data_X15
#
_chem_comp.id X15
_chem_comp.name "1,3-BISPHOSPHOGLYCERIC ACID"
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C3 H8 O10 P2"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2009-12-21
_chem_comp.pdbx_modified_date 2011-06-04
_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 266.037
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code X15
_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 2X15
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site EBI
#
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
X15 OAG OAG O 0 1 N N N N N N 2.464 -7.580 -20.602 3.833 2.065 0.392 OAG X15 1
X15 PAO PAO P 0 1 N N N N N N 1.952 -9.058 -20.530 3.392 0.574 -0.023 PAO X15 2
X15 OAH OAH O 0 1 N N N N N N 3.092 -9.976 -20.170 3.453 0.433 -1.496 OAH X15 3
X15 OAF OAF O 0 1 N N N N N N 1.189 -9.490 -21.779 4.388 -0.491 0.659 OAF X15 4
X15 OAK OAK O 0 1 N N N N N N 0.648 -9.134 -19.118 1.887 0.299 0.480 OAK X15 5
X15 CAM CAM C 0 1 N N N N N N 1.065 -8.982 -17.888 1.328 -0.867 0.122 CAM X15 6
X15 OAB OAB O 0 1 N N N N N N 2.260 -8.859 -17.628 1.952 -1.656 -0.548 OAB X15 7
X15 CAL CAL C 0 1 N N R N N N -0.059 -8.723 -16.857 -0.078 -1.194 0.557 CAL X15 8
X15 OAA OAA O 0 1 N N N N N N 0.495 -8.298 -15.618 -0.403 -2.526 0.155 OAA X15 9
X15 CAI CAI C 0 1 N N N N N N -0.951 -9.922 -16.546 -1.054 -0.212 -0.094 CAI X15 10
X15 OAJ OAJ O 0 1 N N N N N N -0.189 -11.023 -16.251 -2.371 -0.447 0.407 OAJ X15 11
X15 PAN PAN P 0 1 N N N N N N -0.680 -12.433 -16.717 -3.653 0.407 -0.063 PAN X15 12
X15 OAD OAD O 0 1 N N N N N N 0.143 -13.471 -15.901 -4.982 -0.212 0.602 OAD X15 13
X15 OAE OAE O 0 1 N N N N N N -2.179 -12.556 -16.170 -3.480 1.937 0.407 OAE X15 14
X15 OAC OAC O 0 1 N N N N N N -0.485 -12.639 -18.193 -3.768 0.353 -1.537 OAC X15 15
X15 HAG HAG H 0 1 N N N N N N 2.568 -7.237 -19.722 4.731 2.300 0.120 HAG X15 16
X15 HAF HAF H 0 1 N N N N N N 0.266 -9.580 -21.572 4.400 -0.455 1.625 HAF X15 17
X15 HAL HAL H 0 1 N N N N N N -0.683 -7.955 -17.337 -0.151 -1.113 1.641 HAL X15 18
X15 HAA HAA H 0 1 N N N N N N 1.436 -8.203 -15.707 -0.359 -2.671 -0.800 HAA X15 19
X15 HAI1 HAI1 H 0 0 N N N N N N -1.589 -9.683 -15.682 -0.752 0.809 0.140 HAI1 X15 20
X15 HAI2 HAI2 H 0 0 N N N N N N -1.571 -10.143 -17.427 -1.046 -0.354 -1.175 HAI2 X15 21
X15 HAD HAD H 0 1 N N N N N N 0.311 -14.236 -16.439 -5.795 0.253 0.363 HAD X15 22
X15 HAE HAE H 0 1 N N N N N N -2.169 -12.580 -15.220 -3.399 2.048 1.364 HAE X15 23
#
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
X15 OAG PAO SING N N 1
X15 PAO OAH DOUB N N 2
X15 PAO OAF SING N N 3
X15 PAO OAK SING N N 4
X15 OAK CAM SING N N 5
X15 CAM OAB DOUB N N 6
X15 CAM CAL SING N N 7
X15 CAL OAA SING N N 8
X15 CAL CAI SING N N 9
X15 CAI OAJ SING N N 10
X15 OAJ PAN SING N N 11
X15 PAN OAD SING N N 12
X15 PAN OAE SING N N 13
X15 PAN OAC DOUB N N 14
X15 OAG HAG SING N N 15
X15 OAF HAF SING N N 16
X15 CAL HAL SING N N 17
X15 OAA HAA SING N N 18
X15 CAI HAI1 SING N N 19
X15 CAI HAI2 SING N N 20
X15 OAD HAD SING N N 21
X15 OAE HAE SING N N 22
#
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
X15 SMILES ACDLabs 10.04 O=P(O)(O)OCC(O)C(=O)OP(=O)(O)O
X15 SMILES_CANONICAL CACTVS 3.352 O[C@H](CO[P](O)(O)=O)C(=O)O[P](O)(O)=O
X15 SMILES CACTVS 3.352 O[CH](CO[P](O)(O)=O)C(=O)O[P](O)(O)=O
X15 SMILES_CANONICAL "OpenEye OEToolkits" 1.6.1 C([C@H](C(=O)OP(=O)(O)O)O)OP(=O)(O)O
X15 SMILES "OpenEye OEToolkits" 1.6.1 C(C(C(=O)OP(=O)(O)O)O)OP(=O)(O)O
X15 InChI InChI 1.03 InChI=1S/C3H8O10P2/c4-2(1-12-14(6,7)8)3(5)13-15(9,10)11/h2,4H,1H2,(H2,6,7,8)(H2,9,10,11)/t2-/m1/s1
X15 InChIKey InChI 1.03 LJQLQCAXBUHEAZ-UWTATZPHSA-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
X15 "SYSTEMATIC NAME" ACDLabs 10.04 "(2R)-2-hydroxy-1-oxopropane-1,3-diyl bis[dihydrogen (phosphate)]"
X15 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.6.1 "phosphono (2R)-2-hydroxy-3-phosphonooxy-propanoate"
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
X15 'Create component' 2009-12-21 EBI
X15 'Modify descriptor' 2011-06-04 RCSB
#
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
X15 OAG O 3.805 -1.357 1
X15 PAO P 5.104 -0.608 2
X15 OAH O 4.354 0.692 3
X15 OAF O 5.854 -1.907 4
X15 OAK O 6.404 0.142 5
X15 CAM C 7.702 -0.608 6
X15 OAB O 7.702 -2.107 7
X15 CAL C 9.002 0.142 8
X15 OAA O 9.002 1.643 9
X15 CAI C 10.301 -0.608 10
X15 OAJ O 11.600 0.142 11
X15 PAN P 12.899 -0.608 12
X15 OAD O 14.198 -1.357 13
X15 OAE O 13.649 0.692 14
X15 OAC O 12.149 -1.907 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
X15 OAG PAO SINGLE NONE 1
X15 PAO OAH DOUBLE NONE 2
X15 PAO OAF SINGLE NONE 3
X15 PAO OAK SINGLE NONE 4
X15 OAK CAM SINGLE NONE 5
X15 CAM OAB DOUBLE NONE 6
X15 CAM CAL SINGLE NONE 7
X15 CAL OAA SINGLE BEGINDASH 8
X15 CAL CAI SINGLE NONE 9
X15 CAI OAJ SINGLE NONE 10
X15 OAJ PAN SINGLE NONE 11
X15 PAN OAD SINGLE NONE 12
X15 PAN OAE SINGLE NONE 13
X15 PAN OAC DOUBLE NONE 14
#
_pdbe_chem_comp_substructure.comp_id X15
_pdbe_chem_comp_substructure.substructure_name phosphate
_pdbe_chem_comp_substructure.id F1
_pdbe_chem_comp_substructure.substructure_type fragment
_pdbe_chem_comp_substructure.substructure_smiles O=P(O)(O)O
_pdbe_chem_comp_substructure.substructure_inchis InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4)
_pdbe_chem_comp_substructure.substructure_inchikeys NBIIXXVUZAFLBC-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
X15 OAG F1 1
X15 PAO F1 1
X15 OAH F1 1
X15 OAF F1 1
X15 OAK F1 1
X15 OAJ F1 2
X15 PAN F1 2
X15 OAC F1 2
X15 OAD F1 2
X15 OAE F1 2
#
_pdbe_chem_comp_rdkit_properties.comp_id X15
_pdbe_chem_comp_rdkit_properties.exactmw 265.959
_pdbe_chem_comp_rdkit_properties.amw 266.035
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 10
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 5
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 10
_pdbe_chem_comp_rdkit_properties.NumHBD 5
_pdbe_chem_comp_rdkit_properties.NumHBA 10
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 15
_pdbe_chem_comp_rdkit_properties.NumAtoms 23
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 12
_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 94.601
_pdbe_chem_comp_rdkit_properties.tpsa 170.820
_pdbe_chem_comp_rdkit_properties.CrippenClogP -1.908
_pdbe_chem_comp_rdkit_properties.CrippenMR 42.139
_pdbe_chem_comp_rdkit_properties.chi0v 8.266
_pdbe_chem_comp_rdkit_properties.chi1v 5.698
_pdbe_chem_comp_rdkit_properties.chi2v 1.335
_pdbe_chem_comp_rdkit_properties.chi3v 1.335
_pdbe_chem_comp_rdkit_properties.chi4v 0.763
_pdbe_chem_comp_rdkit_properties.chi0n 14.477
_pdbe_chem_comp_rdkit_properties.chi1n 6.318
_pdbe_chem_comp_rdkit_properties.chi2n 0.630
_pdbe_chem_comp_rdkit_properties.chi3n 0.630
_pdbe_chem_comp_rdkit_properties.chi4n 0.282
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.310
_pdbe_chem_comp_rdkit_properties.kappa1 5.852
_pdbe_chem_comp_rdkit_properties.kappa2 5.150
_pdbe_chem_comp_rdkit_properties.kappa3 8.669
_pdbe_chem_comp_rdkit_properties.Phi 2.009
#
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
X15 UniChem PDBe X15
X15 UniChem 'KEGG LIGAND' C00236
X15 UniChem ChEBI 16001
X15 UniChem ZINC ZINC000003869887
X15 UniChem SureChEMBL SCHEMBL4360927
X15 UniChem HMDB HMDB0001270
X15 UniChem NMRShiftDB 60020842
X15 UniChem MetaboLights MTBLC16001
X15 UniChem BRENDA 106202
X15 UniChem BRENDA 15438
X15 UniChem BRENDA 182061
X15 UniChem BRENDA 192334
X15 UniChem BRENDA 2125
X15 UniChem BRENDA 5489
X15 UniChem BRENDA 7076
X15 UniChem BRENDA 562
X15 UniChem PubChem 439191
X15 UniChem ACTor 38168-82-0
X15 UniChem Nikkaji J40.060B
#
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
X15 OAG -4.795 0.770 -0.448 ETKDGv3 1
X15 PAO -3.686 -0.165 0.422 ETKDGv3 2
X15 OAH -4.245 -1.558 0.603 ETKDGv3 3
X15 OAF -3.425 0.547 1.935 ETKDGv3 4
X15 OAK -2.206 -0.242 -0.451 ETKDGv3 5
X15 CAM -1.119 -1.010 -0.026 ETKDGv3 6
X15 OAB -1.190 -1.704 1.026 ETKDGv3 7
X15 CAL 0.160 -0.971 -0.812 ETKDGv3 8
X15 OAA 0.711 -2.260 -0.900 ETKDGv3 9
X15 CAI 1.161 -0.030 -0.142 ETKDGv3 10
X15 OAJ 2.329 0.036 -0.927 ETKDGv3 11
X15 PAN 3.432 1.084 -0.157 ETKDGv3 12
X15 OAD 2.760 2.631 -0.006 ETKDGv3 13
X15 OAE 3.826 0.492 1.379 ETKDGv3 14
X15 OAC 4.690 1.172 -0.990 ETKDGv3 15
X15 HAG -4.357 1.653 -0.545 ETKDGv3 16
X15 HAF -2.870 -0.103 2.434 ETKDGv3 17
X15 HAL -0.054 -0.583 -1.835 ETKDGv3 18
X15 HAA 0.159 -2.763 -1.553 ETKDGv3 19
X15 HAI1 0.692 0.977 -0.055 ETKDGv3 20
X15 HAI2 1.392 -0.423 0.876 ETKDGv3 21
X15 HAD 2.494 2.882 -0.927 ETKDGv3 22
X15 HAE 4.141 -0.434 1.219 ETKDGv3 23
#