data_RPI
#
_chem_comp.id RPI
_chem_comp.name phospho-arginine
_chem_comp.type 'L-peptide linking'
_chem_comp.pdbx_type ATOMP
_chem_comp.formula 'C6 H15 N4 O5 P'
_chem_comp.mon_nstd_parent_comp_id ARG
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2016-01-02
_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 254.181
_chem_comp.one_letter_code R
_chem_comp.three_letter_code RPI
_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 5HBN
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site EBI
_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
RPI P P P 0 1 N N N N N N 22.184 27.498 8.357 -4.405 -0.075 -0.064 P RPI 1
RPI N N N 0 1 N N N Y Y N 25.496 26.248 15.174 4.470 -1.803 0.153 N RPI 2
RPI CA CA C 0 1 N N S Y N N 25.428 27.428 14.360 4.399 -0.449 -0.413 CA RPI 3
RPI CB CB C 0 1 N N N N N N 24.628 27.152 13.104 3.151 0.260 0.115 CB RPI 4
RPI CG CG C 0 1 N N N N N N 25.423 26.301 12.144 1.901 -0.458 -0.398 CG RPI 5
RPI CD CD C 0 1 N N N N N N 25.846 27.139 10.961 0.652 0.250 0.130 CD RPI 6
RPI NE NE N 0 1 N N N N N N 24.723 27.287 10.118 -0.544 -0.438 -0.362 NE RPI 7
RPI CZ CZ C 0 1 N N N N N N 24.909 27.203 8.739 -1.793 0.022 -0.016 CZ RPI 8
RPI NH1 NH1 N 0 1 N N N N N N 26.095 26.994 8.232 -1.912 1.070 0.750 NH1 RPI 9
RPI NH2 NH2 N 0 1 N N N N N N 23.758 27.363 7.890 -2.915 -0.623 -0.477 NH2 RPI 10
RPI O1P O1P O 0 1 N N N N N N 21.571 26.157 8.052 -4.584 1.437 -0.586 O1P RPI 11
RPI O2P O2P O 0 1 N N N N N N 21.592 28.544 7.457 -5.437 -0.936 -0.683 O2P RPI 12
RPI O3P O3P O 0 1 N N N N N N 22.033 27.820 9.814 -4.565 -0.112 1.538 O3P RPI 13
RPI C C C 0 1 N N N Y N Y 24.844 28.624 15.093 5.626 0.328 -0.010 C RPI 14
RPI O O O 0 1 N N N Y N Y 23.736 29.142 14.750 6.282 -0.028 0.940 O RPI 15
RPI OXT OXT O 0 1 N Y N Y N Y 25.506 29.138 16.028 5.990 1.417 -0.706 OXT RPI 16
RPI H H1 H 0 1 N N N Y Y N 26.026 26.442 16.000 5.251 -2.314 -0.230 H1 RPI 17
RPI H2 H2 H 0 1 N Y N Y Y N 24.571 25.966 15.430 4.517 -1.772 1.160 H2 RPI 18
RPI HA H4 H 0 1 N N N Y N N 26.448 27.697 14.050 4.350 -0.511 -1.500 H4 RPI 19
RPI H5 H5 H 0 1 N N N N N N 24.377 28.106 12.618 3.157 0.244 1.205 H5 RPI 20
RPI H6 H6 H 0 1 N N N N N N 23.702 26.623 13.374 3.144 1.293 -0.233 H6 RPI 21
RPI H7 H7 H 0 1 N N N N N N 24.802 25.463 11.796 1.895 -0.442 -1.488 H7 RPI 22
RPI H8 H8 H 0 1 N N N N N N 26.316 25.909 12.654 1.907 -1.491 -0.050 H8 RPI 23
RPI H9 H9 H 0 1 N N N N N N 26.659 26.636 10.417 0.659 0.234 1.219 H9 RPI 24
RPI H10 H10 H 0 1 N N N N N N 26.190 28.126 11.304 0.646 1.283 -0.219 H10 RPI 25
RPI H11 H11 H 0 1 N N N N N N 23.814 27.449 10.502 -0.456 -1.218 -0.932 H11 RPI 26
RPI H12 H12 H 0 1 N N N N N N 26.796 26.910 8.940 -1.120 1.526 1.075 H12 RPI 27
RPI H14 H14 H 0 1 N N N N N N 23.933 27.396 6.906 -2.827 -1.403 -1.047 H14 RPI 28
RPI H15 H15 H 0 1 N N N N N N 20.936 26.251 7.352 -3.939 2.059 -0.221 H15 RPI 29
RPI H16 H16 H 0 1 N N N N N N 21.579 28.649 9.910 -5.424 0.199 1.854 H16 RPI 30
RPI HXT H17 H 0 1 N Y N Y N Y 25.043 29.896 16.365 6.784 1.882 -0.410 H17 RPI 31
#
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
RPI O2P P DOUB N N 1
RPI NH2 P SING N N 2
RPI NH2 CZ SING N N 3
RPI O1P P SING N N 4
RPI NH1 CZ DOUB N N 5
RPI P O3P SING N N 6
RPI CZ NE SING N N 7
RPI NE CD SING N N 8
RPI CD CG SING N N 9
RPI CG CB SING N N 10
RPI CB CA SING N N 11
RPI CA C SING N N 12
RPI CA N SING N N 13
RPI O C DOUB N N 14
RPI C OXT SING N N 15
RPI N H SING N N 16
RPI N H2 SING N N 17
RPI CA HA SING N N 18
RPI CB H5 SING N N 19
RPI CB H6 SING N N 20
RPI CG H7 SING N N 21
RPI CG H8 SING N N 22
RPI CD H9 SING N N 23
RPI CD H10 SING N N 24
RPI NE H11 SING N N 25
RPI NH1 H12 SING N N 26
RPI NH2 H14 SING N N 27
RPI O1P H15 SING N N 28
RPI O3P H16 SING N N 29
RPI OXT HXT SING N N 30
#
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
RPI InChI InChI 1.03 'InChI=1S/C6H15N4O5P/c7-4(5(11)12)2-1-3-9-6(8)10-16(13,14)15/h4H,1-3,7H2,(H,11,12)(H5,8,9,10,13,14,15)/t4-/m0/s1'
RPI InChIKey InChI 1.03 CCTIOCVIZPCTGO-BYPYZUCNSA-N
RPI SMILES_CANONICAL CACTVS 3.385 'N[C@@H](CCCNC(=N)N[P](O)(O)=O)C(O)=O'
RPI SMILES CACTVS 3.385 'N[CH](CCCNC(=N)N[P](O)(O)=O)C(O)=O'
RPI SMILES_CANONICAL 'OpenEye OEToolkits' 2.0.4 '[H]/N=C(/NCCC[C@@H](C(=O)O)N)\NP(=O)(O)O'
RPI SMILES 'OpenEye OEToolkits' 2.0.4 'C(CC(C(=O)O)N)CNC(=N)NP(=O)(O)O'
#
_pdbx_chem_comp_identifier.comp_id RPI
_pdbx_chem_comp_identifier.type 'SYSTEMATIC NAME'
_pdbx_chem_comp_identifier.program 'OpenEye OEToolkits'
_pdbx_chem_comp_identifier.program_version 2.0.4
_pdbx_chem_comp_identifier.identifier '(2~{S})-2-azanyl-5-[(~{N}-phosphonocarbamimidoyl)amino]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
RPI 'Create component' 2016-01-02 EBI
RPI 'Modify name' 2016-01-02 EBI
RPI 'Initial release' 2016-10-12 RCSB
RPI 'Modify backbone' 2023-11-03 PDBE
RPI 'Modify PCM' 2024-09-27 PDBE
#
_pdbx_chem_comp_pcm.pcm_id 1
_pdbx_chem_comp_pcm.comp_id RPI
_pdbx_chem_comp_pcm.modified_residue_id ARG
_pdbx_chem_comp_pcm.type Phosphorylation
_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-0250
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession ?
#
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
RPI P P 5.104 3.518 1
RPI N N 9.002 -3.232 2
RPI CA C 10.301 -2.482 3
RPI CB C 10.301 -0.983 4
RPI CG C 9.002 -0.233 5
RPI CD C 9.002 1.268 6
RPI NE N 7.702 2.018 7
RPI CZ C 7.702 3.518 8
RPI NH1 N 9.002 4.268 9
RPI NH2 N 6.404 4.268 10
RPI O1P O 4.354 4.816 11
RPI O2P O 3.805 2.768 12
RPI O3P O 5.854 2.219 13
RPI C C 11.600 -3.232 14
RPI O O 11.600 -4.732 15
RPI OXT O 12.899 -2.482 16
RPI H12 H 9.001 5.767 17
#
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
RPI O2P P DOUBLE NONE 1
RPI NH2 P SINGLE NONE 2
RPI NH2 CZ SINGLE ENDDOWNRIGHT 3
RPI O1P P SINGLE NONE 4
RPI NH1 CZ DOUBLE NONE 5
RPI P O3P SINGLE NONE 6
RPI CZ NE SINGLE ENDDOWNRIGHT 7
RPI NE CD SINGLE NONE 8
RPI CD CG SINGLE NONE 9
RPI CG CB SINGLE NONE 10
RPI CB CA SINGLE NONE 11
RPI CA C SINGLE NONE 12
RPI CA N SINGLE BEGINWEDGE 13
RPI O C DOUBLE NONE 14
RPI C OXT SINGLE NONE 15
#
_pdbe_chem_comp_substructure.comp_id RPI
_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
RPI O F1 1
RPI C F1 1
RPI CA F1 1
RPI N F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id RPI
_pdbe_chem_comp_rdkit_properties.exactmw 254.078
_pdbe_chem_comp_rdkit_properties.amw 254.183
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 9
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 8
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 9
_pdbe_chem_comp_rdkit_properties.NumHBD 7
_pdbe_chem_comp_rdkit_properties.NumHBA 7
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 16
_pdbe_chem_comp_rdkit_properties.NumAtoms 31
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 10
_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 113.377
_pdbe_chem_comp_rdkit_properties.tpsa 168.760
_pdbe_chem_comp_rdkit_properties.CrippenClogP -1.615
_pdbe_chem_comp_rdkit_properties.CrippenMR 55.754
_pdbe_chem_comp_rdkit_properties.chi0v 8.172
_pdbe_chem_comp_rdkit_properties.chi1v 4.769
_pdbe_chem_comp_rdkit_properties.chi2v 1.222
_pdbe_chem_comp_rdkit_properties.chi3v 1.222
_pdbe_chem_comp_rdkit_properties.chi4v 0.612
_pdbe_chem_comp_rdkit_properties.chi0n 22.277
_pdbe_chem_comp_rdkit_properties.chi1n 10.235
_pdbe_chem_comp_rdkit_properties.chi2n 0.798
_pdbe_chem_comp_rdkit_properties.chi3n 0.798
_pdbe_chem_comp_rdkit_properties.chi4n 0.348
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.150
_pdbe_chem_comp_rdkit_properties.kappa1 3.422
_pdbe_chem_comp_rdkit_properties.kappa2 6.436
_pdbe_chem_comp_rdkit_properties.kappa3 8.183
_pdbe_chem_comp_rdkit_properties.Phi 1.377
#
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
RPI UniChem 'KEGG LIGAND' C05945
RPI UniChem ChEBI 18412
RPI UniChem ZINC ZINC000001530092
RPI UniChem PubChem 92150
RPI UniChem NMRShiftDB 60023632
RPI UniChem ACTor 1189-11-3
RPI UniChem Nikkaji J20.415C
RPI UniChem MetaboLights MTBLC18412
RPI UniChem BRENDA 10583
RPI UniChem BRENDA 114013
RPI UniChem BRENDA 128935
RPI UniChem BRENDA 197747
RPI UniChem BRENDA 37939
RPI UniChem BRENDA 4034
RPI UniChem BRENDA 40791
RPI UniChem BRENDA 4669
RPI UniChem BRENDA 69588
RPI UniChem BRENDA 94766
RPI UniChem 'Probes And Drugs' PD086649
#
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
RPI P 4.252 1.032 -0.402 ETKDGv3 1
RPI N -3.747 -0.750 0.294 ETKDGv3 2
RPI CA -2.605 0.060 0.722 ETKDGv3 3
RPI CB -1.624 0.282 -0.446 ETKDGv3 4
RPI CG -1.087 -1.022 -1.069 ETKDGv3 5
RPI CD -0.245 -1.877 -0.107 ETKDGv3 6
RPI NE 0.847 -1.105 0.488 ETKDGv3 7
RPI CZ 1.992 -0.611 -0.232 ETKDGv3 8
RPI NH1 2.276 -1.036 -1.426 ETKDGv3 9
RPI NH2 2.844 0.354 0.399 ETKDGv3 10
RPI O1P 5.339 -0.208 -0.784 ETKDGv3 11
RPI O2P 4.926 2.026 0.516 ETKDGv3 12
RPI O3P 3.773 1.814 -1.824 ETKDGv3 13
RPI C -3.070 1.385 1.266 ETKDGv3 14
RPI O -2.773 1.722 2.444 ETKDGv3 15
RPI OXT -3.819 2.245 0.468 ETKDGv3 16
RPI H -4.298 -0.227 -0.426 ETKDGv3 17
RPI H2 -4.374 -0.909 1.116 ETKDGv3 18
RPI HA -2.074 -0.480 1.537 ETKDGv3 19
RPI H5 -0.769 0.905 -0.100 ETKDGv3 20
RPI H6 -2.138 0.857 -1.248 ETKDGv3 21
RPI H7 -0.471 -0.755 -1.953 ETKDGv3 22
RPI H8 -1.935 -1.633 -1.446 ETKDGv3 23
RPI H9 -0.897 -2.274 0.700 ETKDGv3 24
RPI H10 0.160 -2.764 -0.638 ETKDGv3 25
RPI H11 0.768 -0.868 1.503 ETKDGv3 26
RPI H12 1.713 -1.749 -1.937 ETKDGv3 27
RPI H14 2.618 0.684 1.364 ETKDGv3 28
RPI H15 5.493 -0.681 0.072 ETKDGv3 29
RPI H16 3.060 2.440 -1.540 ETKDGv3 30
RPI HXT -4.134 3.140 0.823 ETKDGv3 31
#