data_3AG
#
_chem_comp.id 3AG
_chem_comp.name 2-[METHYL-(4-METHYL-PENT-3-ENYL)-AMINO]-ETHYL-DIPHOSPHATE
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C9 H18 N O7 P2"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms "3-AZA-2,3-DIHYDROGERANYL DIPHOSPHATE"
_chem_comp.pdbx_formal_charge -3
_chem_comp.pdbx_initial_date 2002-11-06
_chem_comp.pdbx_modified_date 2020-06-17
_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 314.189
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code 3AG
_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 1N20
_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
3AG C1 C1 C 0 1 N N N N N N 41.644 45.607 45.904 3.679 2.744 -0.821 C1 3AG 1
3AG C2 C2 C 0 1 N N N N N N 41.692 44.655 47.087 4.626 2.101 0.160 C2 3AG 2
3AG C3 C3 C 0 1 N N N N N N 40.337 44.279 47.640 5.426 2.959 1.107 C3 3AG 3
3AG C4 C4 C 0 1 N N N N N N 42.821 44.157 47.640 4.753 0.798 0.190 C4 3AG 4
3AG O1 O1 O 0 1 N N N N N N 46.625 51.599 49.637 -2.609 -1.611 1.242 O1 3AG 5
3AG C5 C5 C 0 1 N N N N N N 44.235 44.439 47.202 3.858 -0.066 -0.661 C5 3AG 6
3AG C6 C6 C 0 1 N N N N N N 44.883 45.568 48.031 3.168 -1.109 0.221 C6 3AG 7
3AG N1 N1 N 0 1 N N S N N N 44.097 46.806 48.228 2.296 -1.951 -0.608 N1 3AG 8
3AG C7 C7 C 0 1 N N N N N N 44.424 47.405 49.548 1.487 -2.759 0.315 C7 3AG 9
3AG C8 C8 C 0 1 N N N N N N 45.910 47.736 49.858 0.300 -1.931 0.811 C8 3AG 10
3AG C9 C9 C 0 1 N N N N N N 44.338 47.771 47.138 3.171 -2.884 -1.329 C9 3AG 11
3AG O2 O2 O 0 1 N N N N N N 46.231 49.041 49.370 -0.541 -1.594 -0.294 O2 3AG 12
3AG P1 P1 P 0 1 N N N N N N 45.798 50.357 50.189 -1.763 -0.729 0.298 P1 3AG 13
3AG O3 O3 O 0 1 N N N N N N 44.223 50.578 49.933 -2.684 -0.202 -0.913 O3 3AG 14
3AG O4 O4 O -1 1 N N N N N N 46.074 50.126 51.747 -1.205 0.479 1.083 O4 3AG 15
3AG P2 P2 P 0 1 N N N N N N 43.530 51.827 50.666 -3.530 1.045 -0.347 P2 3AG 16
3AG O5 O5 O 0 1 N N N N N N 44.068 53.191 50.046 -2.631 2.328 -0.347 O5 3AG 17
3AG O6 O6 O -1 1 N N N N N N 43.859 51.781 52.235 -4.781 1.284 -1.258 O6 3AG 18
3AG O7 O7 O -1 1 N N N N N N 41.951 51.701 50.433 -3.999 0.736 1.116 O7 3AG 19
3AG HC11 1HC1 H 0 0 N N N N N N 42.643 45.884 45.495 2.674 2.759 -0.399 HC11 3AG 20
3AG HC12 2HC1 H 0 0 N N N N N N 40.995 45.192 45.097 4.003 3.765 -1.023 HC12 3AG 21
3AG HC13 3HC1 H 0 0 N N N N N N 41.062 46.522 46.164 3.675 2.173 -1.749 HC13 3AG 22
3AG HC31 1HC3 H 0 0 N N N N N N 40.372 43.580 48.508 6.049 2.322 1.735 HC31 3AG 23
3AG HC32 2HC3 H 0 0 N N N N N N 39.755 45.194 47.900 6.060 3.637 0.535 HC32 3AG 24
3AG HC33 3HC3 H 0 0 N N N N N N 39.688 43.864 46.833 4.748 3.537 1.735 HC33 3AG 25
3AG HC4 HC4 H 0 1 N N N N N N 42.577 43.491 48.485 5.499 0.343 0.825 HC4 3AG 26
3AG HC51 1HC5 H 0 0 N N N N N N 44.857 43.513 47.222 4.456 -0.571 -1.420 HC51 3AG 27
3AG HC52 2HC5 H 0 0 N N N N N N 44.283 44.659 46.110 3.106 0.556 -1.145 HC52 3AG 28
3AG HC61 1HC6 H 0 0 N N N N N N 45.193 45.165 49.023 2.570 -0.604 0.981 HC61 3AG 29
3AG HC62 2HC6 H 0 0 N N N N N N 45.874 45.826 47.591 3.920 -1.731 0.705 HC62 3AG 30
3AG HC71 1HC7 H 0 0 N N N N N N 43.808 48.323 49.693 1.121 -3.645 -0.203 HC71 3AG 31
3AG HC72 2HC7 H 0 0 N N N N N N 44.021 46.749 50.354 2.099 -3.061 1.164 HC72 3AG 32
3AG HC81 1HC8 H 0 0 N N N N N N 46.145 47.625 50.942 -0.269 -2.511 1.537 HC81 3AG 33
3AG HC82 2HC8 H 0 0 N N N N N N 46.603 46.958 49.460 0.665 -1.018 1.282 HC82 3AG 34
3AG HC91 1HC9 H 0 0 N N N N N N 43.745 48.703 47.286 3.733 -2.341 -2.089 HC91 3AG 35
3AG HC92 2HC9 H 0 0 N N N N N N 45.424 47.990 47.017 3.864 -3.348 -0.628 HC92 3AG 36
3AG HC93 3HC9 H 0 0 N N N N N N 44.143 47.317 46.138 2.566 -3.655 -1.807 HC93 3AG 37
#
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
3AG C1 C2 SING N N 1
3AG C1 HC11 SING N N 2
3AG C1 HC12 SING N N 3
3AG C1 HC13 SING N N 4
3AG C2 C3 SING N N 5
3AG C2 C4 DOUB N N 6
3AG C3 HC31 SING N N 7
3AG C3 HC32 SING N N 8
3AG C3 HC33 SING N N 9
3AG C4 C5 SING N N 10
3AG C4 HC4 SING N N 11
3AG O1 P1 DOUB N N 12
3AG C5 C6 SING N N 13
3AG C5 HC51 SING N N 14
3AG C5 HC52 SING N N 15
3AG C6 N1 SING N N 16
3AG C6 HC61 SING N N 17
3AG C6 HC62 SING N N 18
3AG N1 C7 SING N N 19
3AG N1 C9 SING N N 20
3AG C7 C8 SING N N 21
3AG C7 HC71 SING N N 22
3AG C7 HC72 SING N N 23
3AG C8 O2 SING N N 24
3AG C8 HC81 SING N N 25
3AG C8 HC82 SING N N 26
3AG C9 HC91 SING N N 27
3AG C9 HC92 SING N N 28
3AG C9 HC93 SING N N 29
3AG O2 P1 SING N N 30
3AG P1 O3 SING N N 31
3AG P1 O4 SING N N 32
3AG O3 P2 SING N N 33
3AG P2 O5 DOUB N N 34
3AG P2 O6 SING N N 35
3AG P2 O7 SING N N 36
#
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
3AG SMILES_CANONICAL CACTVS 3.341 CN(CCO[P]([O-])(=O)O[P]([O-])([O-])=O)CCC=C(C)C
3AG SMILES CACTVS 3.341 CN(CCO[P]([O-])(=O)O[P]([O-])([O-])=O)CCC=C(C)C
3AG SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 CC(=CCC[N@](C)CCO[P@](=O)([O-])OP(=O)([O-])[O-])C
3AG SMILES "OpenEye OEToolkits" 1.5.0 CC(=CCCN(C)CCOP(=O)([O-])OP(=O)([O-])[O-])C
3AG InChI InChI 1.03 InChI=1S/C9H21NO7P2/c1-9(2)5-4-6-10(3)7-8-16-19(14,15)17-18(11,12)13/h5H,4,6-8H2,1-3H3,(H,14,15)(H2,11,12,13)/p-3
3AG InChIKey InChI 1.03 UWHNDWYDKGVRGE-UHFFFAOYSA-K
#
_pdbx_chem_comp_identifier.comp_id 3AG
_pdbx_chem_comp_identifier.type "SYSTEMATIC NAME"
_pdbx_chem_comp_identifier.program "OpenEye OEToolkits"
_pdbx_chem_comp_identifier.program_version 1.5.0
_pdbx_chem_comp_identifier.identifier "[2-(methyl-(4-methylpent-3-enyl)amino)ethoxy-oxido-phosphoryl] 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
3AG 'Create component' 2002-11-06 RCSB
3AG 'Modify descriptor' 2011-06-04 RCSB
3AG 'Modify synonyms' 2020-06-05 PDBE
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id 3AG
_pdbx_chem_comp_synonyms.name "3-AZA-2,3-DIHYDROGERANYL DIPHOSPHATE"
_pdbx_chem_comp_synonyms.provenance ?
_pdbx_chem_comp_synonyms.type ?
#
_pdbe_chem_comp_drugbank_details.comp_id 3AG
_pdbe_chem_comp_drugbank_details.drugbank_id DB02369
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name '3-Aza-2,3-Dihydrogeranyl Diphosphate'
_pdbe_chem_comp_drugbank_details.description ?
_pdbe_chem_comp_drugbank_details.cas_number ?
_pdbe_chem_comp_drugbank_details.mechanism_of_action ?
#
loop_
_pdbe_chem_comp_synonyms.comp_id
_pdbe_chem_comp_synonyms.name
_pdbe_chem_comp_synonyms.provenance
_pdbe_chem_comp_synonyms.type
3AG '3-AZA-2,3-DIHYDROGERANYL DIPHOSPHATE' wwPDB ?
3AG '3-Aza-2,3-Dihydrogeranyl Diphosphate' DrugBank ?
#
_pdbe_chem_comp_drugbank_classification.comp_id 3AG
_pdbe_chem_comp_drugbank_classification.drugbank_id DB02369
_pdbe_chem_comp_drugbank_classification.parent 'Organic pyrophosphates'
_pdbe_chem_comp_drugbank_classification.kingdom 'Organic compounds'
_pdbe_chem_comp_drugbank_classification.class 'Organic oxoanionic compounds'
_pdbe_chem_comp_drugbank_classification.superclass 'Organic oxygen compounds'
_pdbe_chem_comp_drugbank_classification.description
'This compound belongs to the class of organic compounds known as organic pyrophosphates. These are organic compounds containing the pyrophosphate oxoanion, with the structure OP([O-])(=O)OP(O)([O-])=O.'
#
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
3AG C1 C 3.000 -0.851 1
3AG C2 C 4.299 -0.101 2
3AG C3 C 4.299 1.399 3
3AG C4 C 5.598 -0.851 4
3AG O1 O 13.941 1.198 5
3AG C5 C 6.897 -0.101 6
3AG C6 C 8.196 -0.851 7
3AG N1 N 9.495 -0.101 8
3AG C7 C 10.794 -0.851 9
3AG C8 C 12.093 -0.101 10
3AG C9 C 9.495 1.399 11
3AG O2 O 13.392 -0.851 12
3AG P1 P 14.691 -0.101 13
3AG O3 O 15.990 0.649 14
3AG O4 O 15.441 -1.399 15
3AG P2 P 17.290 -0.101 16
3AG O5 O 18.588 -0.851 17
3AG O6 O 18.040 1.198 18
3AG O7 O 16.540 -1.399 19
#
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
3AG C1 C2 SINGLE NONE 1
3AG C2 C3 SINGLE NONE 2
3AG C2 C4 DOUBLE NONE 3
3AG C4 C5 SINGLE NONE 4
3AG O1 P1 DOUBLE NONE 5
3AG C5 C6 SINGLE NONE 6
3AG C6 N1 SINGLE NONE 7
3AG N1 C7 SINGLE NONE 8
3AG N1 C9 SINGLE NONE 9
3AG C7 C8 SINGLE NONE 10
3AG C8 O2 SINGLE NONE 11
3AG O2 P1 SINGLE NONE 12
3AG P1 O3 SINGLE NONE 13
3AG P1 O4 SINGLE BEGINDASH 14
3AG O3 P2 SINGLE NONE 15
3AG P2 O5 DOUBLE NONE 16
3AG P2 O6 SINGLE NONE 17
3AG P2 O7 SINGLE NONE 18
#
_pdbe_chem_comp_substructure.comp_id 3AG
_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
3AG O2 F1 1
3AG P1 F1 1
3AG O1 F1 1
3AG O3 F1 1
3AG O4 F1 1
3AG O3 F1 2
3AG P2 F1 2
3AG O5 F1 2
3AG O6 F1 2
3AG O7 F1 2
#
_pdbe_chem_comp_rdkit_properties.comp_id 3AG
_pdbe_chem_comp_rdkit_properties.exactmw 314.057
_pdbe_chem_comp_rdkit_properties.amw 314.191
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 8
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 0
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 12
_pdbe_chem_comp_rdkit_properties.NumHBD 0
_pdbe_chem_comp_rdkit_properties.NumHBA 8
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 19
_pdbe_chem_comp_rdkit_properties.NumAtoms 37
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 10
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.778
_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 137.728
_pdbe_chem_comp_rdkit_properties.tpsa 125.020
_pdbe_chem_comp_rdkit_properties.CrippenClogP -0.395
_pdbe_chem_comp_rdkit_properties.CrippenMR 63.795
_pdbe_chem_comp_rdkit_properties.chi0v 10.488
_pdbe_chem_comp_rdkit_properties.chi1v 6.757
_pdbe_chem_comp_rdkit_properties.chi2v 2.785
_pdbe_chem_comp_rdkit_properties.chi3v 2.785
_pdbe_chem_comp_rdkit_properties.chi4v 1.701
_pdbe_chem_comp_rdkit_properties.chi0n 26.699
_pdbe_chem_comp_rdkit_properties.chi1n 12.836
_pdbe_chem_comp_rdkit_properties.chi2n 0.870
_pdbe_chem_comp_rdkit_properties.chi3n 0.870
_pdbe_chem_comp_rdkit_properties.chi4n 0.435
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.040
_pdbe_chem_comp_rdkit_properties.kappa1 4.729
_pdbe_chem_comp_rdkit_properties.kappa2 8.292
_pdbe_chem_comp_rdkit_properties.kappa3 12.726
_pdbe_chem_comp_rdkit_properties.Phi 2.064
#
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
3AG UniChem DrugBank DB02369
3AG UniChem PubChem 4469807
3AG UniChem 'Probes And Drugs' PD008005
#
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
3AG C1 -5.255 -1.061 0.422 ETKDGv3 1
3AG C2 -4.430 0.157 0.094 ETKDGv3 2
3AG C3 -5.116 1.436 -0.325 ETKDGv3 3
3AG C4 -3.086 0.073 0.184 ETKDGv3 4
3AG O1 4.270 0.637 1.759 ETKDGv3 5
3AG C5 -2.165 1.231 -0.121 ETKDGv3 6
3AG C6 -0.689 0.849 0.051 ETKDGv3 7
3AG N1 -0.314 -0.255 -0.861 ETKDGv3 8
3AG C7 0.758 -1.115 -0.310 ETKDGv3 9
3AG C8 2.100 -0.392 -0.103 ETKDGv3 10
3AG C9 -0.003 0.225 -2.220 ETKDGv3 11
3AG O2 3.008 -1.290 0.492 ETKDGv3 12
3AG P1 4.484 -0.475 0.756 ETKDGv3 13
3AG O3 5.599 -1.601 1.380 ETKDGv3 14
3AG O4 5.043 0.174 -0.705 ETKDGv3 15
3AG P2 7.135 -0.866 1.386 ETKDGv3 16
3AG O5 7.650 -0.726 -0.029 ETKDGv3 17
3AG O6 7.084 0.656 2.125 ETKDGv3 18
3AG O7 8.199 -1.851 2.254 ETKDGv3 19
3AG HC11 -5.065 -1.371 1.471 ETKDGv3 20
3AG HC12 -4.981 -1.894 -0.259 ETKDGv3 21
3AG HC13 -6.342 -0.863 0.309 ETKDGv3 22
3AG HC31 -4.792 1.722 -1.347 ETKDGv3 23
3AG HC32 -4.863 2.251 0.385 ETKDGv3 24
3AG HC33 -6.220 1.322 -0.336 ETKDGv3 25
3AG HC4 -2.644 -0.872 0.491 ETKDGv3 26
3AG HC51 -2.393 2.067 0.576 ETKDGv3 27
3AG HC52 -2.342 1.592 -1.155 ETKDGv3 28
3AG HC61 -0.056 1.748 -0.123 ETKDGv3 29
3AG HC62 -0.542 0.552 1.115 ETKDGv3 30
3AG HC71 0.422 -1.540 0.661 ETKDGv3 31
3AG HC72 0.917 -1.985 -0.984 ETKDGv3 32
3AG HC81 1.940 0.490 0.555 ETKDGv3 33
3AG HC82 2.485 -0.061 -1.092 ETKDGv3 34
3AG HC91 0.756 1.037 -2.205 ETKDGv3 35
3AG HC92 -0.923 0.609 -2.706 ETKDGv3 36
3AG HC93 0.371 -0.608 -2.854 ETKDGv3 37
#