data_7ID
#
_chem_comp.id 7ID
_chem_comp.name
"(2~{S})-4-[[(2~{S})-5-[[azanyl($l^{4}-azanylidene)methyl]amino]-1-$l^{1}-oxidanyl-1-oxidanylidene-pentan-2-yl]amino]-2-$l^{2}-azanyl-4-oxidanylidene-butanoic acid"
_chem_comp.type "L-peptide linking"
_chem_comp.pdbx_type ATOMP
_chem_comp.formula "C10 H19 N5 O5"
_chem_comp.mon_nstd_parent_comp_id ASP
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2021-08-11
_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 289.288
_chem_comp.one_letter_code D
_chem_comp.three_letter_code 7ID
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag Y
_chem_comp.pdbx_ideal_coordinates_details Corina
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code 7LGJ
_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
7ID CA C1 C 0 1 N N S Y N N 206.279 160.854 159.130 -3.797 0.841 -0.361 CA 7ID 1
7ID N N1 N 0 1 N N N Y Y N 206.403 162.222 159.638 -3.399 1.484 -1.620 N 7ID 2
7ID CB C2 C 0 1 N N N N N N 206.707 160.909 157.668 -2.556 0.597 0.501 CB 7ID 3
7ID CG C3 C 0 1 N N N N N N 206.165 162.141 156.911 -1.655 -0.397 -0.186 CG 7ID 4
7ID N2 N2 N 0 1 N N N N N N 207.107 163.082 156.307 -0.495 -0.766 0.393 N2 7ID 5
7ID CA2 C4 C 0 1 N N S N N N 206.715 164.309 155.586 0.381 -1.732 -0.275 CA2 7ID 6
7ID CO2 C5 C 0 1 N N N N N N 205.692 163.979 154.507 -0.065 -3.132 0.060 CO2 7ID 7
7ID O2 O1 O 0 1 N N N N N N 205.954 163.064 153.688 -1.018 -3.305 0.784 O2 7ID 8
7ID OX2 O2 O 0 1 N N N N N N 204.608 164.631 154.449 0.595 -4.186 -0.444 OX2 7ID 9
7ID CB2 C6 C 0 1 N N N N N N 207.986 164.966 155.013 1.821 -1.528 0.200 CB2 7ID 10
7ID CG2 C7 C 0 1 N N N N N N 207.873 165.977 153.855 2.317 -0.152 -0.250 CG2 7ID 11
7ID CD2 C8 C 0 1 N N N N N N 208.489 165.398 152.574 3.757 0.052 0.225 CD2 7ID 12
7ID NE2 N3 N 0 1 N N N N N N 208.304 166.271 151.420 4.231 1.369 -0.206 NE2 7ID 13
7ID CZ2 C9 C 0 1 N N N N N N 208.624 165.870 150.049 5.506 1.777 0.108 CZ2 7ID 14
7ID NH1 N4 N 0 1 N N N N N N 208.408 166.791 148.950 6.292 0.992 0.790 NH1 7ID 15
7ID NH2 N5 N 0 1 N N N N N N 209.094 164.751 149.727 5.952 3.013 -0.296 NH2 7ID 16
7ID OD1 O3 O 0 1 N N N N N N 204.997 162.324 156.862 -1.973 -0.863 -1.259 OD1 7ID 17
7ID C C10 C 0 1 N N N Y N Y 207.014 159.867 160.000 -4.755 1.738 0.380 C 7ID 18
7ID O O4 O 0 1 N N N Y N Y 207.852 159.194 159.562 -4.802 2.917 0.121 O 7ID 19
7ID HA H1 H 0 1 N N N Y N N 205.214 160.580 159.148 -4.283 -0.111 -0.576 HA 7ID 20
7ID H H2 H 0 1 N N N Y Y N 206.133 162.246 160.601 -4.192 1.597 -2.234 H 7ID 21
7ID HB2 H5 H 0 1 N N N N N N 206.341 160.002 157.164 -2.022 1.536 0.642 HB2 7ID 22
7ID H22 H7 H 0 1 N N N N N N 208.083 162.881 156.388 -0.241 -0.393 1.251 H22 7ID 23
7ID HA2 H8 H 0 1 N N N N N N 206.256 165.012 156.297 0.330 -1.583 -1.354 HA2 7ID 24
7ID HE H16 H 0 1 N N N N N N 207.940 167.190 151.573 3.646 1.953 -0.713 HE 7ID 25
7ID HH11 H17 H 0 0 N N N N N N 208.037 167.666 149.262 5.978 0.119 1.075 HH11 7ID 26
7ID HH21 H19 H 0 0 N N N N N N 209.274 164.063 150.430 5.366 3.597 -0.803 HH21 7ID 27
7ID HH22 H20 H 0 0 N N N N N N 209.288 164.548 148.767 6.851 3.301 -0.075 HH22 7ID 28
7ID OXT OXT O 0 1 N Y N Y N Y ? ? ? -5.555 1.227 1.329 OXT 7ID 29
7ID HXT HXT H 0 1 N Y N Y N Y ? ? ? -6.153 1.841 1.777 HXT 7ID 30
7ID H2 H11 H 0 1 N Y N Y Y N 207.352 162.525 159.550 -2.946 2.368 -1.447 H2 7ID 31
7ID HB3 H3 H 0 1 N N N N N N 207.806 160.932 157.628 -2.860 0.202 1.471 HB3 7ID 32
7ID HX2 H13 H 0 1 N N N N N N 204.084 164.312 153.723 0.272 -5.064 -0.200 HX2 7ID 33
7ID HBB H6 H 0 1 N N N N N N 208.635 164.150 154.661 1.856 -1.589 1.288 HBB 7ID 34
7ID HBC H15 H 0 1 N N N N N N 208.476 165.490 155.846 2.458 -2.302 -0.228 HBC 7ID 35
7ID HG2 H66 H 0 1 N N N N N N 208.405 166.900 154.127 2.281 -0.092 -1.338 HG2 7ID 36
7ID HG3 H9 H 0 1 N N N N N N 206.812 166.205 153.676 1.680 0.622 0.178 HG3 7ID 37
7ID HD2 H10 H 0 1 N N N N N N 208.015 164.428 152.362 3.792 -0.009 1.313 HD2 7ID 38
7ID HD3 H99 H 0 1 N N N N N N 209.567 165.252 152.736 4.394 -0.722 -0.203 HD3 7ID 39
#
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
7ID NH1 CZ2 DOUB N N 1
7ID NH2 CZ2 SING N N 2
7ID CZ2 NE2 SING N N 3
7ID NE2 CD2 SING N N 4
7ID CD2 CG2 SING N N 5
7ID O2 CO2 DOUB N N 6
7ID CG2 CB2 SING N N 7
7ID OX2 CO2 SING N N 8
7ID CO2 CA2 SING N N 9
7ID CB2 CA2 SING N N 10
7ID CA2 N2 SING N N 11
7ID N2 CG SING N N 12
7ID OD1 CG DOUB N N 13
7ID CG CB SING N N 14
7ID CB CA SING N N 15
7ID CA N SING N N 16
7ID CA C SING N N 17
7ID O C DOUB N N 18
7ID CA HA SING N N 19
7ID N H SING N N 20
7ID CB HB2 SING N N 21
7ID N2 H22 SING N N 22
7ID CA2 HA2 SING N N 23
7ID NE2 HE SING N N 24
7ID NH1 HH11 SING N N 25
7ID NH2 HH21 SING N N 26
7ID NH2 HH22 SING N N 27
7ID C OXT SING N N 28
7ID OXT HXT SING N N 29
7ID N H2 SING N N 30
7ID CB HB3 SING N N 31
7ID OX2 HX2 SING N N 32
7ID CB2 HBB SING N N 33
7ID CB2 HBC SING N N 34
7ID CG2 HG2 SING N N 35
7ID CG2 HG3 SING N N 36
7ID CD2 HD2 SING N N 37
7ID CD2 HD3 SING N N 38
#
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
7ID SMILES ACDLabs 12.01 O=C(NC(CCCNC(=N)N)C(=O)O)CC(N)C(=O)O
7ID InChI InChI 1.03 InChI=1S/C10H19N5O5/c11-5(8(17)18)4-7(16)15-6(9(19)20)2-1-3-14-10(12)13/h5-6H,1-4,11H2,(H,15,16)(H,17,18)(H,19,20)(H4,12,13,14)/t5-,6-/m0/s1
7ID InChIKey InChI 1.03 QCGCETFHYOEVAI-WDSKDSINSA-N
7ID SMILES_CANONICAL CACTVS 3.385 N[C@@H](CC(=O)N[C@@H](CCCNC(N)=N)C(O)=O)C(O)=O
7ID SMILES CACTVS 3.385 N[CH](CC(=O)N[CH](CCCNC(N)=N)C(O)=O)C(O)=O
7ID SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "[H]/N=C(/N)\NCCC[C@@H](C(=O)O)NC(=O)C[C@@H](C(=O)O)N"
7ID SMILES "OpenEye OEToolkits" 2.0.7 C(CC(C(=O)O)NC(=O)CC(C(=O)O)N)CNC(=N)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
7ID "SYSTEMATIC NAME" ACDLabs 12.01 L-beta-aspartyl-L-arginine
7ID "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "(2~{S})-2-[[(3~{S})-3-azanyl-4-oxidanyl-4-oxidanylidene-butanoyl]amino]-5-carbamimidamido-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
7ID 'Create component' 2021-08-11 RCSB
7ID 'Initial release' 2021-08-18 RCSB
7ID '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
7ID CA C 12.899 2.715 1
7ID N N 12.899 1.215 2
7ID CB C 11.600 3.465 3
7ID CG C 10.301 2.715 4
7ID N2 N 9.002 3.465 5
7ID CA2 C 7.702 2.715 6
7ID CO2 C 6.404 3.465 7
7ID O2 O 5.104 2.715 8
7ID OX2 O 6.404 4.965 9
7ID CB2 C 7.702 1.215 10
7ID CG2 C 6.404 0.465 11
7ID CD2 C 6.404 -1.035 12
7ID NE2 N 5.104 -1.785 13
7ID CZ2 C 5.104 -3.285 14
7ID NH1 N 3.805 -4.035 15
7ID NH2 N 6.404 -4.035 16
7ID OD1 O 10.301 1.215 17
7ID C C 14.198 3.465 18
7ID O O 15.497 2.715 19
7ID HH11 H 3.805 -5.535 20
7ID OXT O 14.198 4.965 21
#
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
7ID NH1 CZ2 DOUBLE NONE 1
7ID NH2 CZ2 SINGLE ENDDOWNRIGHT 2
7ID CZ2 NE2 SINGLE ENDDOWNRIGHT 3
7ID NE2 CD2 SINGLE NONE 4
7ID CD2 CG2 SINGLE NONE 5
7ID O2 CO2 DOUBLE NONE 6
7ID CG2 CB2 SINGLE NONE 7
7ID OX2 CO2 SINGLE NONE 8
7ID CO2 CA2 SINGLE NONE 9
7ID CA2 CB2 SINGLE BEGINWEDGE 10
7ID CA2 N2 SINGLE NONE 11
7ID N2 CG SINGLE NONE 12
7ID OD1 CG DOUBLE NONE 13
7ID CG CB SINGLE NONE 14
7ID CB CA SINGLE NONE 15
7ID CA N SINGLE BEGINWEDGE 16
7ID CA C SINGLE NONE 17
7ID O C DOUBLE NONE 18
7ID C OXT SINGLE NONE 19
#
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
7ID amide F1 fragment CC(N)=O InChI=1S/C2H5NO/c1-2(3)4/h1H3,(H2,3,4) DLFVBJFMPXGRIB-UHFFFAOYSA-N
7ID 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
7ID N2 F1 1
7ID CG F1 1
7ID OD1 F1 1
7ID CB F1 1
7ID O2 F2 1
7ID CO2 F2 1
7ID CA2 F2 1
7ID N2 F2 1
7ID O F2 2
7ID C F2 2
7ID CA F2 2
7ID N F2 2
#
_pdbe_chem_comp_rdkit_properties.comp_id 7ID
_pdbe_chem_comp_rdkit_properties.exactmw 289.139
_pdbe_chem_comp_rdkit_properties.amw 289.292
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 10
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 9
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 10
_pdbe_chem_comp_rdkit_properties.NumHBD 7
_pdbe_chem_comp_rdkit_properties.NumHBA 7
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 20
_pdbe_chem_comp_rdkit_properties.NumAtoms 39
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 10
_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 141.836
_pdbe_chem_comp_rdkit_properties.tpsa 191.620
_pdbe_chem_comp_rdkit_properties.CrippenClogP -2.379
_pdbe_chem_comp_rdkit_properties.CrippenMR 68.945
_pdbe_chem_comp_rdkit_properties.chi0v 9.277
_pdbe_chem_comp_rdkit_properties.chi1v 4.336
_pdbe_chem_comp_rdkit_properties.chi2v 1.218
_pdbe_chem_comp_rdkit_properties.chi3v 1.218
_pdbe_chem_comp_rdkit_properties.chi4v 0.572
_pdbe_chem_comp_rdkit_properties.chi0n 28.277
_pdbe_chem_comp_rdkit_properties.chi1n 13.283
_pdbe_chem_comp_rdkit_properties.chi2n 1.218
_pdbe_chem_comp_rdkit_properties.chi3n 1.218
_pdbe_chem_comp_rdkit_properties.chi4n 0.572
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -2.360
_pdbe_chem_comp_rdkit_properties.kappa1 3.845
_pdbe_chem_comp_rdkit_properties.kappa2 8.692
_pdbe_chem_comp_rdkit_properties.kappa3 7.869
_pdbe_chem_comp_rdkit_properties.Phi 1.671
#
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
7ID UniChem PDBe 7ID
7ID UniChem ChEBI 137991
7ID UniChem ChEBI 55435
7ID UniChem ZINC ZINC000050026817
7ID UniChem BRENDA 128763
7ID UniChem BRENDA 135906
7ID UniChem BRENDA 141768
7ID UniChem BRENDA 203106
7ID UniChem BRENDA 225420
7ID UniChem Rhea 137991
7ID UniChem Nikkaji J3.276.558K
7ID UniChem SureChEMBL SCHEMBL18765407
7ID UniChem PubChem 44602459
7ID UniChem PubChem 90658466
#
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
7ID CA -4.063 0.654 0.126 ETKDGv3 1
7ID N -2.983 1.645 0.137 ETKDGv3 2
7ID CB -3.654 -0.604 0.910 ETKDGv3 3
7ID CG -2.473 -1.278 0.275 ETKDGv3 4
7ID N2 -1.140 -0.923 0.671 ETKDGv3 5
7ID CA2 0.044 -1.532 0.059 ETKDGv3 6
7ID CO2 0.196 -2.940 0.563 ETKDGv3 7
7ID O2 0.312 -3.894 -0.253 ETKDGv3 8
7ID OX2 0.223 -3.192 1.932 ETKDGv3 9
7ID CB2 1.299 -0.696 0.380 ETKDGv3 10
7ID CG2 2.536 -1.180 -0.397 ETKDGv3 11
7ID CD2 3.767 -0.307 -0.116 ETKDGv3 12
7ID NE2 3.645 1.016 -0.732 ETKDGv3 13
7ID CZ2 4.639 2.047 -0.593 ETKDGv3 14
7ID NH1 5.732 1.851 0.077 ETKDGv3 15
7ID NH2 4.422 3.317 -1.208 ETKDGv3 16
7ID OD1 -2.661 -2.129 -0.637 ETKDGv3 17
7ID C -5.330 1.239 0.692 ETKDGv3 18
7ID O -5.361 1.665 1.878 ETKDGv3 19
7ID HA -4.258 0.359 -0.930 ETKDGv3 20
7ID H -2.826 1.982 1.116 ETKDGv3 21
7ID HB2 -4.505 -1.321 0.933 ETKDGv3 22
7ID H22 -1.020 -0.209 1.426 ETKDGv3 23
7ID HA2 -0.092 -1.540 -1.046 ETKDGv3 24
7ID HE 2.805 1.234 -1.316 ETKDGv3 25
7ID HH11 5.965 0.951 0.551 ETKDGv3 26
7ID HH21 3.550 3.502 -1.752 ETKDGv3 27
7ID HH22 5.132 4.078 -1.120 ETKDGv3 28
7ID OXT -6.473 1.306 -0.098 ETKDGv3 29
7ID HXT -7.334 1.696 0.266 ETKDGv3 30
7ID H2 -3.277 2.469 -0.436 ETKDGv3 31
7ID HB3 -3.411 -0.341 1.962 ETKDGv3 32
7ID HX2 0.331 -4.135 2.285 ETKDGv3 33
7ID HBB 1.506 -0.731 1.472 ETKDGv3 34
7ID HBC 1.091 0.362 0.110 ETKDGv3 35
7ID HG2 2.774 -2.222 -0.092 ETKDGv3 36
7ID HG3 2.326 -1.184 -1.489 ETKDGv3 37
7ID HD2 4.663 -0.817 -0.532 ETKDGv3 38
7ID HD3 3.901 -0.200 0.983 ETKDGv3 39
#