data_LN5
#
_chem_comp.id LN5
_chem_comp.name N5-(1-iminopropyl)-L-ornithine
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C8 H17 N3 O2"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms "(2S)-2-azanyl-5-(propanimidoylamino)pentanoic acid"
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2009-07-07
_chem_comp.pdbx_modified_date 2021-03-01
_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 187.239
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code LN5
_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 3I4A
_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
LN5 CT1 CT1 C 0 1 N N N N N N 2.386 -22.078 -14.350 -5.944 0.134 0.064 CT1 LN5 1
LN5 CH1 CH1 C 0 1 N N N N N N 1.529 -21.929 -15.597 -4.708 -0.623 -0.427 CH1 LN5 2
LN5 CZ CZ C 0 1 N N N N N N 1.139 -20.498 -15.908 -3.465 0.099 0.025 CZ LN5 3
LN5 NH2 NH2 N 0 1 N N N N N N 1.442 -19.669 -14.796 -3.564 1.185 0.719 NH2 LN5 4
LN5 NE NE N 0 1 N N N N N N 2.019 -19.885 -16.899 -2.229 -0.396 -0.300 NE LN5 5
LN5 CD CD C 0 1 N N N N N N 2.048 -20.462 -18.257 -1.020 0.305 0.140 CD LN5 6
LN5 CG CG C 0 1 N N N N N N 2.875 -19.552 -19.190 0.215 -0.451 -0.352 CG LN5 7
LN5 CB CB C 0 1 N N N N N N 2.878 -20.075 -20.656 1.478 0.281 0.107 CB LN5 8
LN5 CA CA C 0 1 N N S N N N 3.625 -19.146 -21.626 2.714 -0.476 -0.385 CA LN5 9
LN5 C C C 0 1 N N N N N N 5.128 -19.145 -21.340 3.953 0.309 -0.039 C LN5 10
LN5 OA2 OA2 O 0 1 N N N N N N 5.834 -19.925 -22.018 4.612 0.003 0.927 OA2 LN5 11
LN5 OA1 OA1 O 0 1 N N N N N N 5.541 -18.346 -20.471 4.326 1.347 -0.805 OA1 LN5 12
LN5 N N N 0 1 N N N N N N 3.417 -19.588 -23.014 2.771 -1.793 0.263 N LN5 13
LN5 H1H2 H1H2 H 0 0 N N N N N N 1.165 -18.745 -15.059 -2.763 1.650 1.010 H1H2 LN5 14
LN5 H1T1 H1T1 H 0 0 N N N N N N 3.448 -22.114 -14.636 -6.843 -0.388 -0.263 H1T1 LN5 15
LN5 H2T1 H2T1 H 0 0 N N N N N N 2.215 -21.220 -13.683 -5.929 0.185 1.153 H2T1 LN5 16
LN5 H3T1 H3T1 H 0 0 N N N N N N 2.115 -23.008 -13.828 -5.939 1.143 -0.347 H3T1 LN5 17
LN5 H1H1 H1H1 H 0 0 N N N N N N 2.101 -22.319 -16.452 -4.713 -1.632 -0.016 H1H1 LN5 18
LN5 H2H1 H2H1 H 0 0 N N N N N N 0.597 -22.484 -15.414 -4.723 -0.674 -1.516 H2H1 LN5 19
LN5 HNE HNE H 0 1 N N N N N N 2.586 -19.096 -16.664 -2.155 -1.211 -0.821 HNE LN5 20
LN5 H1D H1D H 0 1 N N N N N N 2.507 -21.461 -18.220 -1.016 1.314 -0.272 H1D LN5 21
LN5 H2D H2D H 0 1 N N N N N N 1.021 -20.542 -18.642 -1.006 0.356 1.228 H2D LN5 22
LN5 H1G H1G H 0 1 N N N N N N 2.437 -18.543 -19.177 0.211 -1.461 0.059 H1G LN5 23
LN5 H2G H2G H 0 1 N N N N N N 3.913 -19.543 -18.827 0.201 -0.503 -1.441 H2G LN5 24
LN5 H1B H1B H 0 1 N N N N N N 3.372 -21.058 -20.671 1.482 1.290 -0.305 H1B LN5 25
LN5 H2B H2B H 0 1 N N N N N N 1.831 -20.128 -20.990 1.492 0.332 1.196 H2B LN5 26
LN5 HA HA H 0 1 N N N N N N 3.226 -18.130 -21.485 2.654 -0.605 -1.465 HA LN5 27
LN5 H15 H15 H 0 1 N N N N N N 6.485 -18.417 -20.398 5.128 1.819 -0.543 H15 LN5 28
LN5 H1N H1N H 0 1 N N N N N N 3.370 -18.790 -23.615 2.826 -1.700 1.266 H1N LN5 29
LN5 H2N H2N H 0 1 N N N N N N 4.178 -20.172 -23.295 1.982 -2.362 -0.004 H2N LN5 30
#
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
LN5 CH1 CT1 SING N N 1
LN5 CZ CH1 SING N N 2
LN5 CZ NH2 DOUB N N 3
LN5 NH2 H1H2 SING N N 4
LN5 NE CZ SING N N 5
LN5 CD NE SING N N 6
LN5 CG CD SING N N 7
LN5 CB CG SING N N 8
LN5 CA C SING N N 9
LN5 CA CB SING N N 10
LN5 C OA1 SING N N 11
LN5 OA2 C DOUB N N 12
LN5 N CA SING N N 13
LN5 CT1 H1T1 SING N N 14
LN5 CT1 H2T1 SING N N 15
LN5 CT1 H3T1 SING N N 16
LN5 CH1 H1H1 SING N N 17
LN5 CH1 H2H1 SING N N 18
LN5 NE HNE SING N N 19
LN5 CD H1D SING N N 20
LN5 CD H2D SING N N 21
LN5 CG H1G SING N N 22
LN5 CG H2G SING N N 23
LN5 CB H1B SING N N 24
LN5 CB H2B SING N N 25
LN5 CA HA SING N N 26
LN5 OA1 H15 SING N N 27
LN5 N H1N SING N N 28
LN5 N H2N SING N N 29
#
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
LN5 SMILES ACDLabs 10.04 O=C(O)C(N)CCCNC(=[N@H])CC
LN5 SMILES_CANONICAL CACTVS 3.341 CCC(=N)NCCC[C@H](N)C(O)=O
LN5 SMILES CACTVS 3.341 CCC(=N)NCCC[CH](N)C(O)=O
LN5 SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "[H]/N=C(/CC)\NCCC[C@@H](C(=O)O)N"
LN5 SMILES "OpenEye OEToolkits" 1.5.0 "[H]N=C(CC)NCCCC(C(=O)O)N"
LN5 InChI InChI 1.03 InChI=1S/C8H17N3O2/c1-2-7(10)11-5-3-4-6(9)8(12)13/h6H,2-5,9H2,1H3,(H2,10,11)(H,12,13)/t6-/m0/s1
LN5 InChIKey InChI 1.03 ZYIBCZWVLDODOL-LURJTMIESA-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
LN5 "SYSTEMATIC NAME" ACDLabs 10.04 N~5~-[(1Z)-propanimidoyl]-L-ornithine
LN5 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "(2S)-2-amino-5-(propanimidoylamino)pentanoic acid"
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
LN5 'Create component' 2009-07-07 RCSB
LN5 'Modify descriptor' 2011-06-04 RCSB
LN5 'Modify synonyms' 2021-03-01 PDBE
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id LN5
_pdbx_chem_comp_synonyms.name "(2S)-2-azanyl-5-(propanimidoylamino)pentanoic acid"
_pdbx_chem_comp_synonyms.provenance ?
_pdbx_chem_comp_synonyms.type ?
#
_pdbe_chem_comp_synonyms.comp_id LN5
_pdbe_chem_comp_synonyms.name '(2S)-2-azanyl-5-(propanimidoylamino)pentanoic acid'
_pdbe_chem_comp_synonyms.provenance wwPDB
_pdbe_chem_comp_synonyms.type ?
#
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
LN5 CT1 C 2.506 -3.000 1
LN5 CH1 C 3.805 -3.750 2
LN5 CZ C 5.104 -3.000 3
LN5 NH2 N 6.404 -3.750 4
LN5 NE N 5.104 -1.500 5
LN5 CD C 6.404 -0.750 6
LN5 CG C 6.404 0.750 7
LN5 CB C 7.702 1.500 8
LN5 CA C 7.702 3.000 9
LN5 C C 9.002 3.750 10
LN5 OA2 O 10.301 3.000 11
LN5 OA1 O 9.002 5.250 12
LN5 N N 6.404 3.750 13
LN5 H1H2 H 6.404 -5.250 14
#
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
LN5 CH1 CT1 SINGLE NONE 1
LN5 CZ CH1 SINGLE ENDDOWNRIGHT 2
LN5 CZ NH2 DOUBLE NONE 3
LN5 NE CZ SINGLE ENDDOWNRIGHT 4
LN5 CD NE SINGLE NONE 5
LN5 CG CD SINGLE NONE 6
LN5 CB CG SINGLE NONE 7
LN5 CA C SINGLE NONE 8
LN5 CA CB SINGLE NONE 9
LN5 C OA1 SINGLE NONE 10
LN5 OA2 C DOUBLE NONE 11
LN5 CA N SINGLE BEGINDASH 12
#
_pdbe_chem_comp_substructure.comp_id LN5
_pdbe_chem_comp_substructure.substructure_name peptide
_pdbe_chem_comp_substructure.id F1
_pdbe_chem_comp_substructure.substructure_type fragment
_pdbe_chem_comp_substructure.substructure_smiles NCC=O
_pdbe_chem_comp_substructure.substructure_inchis InChI=1S/C2H5NO/c3-1-2-4/h2H,1,3H2
_pdbe_chem_comp_substructure.substructure_inchikeys LYIIBVSRGJSHAV-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
LN5 OA2 F1 1
LN5 C F1 1
LN5 CA F1 1
LN5 N F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id LN5
_pdbe_chem_comp_rdkit_properties.exactmw 187.132
_pdbe_chem_comp_rdkit_properties.amw 187.243
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 5
_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 4
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 13
_pdbe_chem_comp_rdkit_properties.NumAtoms 30
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 5
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.750
_pdbe_chem_comp_rdkit_properties.NumRings 0
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 0
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 0
_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 1
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 102.028
_pdbe_chem_comp_rdkit_properties.tpsa 99.200
_pdbe_chem_comp_rdkit_properties.CrippenClogP 0.155
_pdbe_chem_comp_rdkit_properties.CrippenMR 50.866
_pdbe_chem_comp_rdkit_properties.chi0v 6.158
_pdbe_chem_comp_rdkit_properties.chi1v 2.803
_pdbe_chem_comp_rdkit_properties.chi2v 0.704
_pdbe_chem_comp_rdkit_properties.chi3v 0.704
_pdbe_chem_comp_rdkit_properties.chi4v 0.247
_pdbe_chem_comp_rdkit_properties.chi0n 23.158
_pdbe_chem_comp_rdkit_properties.chi1n 11.000
_pdbe_chem_comp_rdkit_properties.chi2n 0.704
_pdbe_chem_comp_rdkit_properties.chi3n 0.704
_pdbe_chem_comp_rdkit_properties.chi4n 0.247
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.100
_pdbe_chem_comp_rdkit_properties.kappa1 1.816
_pdbe_chem_comp_rdkit_properties.kappa2 6.420
_pdbe_chem_comp_rdkit_properties.kappa3 6.097
_pdbe_chem_comp_rdkit_properties.Phi 0.897
#
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
LN5 UniChem ChEMBL CHEMBL507472
LN5 UniChem PDBe LN5
LN5 UniChem ZINC ZINC000040380536
LN5 UniChem eMolecules 31239762
LN5 UniChem 'PubChem TPHARMA' 131534375
LN5 UniChem BindingDb 152699
LN5 UniChem BindingDb 50254450
LN5 UniChem BRENDA 38711
LN5 UniChem BRENDA 61104
LN5 UniChem BRENDA 83750
LN5 UniChem 'Probes And Drugs' PD005796
LN5 UniChem Nikkaji J944.483A
LN5 UniChem PubChem 44593548
#
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
LN5 CT1 3.769 0.214 -1.695 ETKDGv3 1
LN5 CH1 3.786 -0.862 -0.615 ETKDGv3 2
LN5 CZ 2.878 -0.487 0.519 ETKDGv3 3
LN5 NH2 3.384 0.089 1.566 ETKDGv3 4
LN5 NE 1.463 -0.724 0.398 ETKDGv3 5
LN5 CD 0.491 -0.325 1.420 ETKDGv3 6
LN5 CG -0.946 -0.649 0.992 ETKDGv3 7
LN5 CB -1.431 0.273 -0.141 ETKDGv3 8
LN5 CA -2.856 -0.078 -0.607 ETKDGv3 9
LN5 C -3.871 0.182 0.477 ETKDGv3 10
LN5 OA2 -4.597 -0.758 0.899 ETKDGv3 11
LN5 OA1 -4.014 1.460 1.010 ETKDGv3 12
LN5 N -3.186 0.689 -1.810 ETKDGv3 13
LN5 H1H2 2.818 0.393 2.387 ETKDGv3 14
LN5 H1T1 4.117 1.184 -1.278 ETKDGv3 15
LN5 H2T1 2.742 0.338 -2.101 ETKDGv3 16
LN5 H3T1 4.446 -0.080 -2.524 ETKDGv3 17
LN5 H1H1 3.456 -1.828 -1.052 ETKDGv3 18
LN5 H2H1 4.826 -0.994 -0.245 ETKDGv3 19
LN5 HNE 1.126 -1.209 -0.464 ETKDGv3 20
LN5 H1D 0.580 0.766 1.619 ETKDGv3 21
LN5 H2D 0.713 -0.873 2.361 ETKDGv3 22
LN5 H1G -1.607 -0.520 1.876 ETKDGv3 23
LN5 H2G -1.008 -1.713 0.674 ETKDGv3 24
LN5 H1B -0.744 0.175 -1.010 ETKDGv3 25
LN5 H2B -1.395 1.332 0.198 ETKDGv3 26
LN5 HA -2.877 -1.159 -0.874 ETKDGv3 27
LN5 H15 -4.693 1.646 1.738 ETKDGv3 28
LN5 H1N -4.133 0.397 -2.145 ETKDGv3 29
LN5 H2N -3.237 1.707 -1.573 ETKDGv3 30
#