data_5GG
#
_chem_comp.id 5GG
_chem_comp.name Deoxyhypusine
_chem_comp.type 'L-peptide linking'
_chem_comp.pdbx_type ATOMP
_chem_comp.formula 'C10 H23 N3 O2'
_chem_comp.mon_nstd_parent_comp_id Lys
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2015-09-23
_chem_comp.pdbx_modified_date 2024-09-27
_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 217.309
_chem_comp.one_letter_code K
_chem_comp.three_letter_code 5GG
_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 5DUB
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site RCSB
_chem_comp.pdbx_pcm Y
#
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
5GG N N N 0 1 N N N Y Y N 37.323 83.597 40.624 -4.258 1.784 0.019 N 5GG 1
5GG CA CA C 0 1 N N S Y N N 37.875 83.480 39.250 -4.202 0.384 -0.423 CA 5GG 2
5GG C C C 0 1 N N N Y N Y 39.371 83.748 39.308 -5.441 -0.339 0.037 C 5GG 3
5GG O O O 0 1 N N N Y N Y 39.800 84.688 39.954 -6.099 0.109 0.947 O 5GG 4
5GG CB CB C 0 1 N N N N N N 37.174 84.485 38.333 -2.966 -0.290 0.176 CB 5GG 5
5GG CG CG C 0 1 N N N N N N 35.702 84.150 38.108 -1.703 0.364 -0.390 CG 5GG 6
5GG CD CD C 0 1 N N N N N N 35.005 85.358 37.472 -0.468 -0.311 0.209 CD 5GG 7
5GG CE CE C 0 1 N N N N N N 33.582 85.070 36.991 0.795 0.343 -0.356 CE 5GG 8
5GG NZ NZ N 0 1 N N N N N N 33.034 86.324 36.406 1.981 -0.304 0.219 NZ 5GG 9
5GG CH CH C 0 1 N N N N N N 31.257 87.357 35.053 4.426 -0.400 0.319 CH 5GG 10
5GG CI CI C 0 1 N N N N N N 29.884 87.223 34.400 5.711 0.229 -0.224 CI 5GG 11
5GG CJ CJ C 0 1 N N N N N N 29.759 88.245 33.262 6.923 -0.471 0.396 CJ 5GG 12
5GG CF CF C 0 1 N N N N N N 31.702 86.095 35.795 3.215 0.299 -0.302 CF 5GG 13
5GG NY NY N 0 1 N N N N N N 28.725 87.805 32.305 8.156 0.133 -0.125 NY 5GG 14
5GG OXT O1 O 0 1 N Y N Y N Y 40.166 82.923 38.634 -5.815 -1.480 -0.562 O1 5GG 15
5GG H H1 H 0 1 N N N Y Y N 37.780 82.941 41.224 -4.312 1.844 1.024 H1 5GG 16
5GG H2 H2 H 0 1 N Y N Y Y N 37.475 84.524 40.966 -3.469 2.306 -0.333 H2 5GG 17
5GG HA H4 H 0 1 N N N Y N N 37.704 82.463 38.867 -4.143 0.349 -1.511 H4 5GG 18
5GG H5 H5 H 0 1 N N N N N N 37.686 84.490 37.360 -2.980 -0.177 1.260 H5 5GG 19
5GG H6 H6 H 0 1 N N N N N N 37.242 85.484 38.789 -2.971 -1.350 -0.079 H6 5GG 20
5GG H7 H7 H 0 1 N N N N N N 35.226 83.915 39.072 -1.690 0.250 -1.474 H7 5GG 21
5GG H8 H8 H 0 1 N N N N N N 35.620 83.282 37.437 -1.698 1.423 -0.135 H8 5GG 22
5GG H9 H9 H 0 1 N N N N N N 35.602 85.688 36.609 -0.481 -0.198 1.293 H9 5GG 23
5GG H10 H10 H 0 1 N N N N N N 34.962 86.165 38.218 -0.473 -1.371 -0.045 H10 5GG 24
5GG H11 H11 H 0 1 N N N N N N 32.959 84.750 37.839 0.808 0.230 -1.440 H11 5GG 25
5GG H12 H12 H 0 1 N N N N N N 33.599 84.278 36.228 0.800 1.403 -0.101 H12 5GG 26
5GG H13 H13 H 0 1 N N N N N N 33.662 86.657 35.703 1.967 -1.299 0.052 H13 5GG 27
5GG H15 H15 H 0 1 N N N N N N 31.996 87.580 34.269 4.404 -1.460 0.064 H15 5GG 28
5GG H16 H16 H 0 1 N N N N N N 31.222 88.190 35.771 4.396 -0.286 1.402 H16 5GG 29
5GG H17 H17 H 0 1 N N N N N N 29.101 87.411 35.150 5.742 0.115 -1.308 H17 5GG 30
5GG H18 H18 H 0 1 N N N N N N 29.768 86.207 33.995 5.733 1.288 0.031 H18 5GG 31
5GG H19 H19 H 0 1 N N N N N N 30.724 88.332 32.742 6.892 -0.357 1.480 H19 5GG 32
5GG H20 H20 H 0 1 N N N N N N 29.478 89.223 33.679 6.901 -1.530 0.141 H20 5GG 33
5GG H21 H21 H 0 1 N N N N N N 30.973 85.857 36.584 3.246 0.185 -1.385 H21 5GG 34
5GG H22 H22 H 0 1 N N N N N N 31.763 85.256 35.087 3.237 1.359 -0.047 H22 5GG 35
5GG H23 H23 H 0 1 N N N N N N 28.648 88.474 31.566 8.171 1.128 0.042 H23 5GG 36
5GG H24 H24 H 0 1 N N N N N N 28.980 86.916 31.924 8.971 -0.312 0.270 H24 5GG 37
5GG HXT H26 H 0 1 N Y N Y N Y 41.070 83.191 38.747 -6.617 -1.907 -0.232 H26 5GG 38
#
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
5GG NY CJ SING N N 1
5GG CJ CI SING N N 2
5GG CI CH SING N N 3
5GG CH CF SING N N 4
5GG CF NZ SING N N 5
5GG NZ CE SING N N 6
5GG CE CD SING N N 7
5GG CD CG SING N N 8
5GG CG CB SING N N 9
5GG CB CA SING N N 10
5GG CA C SING N N 11
5GG CA N SING N N 12
5GG C O DOUB N N 13
5GG C OXT SING N N 14
5GG N H SING N N 15
5GG N H2 SING N N 16
5GG CA HA SING N N 17
5GG CB H5 SING N N 18
5GG CB H6 SING N N 19
5GG CG H7 SING N N 20
5GG CG H8 SING N N 21
5GG CD H9 SING N N 22
5GG CD H10 SING N N 23
5GG CE H11 SING N N 24
5GG CE H12 SING N N 25
5GG NZ H13 SING N N 26
5GG CH H15 SING N N 27
5GG CH H16 SING N N 28
5GG CI H17 SING N N 29
5GG CI H18 SING N N 30
5GG CJ H19 SING N N 31
5GG CJ H20 SING N N 32
5GG CF H21 SING N N 33
5GG CF H22 SING N N 34
5GG NY H23 SING N N 35
5GG NY H24 SING N N 36
5GG OXT HXT SING N N 37
#
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
5GG SMILES ACDLabs 12.01 'NC(C(=O)O)CCCCNCCCCN'
5GG InChI InChI 1.03 'InChI=1S/C10H23N3O2/c11-6-2-4-8-13-7-3-1-5-9(12)10(14)15/h9,13H,1-8,11-12H2,(H,14,15)/t9-/m0/s1'
5GG InChIKey InChI 1.03 PGPFBXMCOQNMJO-VIFPVBQESA-N
5GG SMILES_CANONICAL CACTVS 3.385 'NCCCCNCCCC[C@H](N)C(O)=O'
5GG SMILES CACTVS 3.385 'NCCCCNCCCC[CH](N)C(O)=O'
5GG SMILES_CANONICAL 'OpenEye OEToolkits' 1.9.2 'C(CCNCCCCN)C[C@@H](C(=O)O)N'
5GG SMILES 'OpenEye OEToolkits' 1.9.2 'C(CCNCCCCN)CC(C(=O)O)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
5GG 'SYSTEMATIC NAME' ACDLabs 12.01 'N~6~-(4-aminobutyl)-L-lysine'
5GG 'SYSTEMATIC NAME' 'OpenEye OEToolkits' 1.9.2 '(2S)-2-azanyl-6-(4-azanylbutylamino)hexanoic 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
5GG 'Create component' 2015-09-23 RCSB
5GG 'Initial release' 2016-01-20 RCSB
5GG 'Other modification' 2019-05-08 RCSB
5GG 'Modify backbone' 2023-11-03 PDBE
5GG 'Modify PCM' 2024-09-27 PDBE
#
_pdbx_chem_comp_pcm.pcm_id 1
_pdbx_chem_comp_pcm.comp_id 5GG
_pdbx_chem_comp_pcm.modified_residue_id LYS
_pdbx_chem_comp_pcm.type Deoxyhypusine
_pdbx_chem_comp_pcm.category 'Named protein modification'
_pdbx_chem_comp_pcm.position 'Amino-acid side chain'
_pdbx_chem_comp_pcm.polypeptide_position 'Any position'
_pdbx_chem_comp_pcm.comp_id_linking_atom ?
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom ?
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession PTM-0684
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession ?
_pdbx_chem_comp_pcm.first_instance_model_db_code 5DUB
#
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
5GG N N 9.002 5.715 1
5GG CA C 10.301 4.965 2
5GG C C 11.600 5.715 3
5GG O O 12.899 4.965 4
5GG CB C 10.301 3.465 5
5GG CG C 9.002 2.715 6
5GG CD C 9.002 1.215 7
5GG CE C 7.702 0.465 8
5GG NZ N 7.702 -1.035 9
5GG CH C 6.404 -3.285 10
5GG CI C 5.104 -4.035 11
5GG CJ C 5.104 -5.535 12
5GG CF C 6.404 -1.785 13
5GG NY N 3.805 -6.285 14
5GG OXT O 11.600 7.215 15
#
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
5GG NY CJ SINGLE NONE 1
5GG CJ CI SINGLE NONE 2
5GG CI CH SINGLE NONE 3
5GG CH CF SINGLE NONE 4
5GG CF NZ SINGLE NONE 5
5GG NZ CE SINGLE NONE 6
5GG CE CD SINGLE NONE 7
5GG CD CG SINGLE NONE 8
5GG CG CB SINGLE NONE 9
5GG CB CA SINGLE NONE 10
5GG CA C SINGLE NONE 11
5GG CA N SINGLE BEGINDASH 12
5GG C O DOUBLE NONE 13
5GG C OXT SINGLE NONE 14
#
_pdbe_chem_comp_substructure.comp_id 5GG
_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
5GG O F1 1
5GG C F1 1
5GG CA F1 1
5GG N F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id 5GG
_pdbe_chem_comp_rdkit_properties.exactmw 217.179
_pdbe_chem_comp_rdkit_properties.amw 217.313
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 5
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 6
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 12
_pdbe_chem_comp_rdkit_properties.NumHBD 4
_pdbe_chem_comp_rdkit_properties.NumHBA 5
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 15
_pdbe_chem_comp_rdkit_properties.NumAtoms 38
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 5
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.900
_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 123.900
_pdbe_chem_comp_rdkit_properties.tpsa 101.370
_pdbe_chem_comp_rdkit_properties.CrippenClogP -0.103
_pdbe_chem_comp_rdkit_properties.CrippenMR 60.620
_pdbe_chem_comp_rdkit_properties.chi0v 7.158
_pdbe_chem_comp_rdkit_properties.chi1v 3.303
_pdbe_chem_comp_rdkit_properties.chi2v 0.779
_pdbe_chem_comp_rdkit_properties.chi3v 0.779
_pdbe_chem_comp_rdkit_properties.chi4v 0.309
_pdbe_chem_comp_rdkit_properties.chi0n 30.158
_pdbe_chem_comp_rdkit_properties.chi1n 14.447
_pdbe_chem_comp_rdkit_properties.chi2n 0.779
_pdbe_chem_comp_rdkit_properties.chi3n 0.779
_pdbe_chem_comp_rdkit_properties.chi4n 0.309
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.650
_pdbe_chem_comp_rdkit_properties.kappa1 1.936
_pdbe_chem_comp_rdkit_properties.kappa2 9.888
_pdbe_chem_comp_rdkit_properties.kappa3 9.650
_pdbe_chem_comp_rdkit_properties.Phi 1.276
#
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
5GG UniChem PDBe 5GG
5GG UniChem ChEBI 50038
5GG UniChem SureChEMBL SCHEMBL448753
5GG UniChem HMDB HMDB0011150
5GG UniChem PubChem 122083
5GG UniChem NMRShiftDB 60020862
5GG UniChem ACTor 82543-85-9
5GG UniChem Nikkaji J494.042C
5GG UniChem 'EPA CompTox Dashboard' DTXSID20231839
5GG UniChem MetaboLights MTBLC50038
5GG UniChem BRENDA 114499
5GG UniChem BRENDA 30708
5GG UniChem BRENDA 94105
#
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
5GG N -4.565 -2.120 -0.613 ETKDGv3 1
5GG CA -4.261 -0.755 -0.176 ETKDGv3 2
5GG C -5.148 0.213 -0.908 ETKDGv3 3
5GG O -5.140 0.257 -2.168 ETKDGv3 4
5GG CB -2.766 -0.427 -0.389 ETKDGv3 5
5GG CG -2.367 0.906 0.268 ETKDGv3 6
5GG CD -0.907 1.293 -0.015 ETKDGv3 7
5GG CE 0.099 0.420 0.746 ETKDGv3 8
5GG NZ 1.461 0.917 0.521 ETKDGv3 9
5GG CH 3.874 0.489 0.852 ETKDGv3 10
5GG CI 4.187 0.582 -0.655 ETKDGv3 11
5GG CJ 4.037 -0.742 -1.428 ETKDGv3 12
5GG CF 2.442 0.034 1.166 ETKDGv3 13
5GG NY 4.927 -1.790 -0.930 ETKDGv3 14
5GG OXT -5.974 1.072 -0.190 ETKDGv3 15
5GG H -4.050 -2.791 0.002 ETKDGv3 16
5GG H2 -4.215 -2.261 -1.589 ETKDGv3 17
5GG HA -4.488 -0.684 0.912 ETKDGv3 18
5GG H5 -2.164 -1.245 0.059 ETKDGv3 19
5GG H6 -2.540 -0.393 -1.478 ETKDGv3 20
5GG H7 -2.537 0.853 1.366 ETKDGv3 21
5GG H8 -3.014 1.717 -0.132 ETKDGv3 22
5GG H9 -0.703 1.235 -1.107 ETKDGv3 23
5GG H10 -0.766 2.351 0.295 ETKDGv3 24
5GG H11 -0.139 0.438 1.834 ETKDGv3 25
5GG H12 0.021 -0.626 0.378 ETKDGv3 26
5GG H13 1.539 1.860 0.971 ETKDGv3 27
5GG H15 4.033 1.493 1.302 ETKDGv3 28
5GG H16 4.594 -0.198 1.346 ETKDGv3 29
5GG H17 5.228 0.952 -0.776 ETKDGv3 30
5GG H18 3.523 1.342 -1.120 ETKDGv3 31
5GG H19 4.280 -0.553 -2.495 ETKDGv3 32
5GG H20 2.984 -1.096 -1.399 ETKDGv3 33
5GG H21 2.307 -1.015 0.825 ETKDGv3 34
5GG H22 2.300 0.050 2.270 ETKDGv3 35
5GG H23 4.588 -2.113 0.005 ETKDGv3 36
5GG H24 5.891 -1.401 -0.812 ETKDGv3 37
5GG HXT -6.574 1.735 -0.667 ETKDGv3 38
#