data_AR5
#
_chem_comp.id AR5
_chem_comp.name N~2~-(tert-butoxycarbonyl)-L-arginine
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C11 H22 N4 O4"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2016-03-30
_chem_comp.pdbx_modified_date 2017-03-31
_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 274.317
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code AR5
_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 5J1X
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site EBI
#
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
AR5 O3 O1 O 0 1 N N N N N N 24.121 6.065 12.519 -2.454 0.148 1.073 O3 AR5 1
AR5 C6 C1 C 0 1 N N N N N N 24.871 5.768 13.430 -2.015 -0.199 -0.005 C6 AR5 2
AR5 O2 O2 O 0 1 N N N N N N 24.908 4.581 14.080 -2.636 -1.166 -0.706 O2 AR5 3
AR5 C7 C2 C 0 1 N N N N N N 24.209 3.382 13.553 -3.826 -1.750 -0.112 C7 AR5 4
AR5 C10 C3 C 0 1 N N N N N N 24.337 2.269 14.591 -4.876 -0.659 0.103 C10 AR5 5
AR5 C9 C4 C 0 1 N N N N N N 22.752 3.766 13.332 -4.388 -2.822 -1.047 C9 AR5 6
AR5 C8 C5 C 0 1 N N N N N N 24.911 3.022 12.252 -3.465 -2.384 1.232 C8 AR5 7
AR5 N3 N1 N 0 1 N N N N N N 25.794 6.598 13.942 -0.909 0.389 -0.503 N3 AR5 8
AR5 C4 C6 C 0 1 N N S N N N 26.023 7.890 13.332 -0.236 1.446 0.257 C4 AR5 9
AR5 C5 C7 C 0 1 N N N N N N 26.562 7.722 11.914 -0.894 2.770 -0.032 C5 AR5 10
AR5 O1 O3 O 0 1 N N N N N N 26.429 8.555 11.052 -1.829 2.825 -0.796 O1 AR5 11
AR5 O O4 O 0 1 N N N N N N 27.188 6.591 11.762 -0.442 3.888 0.557 O AR5 12
AR5 C3 C8 C 0 1 N N N N N N 26.955 8.744 14.208 1.237 1.508 -0.151 C3 AR5 13
AR5 C2 C9 C 0 1 N N N N N N 26.307 9.224 15.482 1.935 0.209 0.257 C2 AR5 14
AR5 C1 C10 C 0 1 N N N N N N 25.394 10.386 15.222 3.409 0.272 -0.151 C1 AR5 15
AR5 N2 N2 N 0 1 N N N N N N 26.140 11.638 15.153 4.077 -0.972 0.239 N2 AR5 16
AR5 C C11 C 0 1 N N N N N N 25.765 12.764 15.771 5.415 -1.146 -0.027 C AR5 17
AR5 N1 N3 N 0 1 N N N N N N 26.667 13.738 15.905 6.088 -0.205 -0.626 N1 AR5 18
AR5 N N4 N 0 1 N N N N N N 24.534 12.873 16.210 6.042 -2.314 0.340 N AR5 19
AR5 H1 H1 H 0 1 N N N N N N 23.818 2.566 15.514 -5.133 -0.207 -0.855 H1 AR5 20
AR5 H2 H2 H 0 1 N N N N N N 23.885 1.347 14.197 -5.769 -1.097 0.549 H2 AR5 21
AR5 H3 H3 H 0 1 N N N N N N 25.400 2.092 14.809 -4.475 0.105 0.769 H3 AR5 22
AR5 H4 H4 H 0 1 N N N N N N 22.288 4.017 14.297 -3.640 -3.599 -1.201 H4 AR5 23
AR5 H5 H5 H 0 1 N N N N N N 22.700 4.637 12.663 -5.281 -3.260 -0.601 H5 AR5 24
AR5 H6 H6 H 0 1 N N N N N N 22.215 2.921 12.876 -4.645 -2.370 -2.006 H6 AR5 25
AR5 H7 H7 H 0 1 N N N N N N 25.957 2.753 12.461 -3.064 -1.620 1.898 H7 AR5 26
AR5 H8 H8 H 0 1 N N N N N N 24.399 2.168 11.784 -4.358 -2.822 1.678 H8 AR5 27
AR5 H9 H9 H 0 1 N N N N N N 24.884 3.885 11.570 -2.716 -3.161 1.079 H9 AR5 28
AR5 H10 H10 H 0 1 N N N N N N 26.323 6.323 14.745 -0.558 0.113 -1.364 H10 AR5 29
AR5 H11 H11 H 0 1 N N N N N N 25.061 8.419 13.261 -0.309 1.229 1.323 H11 AR5 30
AR5 H12 H12 H 0 1 N N N N N N 27.519 6.529 10.874 -0.896 4.713 0.340 H12 AR5 31
AR5 H13 H13 H 0 1 N N N N N N 27.836 8.140 14.471 1.310 1.636 -1.231 H13 AR5 32
AR5 H14 H14 H 0 1 N N N N N N 27.273 9.622 13.626 1.717 2.351 0.348 H14 AR5 33
AR5 H15 H15 H 0 1 N N N N N N 25.724 8.401 15.920 1.863 0.081 1.337 H15 AR5 34
AR5 H16 H16 H 0 1 N N N N N N 27.091 9.535 16.188 1.456 -0.633 -0.242 H16 AR5 35
AR5 H17 H17 H 0 1 N N N N N N 24.657 10.452 16.036 3.481 0.400 -1.231 H17 AR5 36
AR5 H18 H18 H 0 1 N N N N N N 24.873 10.226 14.267 3.888 1.114 0.348 H18 AR5 37
AR5 H19 H19 H 0 1 N N N N N N 26.981 11.656 14.612 3.576 -1.672 0.685 H19 AR5 38
AR5 H20 H20 H 0 1 N N N N N N 26.288 14.538 16.371 7.032 -0.328 -0.814 H20 AR5 39
AR5 H22 H22 H 0 1 N N N N N N 24.239 13.712 16.667 5.540 -3.014 0.786 H22 AR5 40
AR5 H23 H23 H 0 1 N N N N N N 23.891 12.117 16.088 6.985 -2.437 0.152 H23 AR5 41
#
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
AR5 O1 C5 DOUB N N 1
AR5 O C5 SING N N 2
AR5 C5 C4 SING N N 3
AR5 C8 C7 SING N N 4
AR5 O3 C6 DOUB N N 5
AR5 C9 C7 SING N N 6
AR5 C4 N3 SING N N 7
AR5 C4 C3 SING N N 8
AR5 C6 N3 SING N N 9
AR5 C6 O2 SING N N 10
AR5 C7 O2 SING N N 11
AR5 C7 C10 SING N N 12
AR5 C3 C2 SING N N 13
AR5 N2 C1 SING N N 14
AR5 N2 C SING N N 15
AR5 C1 C2 SING N N 16
AR5 C N1 DOUB N N 17
AR5 C N SING N N 18
AR5 C10 H1 SING N N 19
AR5 C10 H2 SING N N 20
AR5 C10 H3 SING N N 21
AR5 C9 H4 SING N N 22
AR5 C9 H5 SING N N 23
AR5 C9 H6 SING N N 24
AR5 C8 H7 SING N N 25
AR5 C8 H8 SING N N 26
AR5 C8 H9 SING N N 27
AR5 N3 H10 SING N N 28
AR5 C4 H11 SING N N 29
AR5 O H12 SING N N 30
AR5 C3 H13 SING N N 31
AR5 C3 H14 SING N N 32
AR5 C2 H15 SING N N 33
AR5 C2 H16 SING N N 34
AR5 C1 H17 SING N N 35
AR5 C1 H18 SING N N 36
AR5 N2 H19 SING N N 37
AR5 N1 H20 SING N N 38
AR5 N H22 SING N N 39
AR5 N H23 SING N N 40
#
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
AR5 SMILES ACDLabs 12.01 O=C(NC(CCCN\C(=N)N)C(=O)O)OC(C)(C)C
AR5 InChI InChI 1.03 InChI=1S/C11H22N4O4/c1-11(2,3)19-10(18)15-7(8(16)17)5-4-6-14-9(12)13/h7H,4-6H2,1-3H3,(H,15,18)(H,16,17)(H4,12,13,14)/t7-/m0/s1
AR5 InChIKey InChI 1.03 HSQIYOPBCOPMSS-ZETCQYMHSA-N
AR5 SMILES_CANONICAL CACTVS 3.385 CC(C)(C)OC(=O)N[C@@H](CCCNC(N)=N)C(O)=O
AR5 SMILES CACTVS 3.385 CC(C)(C)OC(=O)N[CH](CCCNC(N)=N)C(O)=O
AR5 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.4 "[H]/N=C(/N)\NCCC[C@@H](C(=O)O)NC(=O)OC(C)(C)C"
AR5 SMILES "OpenEye OEToolkits" 2.0.4 CC(C)(C)OC(=O)NC(CCCNC(=N)N)C(=O)O
#
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
AR5 "SYSTEMATIC NAME" ACDLabs 12.01 N~2~-(tert-butoxycarbonyl)-L-arginine
AR5 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.4 "(2~{S})-5-carbamimidamido-2-[(2-methylpropan-2-yl)oxycarbonylamino]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
AR5 'Create component' 2016-03-30 EBI
AR5 'Initial release' 2017-04-05 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
AR5 O3 O 10.301 1.215 1
AR5 C6 C 10.301 2.715 2
AR5 O2 O 11.600 3.465 3
AR5 C7 C 12.899 2.715 4
AR5 C10 C 12.149 1.416 5
AR5 C9 C 13.649 4.014 6
AR5 C8 C 14.198 1.965 7
AR5 N3 N 9.002 3.465 8
AR5 C4 C 7.702 2.715 9
AR5 C5 C 6.404 3.465 10
AR5 O1 O 5.104 2.715 11
AR5 O O 6.404 4.965 12
AR5 C3 C 7.702 1.215 13
AR5 C2 C 6.404 0.465 14
AR5 C1 C 6.404 -1.035 15
AR5 N2 N 5.104 -1.785 16
AR5 C C 5.104 -3.285 17
AR5 N1 N 3.805 -4.035 18
AR5 N N 6.404 -4.035 19
AR5 H20 H 3.805 -5.535 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
AR5 O1 C5 DOUBLE NONE 1
AR5 O C5 SINGLE NONE 2
AR5 C5 C4 SINGLE NONE 3
AR5 C8 C7 SINGLE NONE 4
AR5 O3 C6 DOUBLE NONE 5
AR5 C9 C7 SINGLE NONE 6
AR5 C4 N3 SINGLE NONE 7
AR5 C4 C3 SINGLE BEGINWEDGE 8
AR5 C6 N3 SINGLE NONE 9
AR5 C6 O2 SINGLE NONE 10
AR5 C7 O2 SINGLE NONE 11
AR5 C7 C10 SINGLE NONE 12
AR5 C3 C2 SINGLE NONE 13
AR5 N2 C1 SINGLE NONE 14
AR5 N2 C SINGLE ENDUPRIGHT 15
AR5 C1 C2 SINGLE NONE 16
AR5 C N1 DOUBLE NONE 17
AR5 C N SINGLE ENDUPRIGHT 18
#
_pdbe_chem_comp_substructure.comp_id AR5
_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
AR5 O1 F1 1
AR5 C5 F1 1
AR5 C4 F1 1
AR5 N3 F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id AR5
_pdbe_chem_comp_rdkit_properties.exactmw 274.164
_pdbe_chem_comp_rdkit_properties.amw 274.321
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 8
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 6
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 6
_pdbe_chem_comp_rdkit_properties.NumHBD 5
_pdbe_chem_comp_rdkit_properties.NumHBA 5
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 19
_pdbe_chem_comp_rdkit_properties.NumAtoms 41
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 8
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 1
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.727
_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 143.031
_pdbe_chem_comp_rdkit_properties.tpsa 137.530
_pdbe_chem_comp_rdkit_properties.CrippenClogP 0.228
_pdbe_chem_comp_rdkit_properties.CrippenMR 69.944
_pdbe_chem_comp_rdkit_properties.chi0v 8.922
_pdbe_chem_comp_rdkit_properties.chi1v 4.112
_pdbe_chem_comp_rdkit_properties.chi2v 1.030
_pdbe_chem_comp_rdkit_properties.chi3v 1.030
_pdbe_chem_comp_rdkit_properties.chi4v 0.535
_pdbe_chem_comp_rdkit_properties.chi0n 30.922
_pdbe_chem_comp_rdkit_properties.chi1n 14.757
_pdbe_chem_comp_rdkit_properties.chi2n 1.030
_pdbe_chem_comp_rdkit_properties.chi3n 1.030
_pdbe_chem_comp_rdkit_properties.chi4n 0.535
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.990
_pdbe_chem_comp_rdkit_properties.kappa1 3.018
_pdbe_chem_comp_rdkit_properties.kappa2 7.446
_pdbe_chem_comp_rdkit_properties.kappa3 9.688
_pdbe_chem_comp_rdkit_properties.Phi 1.183
#
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
AR5 UniChem ChEMBL CHEMBL1229088
AR5 UniChem PDBe AR5
AR5 UniChem ZINC ZINC000001576309
AR5 UniChem 'EPA CompTox Dashboard' DTXSID30160126
AR5 UniChem ChemicalBook CB3707720
AR5 UniChem 'Probes And Drugs' PD131236
AR5 UniChem Nikkaji J278.017H
AR5 UniChem eMolecules 505488
AR5 UniChem SureChEMBL SCHEMBL1486276
AR5 UniChem 'PubChem TPHARMA' 16205684
AR5 UniChem PubChem 114667
AR5 UniChem PubChem 6992570
AR5 UniChem Mcule MCULE-3451096482
AR5 UniChem ACTor 114622-81-0
AR5 UniChem ACTor 13726-76-6
AR5 UniChem ACTor 35897-34-8
#
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
AR5 O3 0.926 1.325 0.303 ETKDGv3 1
AR5 C6 1.551 0.230 0.295 ETKDGv3 2
AR5 O2 2.942 0.192 0.115 ETKDGv3 3
AR5 C7 3.806 1.324 -0.069 ETKDGv3 4
AR5 C10 3.752 2.253 1.159 ETKDGv3 5
AR5 C9 5.236 0.783 -0.220 ETKDGv3 6
AR5 C8 3.427 2.094 -1.349 ETKDGv3 7
AR5 N3 0.842 -1.002 0.472 ETKDGv3 8
AR5 C4 -0.606 -1.049 0.692 ETKDGv3 9
AR5 C5 -0.904 -0.597 2.096 ETKDGv3 10
AR5 O1 -1.535 0.475 2.294 ETKDGv3 11
AR5 O -0.457 -1.347 3.180 ETKDGv3 12
AR5 C3 -1.132 -2.479 0.444 ETKDGv3 13
AR5 C2 -2.665 -2.621 0.531 ETKDGv3 14
AR5 C1 -3.412 -1.961 -0.643 ETKDGv3 15
AR5 N2 -3.692 -0.547 -0.389 ETKDGv3 16
AR5 C -4.284 0.300 -1.383 ETKDGv3 17
AR5 N1 -4.597 -0.177 -2.546 ETKDGv3 18
AR5 N -4.528 1.677 -1.084 ETKDGv3 19
AR5 H1 3.951 1.674 2.086 ETKDGv3 20
AR5 H2 2.760 2.738 1.258 ETKDGv3 21
AR5 H3 4.514 3.058 1.074 ETKDGv3 22
AR5 H4 5.963 1.612 -0.367 ETKDGv3 23
AR5 H5 5.299 0.099 -1.093 ETKDGv3 24
AR5 H6 5.530 0.212 0.687 ETKDGv3 25
AR5 H7 4.173 2.890 -1.560 ETKDGv3 26
AR5 H8 2.435 2.580 -1.251 ETKDGv3 27
AR5 H9 3.393 1.401 -2.217 ETKDGv3 28
AR5 H10 1.396 -1.889 0.457 ETKDGv3 29
AR5 H11 -1.091 -0.367 -0.038 ETKDGv3 30
AR5 H12 -0.642 -1.049 4.130 ETKDGv3 31
AR5 H13 -0.794 -2.822 -0.558 ETKDGv3 32
AR5 H14 -0.674 -3.169 1.187 ETKDGv3 33
AR5 H15 -3.044 -2.244 1.506 ETKDGv3 34
AR5 H16 -2.894 -3.708 0.506 ETKDGv3 35
AR5 H17 -2.822 -2.067 -1.580 ETKDGv3 36
AR5 H18 -4.379 -2.489 -0.792 ETKDGv3 37
AR5 H19 -3.482 -0.132 0.546 ETKDGv3 38
AR5 H20 -5.029 0.420 -3.287 ETKDGv3 39
AR5 H22 -4.959 2.312 -1.793 ETKDGv3 40
AR5 H23 -4.274 2.068 -0.150 ETKDGv3 41
#