data_GND
#
_chem_comp.id GND
_chem_comp.name "2-AMINO-5-GUANIDINO-PENTANOIC ACID"
_chem_comp.type "L-PEPTIDE LINKING"
_chem_comp.pdbx_type ATOMP
_chem_comp.formula "C6 H15 N4 O2"
_chem_comp.mon_nstd_parent_comp_id LYS
_chem_comp.pdbx_synonyms "L-argininium(2+); L-argininediium"
_chem_comp.pdbx_formal_charge 1
_chem_comp.pdbx_initial_date 2003-01-17
_chem_comp.pdbx_modified_date 2024-09-05
_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 175.209
_chem_comp.one_letter_code K
_chem_comp.three_letter_code GND
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag N
_chem_comp.pdbx_ideal_coordinates_details "OpenEye/OEToolkits V1.4.2"
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code ?
_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
GND CA CA C 0 1 N N S Y N N 56.100 0.107 -2.538 1.495 1.476 2.040 CA GND 1
GND CB CB C 0 1 N N N N N N 56.860 1.174 -3.327 2.375 0.247 2.292 CB GND 2
GND CG CG C 0 1 N N N N N N 58.341 1.091 -2.993 1.615 -0.927 2.923 CG GND 3
GND CD CD C 0 1 N N N N N N 59.120 1.865 -4.039 2.517 -2.129 3.197 CD GND 4
GND NE NE N 0 1 N N N N N N 60.419 2.204 -3.408 1.763 -3.210 3.785 NE GND 5
GND CZ CZ C 0 1 N N N N N N 60.587 3.363 -2.847 2.243 -4.445 4.168 CZ GND 6
GND NH1 NH1 N 0 1 N N N N N N 61.767 3.711 -2.417 1.454 -5.347 4.690 NH1 GND 7
GND NH2 NH2 N 0 1 N N N N N N 59.574 4.161 -2.681 3.581 -4.681 3.974 NH2 GND 8
GND C C C 0 1 N N N Y N Y 54.619 0.477 -2.418 0.371 1.146 1.081 C GND 9
GND OXT OXT O 0 1 N Y N Y N Y 54.227 1.470 -3.008 0.835 0.810 -0.151 OXT GND 10
GND O O O 0 1 N N N Y N Y 53.904 -0.240 -1.739 -0.820 1.171 1.360 O GND 11
GND N N N 1 1 N N N Y Y N 56.255 -1.144 -3.334 0.923 1.950 3.335 N GND 12
GND HA HA H 0 1 N N N Y N N 56.542 -0.011 -1.561 2.067 2.322 1.645 HA GND 13
GND HB1 1HB H 0 1 N N N N N N 56.492 2.153 -3.064 2.805 -0.087 1.339 HB1 GND 14
GND HB2 2HB H 0 1 N N N N N N 56.725 1.008 -4.385 3.226 0.527 2.926 HB2 GND 15
GND HG1 1HG H 0 1 N N N N N N 58.656 0.061 -3.006 1.139 -0.611 3.859 HG1 GND 16
GND HG2 2HG H 0 1 N N N N N N 58.516 1.520 -2.022 0.815 -1.242 2.242 HG2 GND 17
GND HD1 1HD H 0 1 N N N N N N 58.592 2.764 -4.302 2.954 -2.477 2.256 HD1 GND 18
GND HD2 2HD H 0 1 N N N N N N 59.277 1.249 -4.903 3.343 -1.852 3.860 HD2 GND 19
GND HE HE H 0 1 N N N N N N 61.164 1.578 -3.462 0.772 -3.031 3.926 HE GND 20
GND HH11 1HH1 H 0 0 N N N N N N 62.540 3.089 -2.525 0.506 -4.960 4.742 HH11 GND 21
GND HH21 1HH2 H 0 0 N N N N N N 58.660 3.888 -2.971 4.201 -3.988 3.571 HH21 GND 22
GND HH22 2HH2 H 0 0 N N N N N N 59.713 5.057 -2.259 3.998 -5.569 4.234 HH22 GND 23
GND HXT HXT H 0 1 N Y N Y N Y 53.308 1.699 -2.933 0.143 0.587 -0.810 HXT GND 24
GND HN1 1HN H 0 1 N N N Y Y N 57.186 -1.566 -3.141 1.600 1.830 4.091 HN1 GND 25
GND HN2 2HN H 0 1 N Y N Y Y N 56.178 -0.921 -4.348 0.080 1.421 3.568 HN2 GND 26
GND HN3 3HN H 0 1 N N N Y Y N 55.510 -1.818 -3.070 0.677 2.941 3.276 HN3 GND 27
#
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
GND CA CB SING N N 1
GND CA C SING N N 2
GND CA N SING N N 3
GND CA HA SING N N 4
GND CB CG SING N N 5
GND CB HB1 SING N N 6
GND CB HB2 SING N N 7
GND CG CD SING N N 8
GND CG HG1 SING N N 9
GND CG HG2 SING N N 10
GND CD NE SING N N 11
GND CD HD1 SING N N 12
GND CD HD2 SING N N 13
GND NE CZ SING N N 14
GND NE HE SING N N 15
GND CZ NH1 DOUB N N 16
GND CZ NH2 SING N N 17
GND NH1 HH11 SING N N 18
GND NH2 HH21 SING N N 19
GND NH2 HH22 SING N N 20
GND C OXT SING N N 21
GND C O DOUB N N 22
GND OXT HXT SING N N 23
GND N HN1 SING N N 24
GND N HN2 SING N N 25
GND N HN3 SING N N 26
#
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
GND SMILES ACDLabs 10.04 O=C(O)C(CCCNC(=[N@H])N)[NH3+]
GND SMILES_CANONICAL CACTVS 3.341 NC(=N)NCCC[C@H]([NH3+])C(O)=O
GND SMILES CACTVS 3.341 NC(=N)NCCC[CH]([NH3+])C(O)=O
GND SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "[H]/N=C(/N)\NCCC[C@@H](C(=O)O)[NH3+]"
GND SMILES "OpenEye OEToolkits" 1.5.0 "[H]N=C(N)NCCCC(C(=O)O)[NH3+]"
GND InChI InChI 1.03 InChI=1S/C6H14N4O2/c7-4(5(11)12)2-1-3-10-6(8)9/h4H,1-3,7H2,(H,11,12)(H4,8,9,10)/p+1/t4-/m0/s1
GND InChIKey InChI 1.03 ODKSFYDXXFIFQN-BYPYZUCNSA-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
GND "SYSTEMATIC NAME" ACDLabs 10.04 (1S)-4-carbamimidamido-1-carboxybutan-1-aminium
GND "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2S)-5-carbamimidamido-1-hydroxy-1-oxo-pentan-2-yl]azanium"
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
GND 'Create component' 2003-01-17 RCSB
GND 'Modify descriptor' 2011-06-04 RCSB
GND 'Modify parent residue' 2024-09-05 PDBE
#
loop_
_pdbx_chem_comp_synonyms.ordinal
_pdbx_chem_comp_synonyms.comp_id
_pdbx_chem_comp_synonyms.name
_pdbx_chem_comp_synonyms.provenance
_pdbx_chem_comp_synonyms.type
1 GND L-argininium(2+) PUBCHEM ?
2 GND L-argininediium PUBCHEM ?
#
loop_
_pdbe_chem_comp_synonyms.comp_id
_pdbe_chem_comp_synonyms.name
_pdbe_chem_comp_synonyms.provenance
_pdbe_chem_comp_synonyms.type
GND L-argininium(2+) wwPDB ?
GND L-argininediium wwPDB ?
#
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
GND CA C 8.453 7.680 1
GND CB C 8.453 6.180 2
GND CG C 7.154 5.430 3
GND CD C 7.154 3.930 4
GND NE N 5.854 3.180 5
GND CZ C 5.854 1.680 6
GND NH1 N 4.555 0.930 7
GND NH2 N 7.154 0.930 8
GND C C 9.752 8.430 9
GND OXT O 11.051 7.680 10
GND O O 9.752 9.930 11
GND N N 7.154 8.430 12
GND HH11 H 0.000 4.590 13
#
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
GND CA CB SINGLE NONE 1
GND CA C SINGLE NONE 2
GND CA N SINGLE BEGINDASH 3
GND CB CG SINGLE NONE 4
GND CG CD SINGLE NONE 5
GND CD NE SINGLE NONE 6
GND NE CZ SINGLE ENDUPRIGHT 7
GND CZ NH1 DOUBLE NONE 8
GND CZ NH2 SINGLE ENDUPRIGHT 9
GND C OXT SINGLE NONE 10
GND C O DOUBLE NONE 11
#
_pdbe_chem_comp_substructure.comp_id GND
_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
GND O F1 1
GND C F1 1
GND CA F1 1
GND N F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id GND
_pdbe_chem_comp_rdkit_properties.exactmw 175.119
_pdbe_chem_comp_rdkit_properties.amw 175.212
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 6
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 8
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 6
_pdbe_chem_comp_rdkit_properties.NumHBD 5
_pdbe_chem_comp_rdkit_properties.NumHBA 3
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 12
_pdbe_chem_comp_rdkit_properties.NumAtoms 27
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 6
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.667
_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 92.002
_pdbe_chem_comp_rdkit_properties.tpsa 126.840
_pdbe_chem_comp_rdkit_properties.CrippenClogP -2.055
_pdbe_chem_comp_rdkit_properties.CrippenMR 43.463
_pdbe_chem_comp_rdkit_properties.chi0v 5.605
_pdbe_chem_comp_rdkit_properties.chi1v 2.526
_pdbe_chem_comp_rdkit_properties.chi2v 0.586
_pdbe_chem_comp_rdkit_properties.chi3v 0.586
_pdbe_chem_comp_rdkit_properties.chi4v 0.216
_pdbe_chem_comp_rdkit_properties.chi0n 20.605
_pdbe_chem_comp_rdkit_properties.chi1n 9.565
_pdbe_chem_comp_rdkit_properties.chi2n 0.586
_pdbe_chem_comp_rdkit_properties.chi3n 0.586
_pdbe_chem_comp_rdkit_properties.chi4n 0.216
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.300
_pdbe_chem_comp_rdkit_properties.kappa1 1.650
_pdbe_chem_comp_rdkit_properties.kappa2 5.363
_pdbe_chem_comp_rdkit_properties.kappa3 5.482
_pdbe_chem_comp_rdkit_properties.Phi 0.738
#
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
GND UniChem ChEBI 32682
GND UniChem SureChEMBL SCHEMBL6703134
GND UniChem HMDB HMDB0062762
GND UniChem PubChem 1549073
GND UniChem PubChem 5287702
GND UniChem PubChem 52941769
GND UniChem PubChem 88031296
GND UniChem Recon 'arg_L'
GND UniChem Nikkaji J2.241.252C
GND UniChem Nikkaji J2.345.823C
GND UniChem MetaboLights MTBLC32682
GND UniChem Rhea 32682
GND UniChem CCDC ARGBRH
#
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
GND CA -2.182 0.083 -0.066 ETKDGv3 1
GND CB -0.831 -0.356 -0.670 ETKDGv3 2
GND CG -0.007 -1.210 0.309 ETKDGv3 3
GND CD 1.303 -1.698 -0.324 ETKDGv3 4
GND NE 2.183 -0.577 -0.661 ETKDGv3 5
GND CZ 2.879 0.239 0.299 ETKDGv3 6
GND NH1 2.931 -0.079 1.556 ETKDGv3 7
GND NH2 3.550 1.418 -0.144 ETKDGv3 8
GND C -1.979 1.017 1.099 ETKDGv3 9
GND OXT -2.361 0.620 2.377 ETKDGv3 10
GND O -1.454 2.149 0.925 ETKDGv3 11
GND N -3.018 0.726 -1.088 ETKDGv3 12
GND HA -2.716 -0.824 0.298 ETKDGv3 13
GND HB1 -1.026 -0.957 -1.586 ETKDGv3 14
GND HB2 -0.248 0.542 -0.973 ETKDGv3 15
GND HG1 -0.603 -2.099 0.609 ETKDGv3 16
GND HG2 0.215 -0.626 1.226 ETKDGv3 17
GND HD1 1.824 -2.401 0.360 ETKDGv3 18
GND HD2 1.067 -2.270 -1.248 ETKDGv3 19
GND HE 2.304 -0.351 -1.674 ETKDGv3 20
GND HH11 2.483 -0.929 1.958 ETKDGv3 21
GND HH21 4.070 2.021 0.533 ETKDGv3 22
GND HH22 3.526 1.697 -1.150 ETKDGv3 23
GND HXT -2.226 1.232 3.173 ETKDGv3 24
GND HN1 -3.927 1.027 -0.666 ETKDGv3 25
GND HN2 -3.224 0.046 -1.856 ETKDGv3 26
GND HN3 -2.532 1.560 -1.492 ETKDGv3 27
#