data_DMA
#
_chem_comp.id DMA
_chem_comp.name "DIMETHYLALLYL DIPHOSPHATE"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C5 H12 O7 P2"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 1999-07-08
_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 246.092
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code DMA
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag N
_chem_comp.pdbx_ideal_coordinates_details ?
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code 1UBY
_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
DMA C1 C1 C 0 1 N N N N N N 4.737 31.264 103.084 -0.208 0.429 2.127 C1 DMA 1
DMA O1 O1 O 0 1 N N N N N N 4.703 29.962 103.681 -0.770 -0.377 1.089 O1 DMA 2
DMA C2 C2 C 0 1 N N N N N N 5.398 31.119 101.745 -0.790 0.015 3.454 C2 DMA 3
DMA C3 C3 C 0 1 N N N N N N 4.905 31.586 100.602 -0.008 -0.128 4.495 C3 DMA 4
DMA C4 C4 C 0 1 N N N N N N 3.637 32.376 100.596 -0.565 -0.667 5.787 C4 DMA 5
DMA C5 C5 C 0 1 N N N N N N 5.760 31.292 99.334 1.448 0.244 4.400 C5 DMA 6
DMA PA PA P 0 1 N N R N N N 4.575 29.715 105.278 -0.108 0.116 -0.293 PA DMA 7
DMA O1A O1A O 0 1 N N N N N N 3.463 30.681 105.909 -0.425 1.545 -0.508 O1A DMA 8
DMA O2A O2A O 0 1 N N N N N N 4.096 28.176 105.341 1.488 -0.075 -0.221 O2A DMA 9
DMA O3A O3A O 0 1 N N N N N N 5.906 30.016 106.132 -0.700 -0.754 -1.511 O3A DMA 10
DMA PB PB P 0 1 N N N N N N 7.387 29.726 105.702 0.001 -0.210 -2.854 PB DMA 11
DMA O1B O1B O 0 1 N N N N N N 8.229 28.854 106.747 1.467 -0.381 -2.750 O1B DMA 12
DMA O2B O2B O 0 1 N N N N N N 8.081 31.146 105.413 -0.546 -1.041 -4.120 O2B DMA 13
DMA O3B O3B O 0 1 N N N N N N 7.216 28.875 104.364 -0.344 1.350 -3.046 O3B DMA 14
DMA H11 1H1 H 0 1 N N N N N N 3.732 31.744 103.026 -0.441 1.477 1.939 H11 DMA 15
DMA H12 2H1 H 0 1 N N N N N N 5.224 32.029 103.731 0.872 0.294 2.146 H12 DMA 16
DMA H2 H2 H 0 1 N N N N N N 6.361 30.607 101.581 -1.851 -0.161 3.547 H2 DMA 17
DMA H41 1H4 H 0 1 N N N N N N 3.223 32.767 99.637 0.227 -0.715 6.533 H41 DMA 18
DMA H42 2H4 H 0 1 N N N N N N 2.845 31.773 101.099 -1.358 -0.009 6.143 H42 DMA 19
DMA H43 3H4 H 0 1 N N N N N N 3.752 33.230 101.303 -0.968 -1.665 5.621 H43 DMA 20
DMA H51 1H5 H 0 1 N N N N N N 5.346 31.683 98.375 1.538 1.276 4.060 H51 DMA 21
DMA H52 2H5 H 0 1 N N N N N N 6.801 31.663 99.480 1.914 0.143 5.381 H52 DMA 22
DMA H53 3H5 H 0 1 N N N N N N 5.951 30.196 99.248 1.947 -0.416 3.692 H53 DMA 23
DMA HOA2 2HOA H 0 0 N N N N N N 4.021 28.031 106.276 1.650 -1.018 -0.080 HOA2 DMA 24
DMA HOB2 2HOB H 0 0 N N N N N N 8.977 30.970 105.152 -0.103 -0.685 -4.902 HOB2 DMA 25
DMA HOB3 3HOB H 0 0 N N N N N N 8.112 28.699 104.103 -1.307 1.417 -3.110 HOB3 DMA 26
#
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
DMA C1 O1 SING N N 1
DMA C1 C2 SING N N 2
DMA C1 H11 SING N N 3
DMA C1 H12 SING N N 4
DMA O1 PA SING N N 5
DMA C2 C3 DOUB N N 6
DMA C2 H2 SING N N 7
DMA C3 C4 SING N N 8
DMA C3 C5 SING N N 9
DMA C4 H41 SING N N 10
DMA C4 H42 SING N N 11
DMA C4 H43 SING N N 12
DMA C5 H51 SING N N 13
DMA C5 H52 SING N N 14
DMA C5 H53 SING N N 15
DMA PA O1A DOUB N N 16
DMA PA O2A SING N N 17
DMA PA O3A SING N N 18
DMA O2A HOA2 SING N N 19
DMA O3A PB SING N N 20
DMA PB O1B DOUB N N 21
DMA PB O2B SING N N 22
DMA PB O3B SING N N 23
DMA O2B HOB2 SING N N 24
DMA O3B HOB3 SING N N 25
#
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
DMA SMILES ACDLabs 10.04 O=P(OP(=O)(OC/C=C(/C)C)O)(O)O
DMA SMILES_CANONICAL CACTVS 3.341 CC(C)=CCO[P@](O)(=O)O[P](O)(O)=O
DMA SMILES CACTVS 3.341 CC(C)=CCO[P](O)(=O)O[P](O)(O)=O
DMA SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 CC(=CCO[P@@](=O)(O)OP(=O)(O)O)C
DMA SMILES "OpenEye OEToolkits" 1.5.0 CC(=CCOP(=O)(O)OP(=O)(O)O)C
DMA InChI InChI 1.03 InChI=1S/C5H12O7P2/c1-5(2)3-4-11-14(9,10)12-13(6,7)8/h3H,4H2,1-2H3,(H,9,10)(H2,6,7,8)
DMA InChIKey InChI 1.03 CBIDRCWHNCKSTO-UHFFFAOYSA-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
DMA "SYSTEMATIC NAME" ACDLabs 10.04 "3-methylbut-2-en-1-yl trihydrogen diphosphate"
DMA "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "3-methylbut-2-enyl phosphono hydrogen phosphate"
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
DMA 'Create component' 1999-07-08 RCSB
DMA 'Modify descriptor' 2011-06-04 RCSB
#
_pdbe_chem_comp_drugbank_details.comp_id DMA
_pdbe_chem_comp_drugbank_details.drugbank_id DB01785
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name 'Dimethylallyl Diphosphate'
_pdbe_chem_comp_drugbank_details.description ?
_pdbe_chem_comp_drugbank_details.cas_number 358-72-5
_pdbe_chem_comp_drugbank_details.mechanism_of_action ?
#
_pdbe_chem_comp_synonyms.comp_id DMA
_pdbe_chem_comp_synonyms.name 'Dimethylallyl Diphosphate'
_pdbe_chem_comp_synonyms.provenance DrugBank
_pdbe_chem_comp_synonyms.type ?
#
_pdbe_chem_comp_drugbank_classification.comp_id DMA
_pdbe_chem_comp_drugbank_classification.drugbank_id DB01785
_pdbe_chem_comp_drugbank_classification.parent 'Isoprenoid phosphates'
_pdbe_chem_comp_drugbank_classification.kingdom 'Organic compounds'
_pdbe_chem_comp_drugbank_classification.class 'Prenol lipids'
_pdbe_chem_comp_drugbank_classification.superclass 'Lipids and lipid-like molecules'
_pdbe_chem_comp_drugbank_classification.description
'This compound belongs to the class of organic compounds known as isoprenoid phosphates. These are prenol lipids containing a phosphate group linked to an isoprene (2-methylbuta-1,3-diene) unit.'
#
loop_
_pdbe_chem_comp_drugbank_targets.comp_id
_pdbe_chem_comp_drugbank_targets.drugbank_id
_pdbe_chem_comp_drugbank_targets.name
_pdbe_chem_comp_drugbank_targets.organism
_pdbe_chem_comp_drugbank_targets.uniprot_id
_pdbe_chem_comp_drugbank_targets.pharmacologically_active
_pdbe_chem_comp_drugbank_targets.ordinal
DMA DB01785 'Farnesyl pyrophosphate synthase' Humans P14324 yes 1
DMA DB01785 'Isopentenyl-diphosphate Delta-isomerase 1' Humans Q13907 unknown 2
DMA DB01785 '4-hydroxy-3-methylbut-2-enyl diphosphate reductase' 'Escherichia coli (strain K12)' P62623 unknown 3
#
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
DMA C1 C 6.897 -0.403 1
DMA O1 O 8.196 -1.153 2
DMA C2 C 5.598 -1.153 3
DMA C3 C 4.299 -0.403 4
DMA C4 C 3.000 -1.153 5
DMA C5 C 4.299 1.097 6
DMA PA P 9.495 -0.403 7
DMA O1A O 8.745 0.896 8
DMA O2A O 10.245 -1.702 9
DMA O3A O 10.794 0.347 10
DMA PB P 12.093 -0.403 11
DMA O1B O 13.392 -1.153 12
DMA O2B O 12.843 0.896 13
DMA O3B O 11.343 -1.702 14
#
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
DMA C1 O1 SINGLE NONE 1
DMA C1 C2 SINGLE NONE 2
DMA O1 PA SINGLE NONE 3
DMA C2 C3 DOUBLE NONE 4
DMA C3 C4 SINGLE NONE 5
DMA C3 C5 SINGLE NONE 6
DMA PA O1A DOUBLE NONE 7
DMA PA O2A SINGLE BEGINWEDGE 8
DMA PA O3A SINGLE NONE 9
DMA O3A PB SINGLE NONE 10
DMA PB O1B DOUBLE NONE 11
DMA PB O2B SINGLE NONE 12
DMA PB O3B SINGLE NONE 13
#
_pdbe_chem_comp_substructure.comp_id DMA
_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
DMA O1 F1 1
DMA PA F1 1
DMA O1A F1 1
DMA O2A F1 1
DMA O3A F1 1
DMA O3A F1 2
DMA PB F1 2
DMA O1B F1 2
DMA O2B F1 2
DMA O3B F1 2
#
_pdbe_chem_comp_rdkit_properties.comp_id DMA
_pdbe_chem_comp_rdkit_properties.exactmw 246.006
_pdbe_chem_comp_rdkit_properties.amw 246.092
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 7
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 3
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 10
_pdbe_chem_comp_rdkit_properties.NumHBD 3
_pdbe_chem_comp_rdkit_properties.NumHBA 7
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 14
_pdbe_chem_comp_rdkit_properties.NumAtoms 26
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 9
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_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 1
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 98.338
_pdbe_chem_comp_rdkit_properties.tpsa 113.290
_pdbe_chem_comp_rdkit_properties.CrippenClogP 1.179
_pdbe_chem_comp_rdkit_properties.CrippenMR 48.337
_pdbe_chem_comp_rdkit_properties.chi0v 8.041
_pdbe_chem_comp_rdkit_properties.chi1v 5.586
_pdbe_chem_comp_rdkit_properties.chi2v 2.448
_pdbe_chem_comp_rdkit_properties.chi3v 2.448
_pdbe_chem_comp_rdkit_properties.chi4v 1.539
_pdbe_chem_comp_rdkit_properties.chi0n 18.252
_pdbe_chem_comp_rdkit_properties.chi1n 8.389
_pdbe_chem_comp_rdkit_properties.chi2n 0.533
_pdbe_chem_comp_rdkit_properties.chi3n 0.533
_pdbe_chem_comp_rdkit_properties.chi4n 0.269
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.000
_pdbe_chem_comp_rdkit_properties.kappa1 3.786
_pdbe_chem_comp_rdkit_properties.kappa2 5.186
_pdbe_chem_comp_rdkit_properties.kappa3 8.592
_pdbe_chem_comp_rdkit_properties.Phi 1.402
#
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
DMA UniChem DrugBank DB01785
DMA UniChem 'KEGG LIGAND' C00235
DMA UniChem ChEBI 16057
DMA UniChem ZINC ZINC000008215740
DMA UniChem SureChEMBL SCHEMBL153577
DMA UniChem HMDB HMDB0001120
DMA UniChem 'PubChem TPHARMA' 14847589
DMA UniChem NMRShiftDB 60021128
DMA UniChem ACTor 358-72-5
DMA UniChem Nikkaji J39.581A
DMA UniChem BindingDb 50516699
DMA UniChem LipidMaps LMPR01010001
DMA UniChem MetaboLights MTBLC16057
DMA UniChem BRENDA 112067
DMA UniChem BRENDA 127354
DMA UniChem BRENDA 157
DMA UniChem BRENDA 161162
DMA UniChem BRENDA 20236
DMA UniChem BRENDA 44726
DMA UniChem BRENDA 4666
DMA UniChem 'Probes And Drugs' PD008428
DMA UniChem 'EPA CompTox Dashboard' DTXSID70189331
DMA UniChem PubChem 647
#
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
DMA C1 -0.658 -1.103 -0.628 ETKDGv3 1
DMA O1 0.448 -0.310 -0.270 ETKDGv3 2
DMA C2 -1.765 -0.885 0.367 ETKDGv3 3
DMA C3 -2.433 0.281 0.504 ETKDGv3 4
DMA C4 -2.115 1.485 -0.352 ETKDGv3 5
DMA C5 -3.529 0.368 1.535 ETKDGv3 6
DMA PA 1.649 -0.478 -1.471 ETKDGv3 7
DMA O1A 2.053 -1.929 -1.611 ETKDGv3 8
DMA O2A 1.038 0.064 -2.954 ETKDGv3 9
DMA O3A 3.015 0.462 -1.086 ETKDGv3 10
DMA PB 3.467 0.094 0.515 ETKDGv3 11
DMA O1B 3.666 -1.395 0.691 ETKDGv3 12
DMA O2B 2.287 0.645 1.597 ETKDGv3 13
DMA O3B 4.923 0.884 0.859 ETKDGv3 14
DMA H11 -1.038 -0.853 -1.644 ETKDGv3 15
DMA H12 -0.380 -2.180 -0.601 ETKDGv3 16
DMA H2 -2.042 -1.729 0.995 ETKDGv3 17
DMA H41 -1.069 1.813 -0.175 ETKDGv3 18
DMA H42 -2.783 2.339 -0.116 ETKDGv3 19
DMA H43 -2.248 1.236 -1.425 ETKDGv3 20
DMA H51 -3.999 1.373 1.552 ETKDGv3 21
DMA H52 -4.317 -0.382 1.310 ETKDGv3 22
DMA H53 -3.111 0.163 2.544 ETKDGv3 23
DMA HOA2 0.744 0.993 -2.779 ETKDGv3 24
DMA HOB2 2.649 0.436 2.495 ETKDGv3 25
DMA HOB3 5.547 0.581 0.151 ETKDGv3 26
#