143 -0.493 ETKDGv3 17
PA2 H41 1.886 1.690 -0.710 ETKDGv3 18
PA2 H42 1.446 1.180 0.958 ETKDGv3 19
PA2 H5 1.273 -0.550 -1.608 ETKDGv3 20
PA2 HN51 3.477 -0.241 -0.820 ETKDGv3 21
PA2 HN52 3.062 -0.637 0.765 ETKDGv3 22
PA2 H61 0.698 -1.319 1.331 ETKDGv3 23
PA2 H62 0.656 -2.409 -0.100 ETKDGv3 24
#