data_GHG
#
_chem_comp.id GHG
_chem_comp.name "(2S,4S)-2,5-diamino-4-hydroxy-5-oxopentanoic acid (non-preferred name)"
_chem_comp.type "L-PEPTIDE LINKING"
_chem_comp.pdbx_type ATOMP
_chem_comp.formula "C5 H10 N2 O4"
_chem_comp.mon_nstd_parent_comp_id GLN
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2004-01-20
_chem_comp.pdbx_modified_date 2023-11-03
_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 162.144
_chem_comp.one_letter_code Q
_chem_comp.three_letter_code GHG
_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 1RU9
_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
GHG N N N 0 1 N N N Y Y N 48.924 37.391 21.202 1.305 0.925 1.565 N GHG 1
GHG CA CA C 0 1 N N S Y N N 49.236 38.768 21.485 1.227 -0.134 0.550 CA GHG 2
GHG C C C 0 1 N N N Y N Y 48.858 39.767 20.447 2.456 -0.085 -0.321 C GHG 3
GHG O O O 0 1 N N N Y N Y 48.567 39.454 19.297 3.121 0.922 -0.372 O GHG 4
GHG CB CB C 0 1 N N N N N N 50.670 38.950 22.135 -0.018 0.078 -0.314 CB GHG 5
GHG CG CG C 0 1 N N S N N N 51.498 37.761 22.674 -1.271 -0.094 0.547 CG GHG 6
GHG OG1 OG1 O 0 1 N N N N N N 52.624 38.538 22.953 -1.353 -1.446 1.003 OG1 GHG 7
GHG CD CD C 0 1 N N N N N N 52.112 36.636 21.812 -2.493 0.234 -0.272 CD GHG 8
GHG OE1 OE1 O 0 1 N N N N N N 51.596 36.295 20.741 -3.304 -0.631 -0.524 OE1 GHG 9
GHG NE2 NE2 N 0 1 N N N N N N 53.158 35.905 22.232 -2.683 1.490 -0.725 NE2 GHG 10
GHG H H H 0 1 N N N Y Y N 49.222 36.818 21.965 2.083 0.771 2.189 H GHG 11
GHG H2 H2 H 0 1 N Y N Y Y N 47.937 37.292 21.077 1.361 1.836 1.135 H2 GHG 12
GHG HA HA H 0 1 N N N Y N N 48.525 39.047 22.276 1.168 -1.105 1.041 HA GHG 13
GHG HB2 HB2 H 0 1 N N N N N N 51.290 39.402 21.347 -0.002 1.084 -0.734 HB2 GHG 14
GHG HB3 HB3 H 0 1 N N N N N N 50.515 39.611 23.000 -0.029 -0.653 -1.122 HB3 GHG 15
GHG HG HG H 0 1 N N N N N N 50.854 37.185 23.355 -1.218 0.576 1.405 HG GHG 16
GHG HG1 HG1 H 0 1 N N N N N N 53.307 37.987 23.316 -1.404 -2.099 0.292 HG1 GHG 17
GHG HE21 HE21 H 0 0 N N N N N N 53.479 35.132 21.685 -2.033 2.181 -0.523 HE21 GHG 18
GHG HE22 HE22 H 0 0 N N N N N N 53.615 36.134 23.091 -3.469 1.701 -1.252 HE22 GHG 19
GHG OXT OXT O 0 1 N Y N Y N Y 48.764 41.189 20.568 2.812 -1.162 -1.039 OXT GHG 20
GHG HXT HXT H 0 1 N Y N Y N Y 48.499 41.561 19.735 3.608 -1.083 -1.583 HXT GHG 21
#
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
GHG N CA SING N N 1
GHG N H SING N N 2
GHG N H2 SING N N 3
GHG CA C SING N N 4
GHG CA CB SING N N 5
GHG CA HA SING N N 6
GHG C O DOUB N N 7
GHG CB CG SING N N 8
GHG CB HB2 SING N N 9
GHG CB HB3 SING N N 10
GHG CG OG1 SING N N 11
GHG CG CD SING N N 12
GHG CG HG SING N N 13
GHG OG1 HG1 SING N N 14
GHG CD OE1 DOUB N N 15
GHG CD NE2 SING N N 16
GHG NE2 HE21 SING N N 17
GHG NE2 HE22 SING N N 18
GHG C OXT SING N N 19
GHG OXT HXT SING N N 20
#
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
GHG SMILES ACDLabs 12.01 O=C(N)C(O)CC(C(=O)O)N
GHG SMILES_CANONICAL CACTVS 3.370 N[C@@H](C[C@H](O)C(N)=O)C(O)=O
GHG SMILES CACTVS 3.370 N[CH](C[CH](O)C(N)=O)C(O)=O
GHG SMILES_CANONICAL "OpenEye OEToolkits" 1.7.0 C([C@@H](C(=O)O)N)[C@@H](C(=O)N)O
GHG SMILES "OpenEye OEToolkits" 1.7.0 C(C(C(=O)O)N)C(C(=O)N)O
GHG InChI InChI 1.03 InChI=1S/C5H10N2O4/c6-2(5(10)11)1-3(8)4(7)9/h2-3,8H,1,6H2,(H2,7,9)(H,10,11)/t2-,3-/m0/s1
GHG InChIKey InChI 1.03 VTJRNXQBJNWLRA-HRFVKAFMSA-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
GHG "SYSTEMATIC NAME" ACDLabs 12.01 "(2S,4S)-2,5-diamino-4-hydroxy-5-oxopentanoic acid (non-preferred name)"
GHG "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.0 "(2S,4S)-2,5-bis(azanyl)-4-hydroxy-5-oxo-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
GHG 'Create component' 2004-01-20 RCSB
GHG 'Modify descriptor' 2011-06-04 RCSB
GHG 'Modify backbone' 2023-11-03 PDBE
#
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
GHG N N 9.002 -1.643 1
GHG CA C 9.002 -0.142 2
GHG C C 10.301 0.608 3
GHG O O 10.301 2.107 4
GHG CB C 7.702 0.608 5
GHG CG C 6.404 -0.142 6
GHG OG1 O 6.404 -1.643 7
GHG CD C 5.104 0.608 8
GHG OE1 O 3.805 -0.142 9
GHG NE2 N 5.104 2.107 10
GHG OXT O 11.600 -0.142 11
#
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
GHG CA N SINGLE BEGINWEDGE 1
GHG CA C SINGLE NONE 2
GHG CA CB SINGLE NONE 3
GHG C O DOUBLE NONE 4
GHG CB CG SINGLE NONE 5
GHG CG OG1 SINGLE BEGINDASH 6
GHG CG CD SINGLE NONE 7
GHG CD OE1 DOUBLE NONE 8
GHG CD NE2 SINGLE NONE 9
GHG C OXT 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
GHG amide F1 fragment CC(N)=O InChI=1S/C2H5NO/c1-2(3)4/h1H3,(H2,3,4) DLFVBJFMPXGRIB-UHFFFAOYSA-N
GHG peptide F2 fragment NCC=O InChI=1S/C2H5NO/c3-1-2-4/h2H,1,3H2 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
GHG NE2 F1 1
GHG CD F1 1
GHG OE1 F1 1
GHG CG F1 1
GHG O F2 1
GHG C F2 1
GHG CA F2 1
GHG N F2 1
#
_pdbe_chem_comp_rdkit_properties.comp_id GHG
_pdbe_chem_comp_rdkit_properties.exactmw 162.064
_pdbe_chem_comp_rdkit_properties.amw 162.145
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 6
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 6
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 6
_pdbe_chem_comp_rdkit_properties.NumHBD 4
_pdbe_chem_comp_rdkit_properties.NumHBA 5
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 11
_pdbe_chem_comp_rdkit_properties.NumAtoms 21
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 6
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 1
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.600
_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 2
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 77.246
_pdbe_chem_comp_rdkit_properties.tpsa 126.640
_pdbe_chem_comp_rdkit_properties.CrippenClogP -2.365
_pdbe_chem_comp_rdkit_properties.CrippenMR 35.429
_pdbe_chem_comp_rdkit_properties.chi0v 5.027
_pdbe_chem_comp_rdkit_properties.chi1v 2.264
_pdbe_chem_comp_rdkit_properties.chi2v 0.620
_pdbe_chem_comp_rdkit_properties.chi3v 0.620
_pdbe_chem_comp_rdkit_properties.chi4v 0.212
_pdbe_chem_comp_rdkit_properties.chi0n 15.027
_pdbe_chem_comp_rdkit_properties.chi1n 6.869
_pdbe_chem_comp_rdkit_properties.chi2n 0.620
_pdbe_chem_comp_rdkit_properties.chi3n 0.620
_pdbe_chem_comp_rdkit_properties.chi4n 0.212
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.140
_pdbe_chem_comp_rdkit_properties.kappa1 2.176
_pdbe_chem_comp_rdkit_properties.kappa2 3.891
_pdbe_chem_comp_rdkit_properties.kappa3 3.535
_pdbe_chem_comp_rdkit_properties.Phi 0.770
#
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
GHG UniChem PDBe GHG
GHG UniChem SureChEMBL SCHEMBL5813046
GHG UniChem PubChem 49867033
#
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
GHG N -1.955 -1.299 -0.723 ETKDGv3 1
GHG CA -1.099 -0.688 0.298 ETKDGv3 2
GHG C -1.950 -0.089 1.384 ETKDGv3 3
GHG O -2.907 0.679 1.092 ETKDGv3 4
GHG CB -0.208 0.413 -0.316 ETKDGv3 5
GHG CG 0.863 -0.131 -1.279 ETKDGv3 6
GHG OG1 1.699 -1.035 -0.604 ETKDGv3 7
GHG CD 1.682 1.007 -1.829 ETKDGv3 8
GHG OE1 1.482 1.409 -3.006 ETKDGv3 9
GHG NE2 2.661 1.659 -1.018 ETKDGv3 10
GHG H -1.363 -1.909 -1.331 ETKDGv3 11
GHG H2 -2.623 -1.952 -0.251 ETKDGv3 12
GHG HA -0.457 -1.473 0.758 ETKDGv3 13
GHG HB2 -0.851 1.143 -0.859 ETKDGv3 14
GHG HB3 0.303 0.962 0.507 ETKDGv3 15
GHG HG 0.359 -0.646 -2.129 ETKDGv3 16
GHG HG1 2.193 -1.543 -1.300 ETKDGv3 17
GHG HE21 3.218 2.454 -1.403 ETKDGv3 18
GHG HE22 2.830 1.355 -0.034 ETKDGv3 19
GHG OXT -1.662 -0.360 2.718 ETKDGv3 20
GHG HXT -2.218 0.044 3.462 ETKDGv3 21
#