data_U2F
#
_chem_comp.id U2F
_chem_comp.name "URIDINE-5'-DIPHOSPHATE-2-DEOXY-2-FLUORO-ALPHA-D-GLUCOSE"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C15 H23 F N2 O16 P2"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2003-10-20
_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 568.293
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code U2F
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag N
_chem_comp.pdbx_ideal_coordinates_details "OpenEye/OEToolkits V1.4.2"
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code 1UQT
_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
U2F C1 C1 C 0 1 N N R N N N 36.379 25.672 14.627 6.957 2.761 -5.048 C1 U2F 1
U2F O1 O1 O 0 1 N N N N N N 35.007 24.869 14.537 6.982 1.513 -5.737 O1 U2F 2
U2F PB PB P 0 1 N N R N N N 34.271 24.121 15.744 6.790 0.139 -4.913 PB U2F 3
U2F O1B O1B O 0 1 N N N N N N 33.864 22.753 15.262 6.835 -1.107 -5.748 O1B U2F 4
U2F O2B O2B O 0 1 N N N N N N 35.512 23.768 16.530 7.903 0.198 -3.740 O2B U2F 5
U2F O3A O3A O 0 1 N N N N N N 33.206 24.597 16.791 5.396 0.374 -4.128 O3A U2F 6
U2F PA PA P 0 1 N N R N N N 32.010 25.602 16.518 4.636 -0.528 -3.023 PA U2F 7
U2F O1A O1A O 0 1 N N N N N N 32.540 26.905 16.243 5.422 -0.774 -1.769 O1A U2F 8
U2F O2A O2A O 0 1 N N N N N N 31.145 25.510 17.757 4.237 -1.859 -3.852 O2A U2F 9
U2F "O5'" "O5'" O 0 1 N N N N N N 31.275 25.113 15.183 3.228 0.245 -2.828 "O5'" U2F 10
U2F "C5'" "C5'" C 0 1 N N N N N N 30.558 23.901 15.258 3.242 1.544 -2.262 "C5'" U2F 11
U2F "C4'" "C4'" C 0 1 N N R N N N 29.541 24.033 14.120 1.814 2.065 -2.179 "C4'" U2F 12
U2F "O4'" "O4'" O 0 1 N N N N N N 29.072 22.750 13.718 1.855 3.410 -1.654 "O4'" U2F 13
U2F "C1'" "C1'" C 0 1 N N R N N N 27.650 22.725 13.868 1.528 4.335 -2.703 "C1'" U2F 14
U2F "C2'" "C2'" C 0 1 N N R N N N 27.339 23.649 14.994 1.551 3.545 -4.000 "C2'" U2F 15
U2F "C3'" "C3'" C 0 1 N N S N N N 28.314 24.752 14.654 1.130 2.167 -3.536 "C3'" U2F 16
U2F "O3'" "O3'" O 0 1 N N N N N N 27.779 25.605 13.673 -0.280 2.126 -3.322 "O3'" U2F 17
U2F "O2'" "O2'" O 0 1 N N N N N N 26.024 24.071 14.948 0.676 4.073 -4.975 "O2'" U2F 18
U2F N1 N1 N 0 1 N N N N N N 27.357 21.329 14.136 2.484 5.405 -2.696 N1 U2F 19
U2F "C6'" "C6'" C 0 1 N N N N N N 26.320 20.741 13.419 2.120 6.719 -3.075 "C6'" U2F 20
U2F "O6'" "O6'" O 0 1 N N N N N N 25.769 21.338 12.539 0.984 7.039 -3.432 "O6'" U2F 21
U2F N3 N3 N 0 1 N N N N N N 26.038 19.394 13.603 3.155 7.663 -3.021 N3 U2F 22
U2F "C7'" "C7'" C 0 1 N N N N N N 26.713 18.660 14.534 4.468 7.434 -2.640 "C7'" U2F 23
U2F "O7'" "O7'" O 0 1 N N N N N N 26.416 17.603 14.679 5.342 8.295 -2.609 "O7'" U2F 24
U2F "C8'" "C8'" C 0 1 N N N N N N 27.695 19.271 15.309 4.765 6.038 -2.260 "C8'" U2F 25
U2F "C9'" "C9'" C 0 1 N N N N N N 28.036 20.608 15.102 3.789 5.128 -2.306 "C9'" U2F 26
U2F C2 C2 C 0 1 N N R N N N 36.988 26.374 15.780 5.815 3.655 -5.517 C2 U2F 27
U2F F1 F1 F 0 1 N N N N N N 37.493 25.417 16.691 4.661 2.935 -5.523 F1 U2F 28
U2F C3 C3 C 0 1 N N S N N N 35.936 27.231 16.670 6.057 4.219 -6.911 C3 U2F 29
U2F O3 O3 O 0 1 N N N N N N 36.299 27.727 18.113 5.072 5.224 -7.152 O3 U2F 30
U2F C4 C4 C 0 1 N N S N N N 35.436 28.438 15.809 7.452 4.842 -6.999 C4 U2F 31
U2F O4 O4 O 0 1 N N N N N N 34.176 29.006 16.498 7.751 5.150 -8.358 O4 U2F 32
U2F C5 C5 C 0 1 N N R N N N 35.068 27.864 14.263 8.522 3.884 -6.460 C5 U2F 33
U2F C6 C6 C 0 1 N N N N N N 34.825 29.128 13.332 9.894 4.550 -6.405 C6 U2F 34
U2F O6 O6 O 0 1 N N N N N N 35.769 30.193 13.418 10.827 3.617 -5.891 O6 U2F 35
U2F O5 O5 O 0 1 N N N N N N 36.183 27.019 13.860 8.204 3.453 -5.133 O5 U2F 36
U2F H1 H1 H 0 1 N N N N N N 37.172 25.081 14.111 6.797 2.514 -3.994 H1 U2F 37
U2F "H5'1" "1H5'" H 0 0 N N N N N N 30.113 23.684 16.257 3.689 1.489 -1.265 "H5'1" U2F 38
U2F "H5'2" "2H5'" H 0 0 N N N N N N 31.189 22.983 15.214 3.853 2.197 -2.893 "H5'2" U2F 39
U2F "H4'" "H4'" H 0 1 N N N N N N 29.980 24.584 13.256 1.244 1.450 -1.474 "H4'" U2F 40
U2F "H1'" "H1'" H 0 1 N N N N N N 27.148 23.061 12.931 0.546 4.774 -2.496 "H1'" U2F 41
U2F "H2'" "H2'" H 0 1 N N N N N N 27.581 23.184 15.978 2.563 3.508 -4.422 "H2'" U2F 42
U2F "H3'" "H3'" H 0 1 N N N N N N 28.575 25.332 15.570 1.386 1.365 -4.234 "H3'" U2F 43
U2F HB HB H 0 1 N N N N N N 27.012 26.055 14.007 -0.683 2.615 -4.055 HB U2F 44
U2F HA HA H 0 1 N N N N N N 25.411 23.378 15.162 1.227 4.445 -5.686 HA U2F 45
U2F H3 H3 H 0 1 N N N N N N 25.317 18.948 13.035 2.917 8.614 -3.289 H3 U2F 46
U2F "H8'" "H8'" H 0 1 N N N N N N 28.209 18.692 16.095 5.771 5.785 -1.951 "H8'" U2F 47
U2F "H9'" "H9'" H 0 1 N N N N N N 28.833 21.082 15.698 3.986 4.097 -2.031 "H9'" U2F 48
U2F H2 H2 H 0 1 N N N N N N 37.814 27.035 15.428 5.677 4.483 -4.811 H2 U2F 49
U2F HC HC H 0 1 N N N N N N 35.048 26.569 16.798 5.916 3.448 -7.677 HC U2F 50
U2F HD HD H 0 1 N N N N N N 35.683 28.229 18.634 4.742 5.498 -6.283 HD U2F 51
U2F H4 H4 H 0 1 N N N N N N 36.227 29.221 15.750 7.466 5.785 -6.439 H4 U2F 52
U2F HE HE H 0 1 N N N N N N 33.872 29.739 15.975 7.869 4.302 -8.814 HE U2F 53
U2F H5 H5 H 0 1 N N N N N N 34.137 27.252 14.307 8.615 3.008 -7.114 H5 U2F 54
U2F H6C1 1H6C H 0 0 N N N N N N 33.799 29.527 13.510 9.858 5.421 -5.751 H6C1 U2F 55
U2F H6C2 2H6C H 0 0 N N N N N N 34.737 28.795 12.271 10.201 4.853 -7.406 H6C2 U2F 56
U2F H6 H6 H 0 1 N N N N N N 35.624 30.949 12.861 10.720 3.610 -4.924 H6 U2F 57
U2F HO1 HO1 H 0 1 N N N N N N 31.698 25.491 18.529 3.836 -2.615 -3.373 HO1 U2F 58
U2F HO2 HO2 H 0 1 N N N N N N 36.252 23.694 15.938 8.039 -0.592 -3.176 HO2 U2F 59
#
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
U2F C1 O1 SING N N 1
U2F C1 C2 SING N N 2
U2F C1 O5 SING N N 3
U2F C1 H1 SING N N 4
U2F O1 PB SING N N 5
U2F PB O1B DOUB N N 6
U2F PB O2B SING N N 7
U2F PB O3A SING N N 8
U2F O3A PA SING N N 9
U2F PA O1A DOUB N N 10
U2F PA O2A SING N N 11
U2F PA "O5'" SING N N 12
U2F "O5'" "C5'" SING N N 13
U2F "C5'" "C4'" SING N N 14
U2F "C5'" "H5'1" SING N N 15
U2F "C5'" "H5'2" SING N N 16
U2F "C4'" "O4'" SING N N 17
U2F "C4'" "C3'" SING N N 18
U2F "C4'" "H4'" SING N N 19
U2F "O4'" "C1'" SING N N 20
U2F "C1'" "C2'" SING N N 21
U2F "C1'" N1 SING N N 22
U2F "C1'" "H1'" SING N N 23
U2F "C2'" "C3'" SING N N 24
U2F "C2'" "O2'" SING N N 25
U2F "C2'" "H2'" SING N N 26
U2F "C3'" "O3'" SING N N 27
U2F "C3'" "H3'" SING N N 28
U2F "O3'" HB SING N N 29
U2F "O2'" HA SING N N 30
U2F N1 "C6'" SING N N 31
U2F N1 "C9'" SING N N 32
U2F "C6'" "O6'" DOUB N N 33
U2F "C6'" N3 SING N N 34
U2F N3 "C7'" SING N N 35
U2F N3 H3 SING N N 36
U2F "C7'" "O7'" DOUB N N 37
U2F "C7'" "C8'" SING N N 38
U2F "C8'" "C9'" DOUB N N 39
U2F "C8'" "H8'" SING N N 40
U2F "C9'" "H9'" SING N N 41
U2F C2 F1 SING N N 42
U2F C2 C3 SING N N 43
U2F C2 H2 SING N N 44
U2F C3 O3 SING N N 45
U2F C3 C4 SING N N 46
U2F C3 HC SING N N 47
U2F O3 HD SING N N 48
U2F C4 O4 SING N N 49
U2F C4 C5 SING N N 50
U2F C4 H4 SING N N 51
U2F O4 HE SING N N 52
U2F C5 C6 SING N N 53
U2F C5 O5 SING N N 54
U2F C5 H5 SING N N 55
U2F C6 O6 SING N N 56
U2F C6 H6C1 SING N N 57
U2F C6 H6C2 SING N N 58
U2F O6 H6 SING N N 59
U2F HO1 O2A SING N N 60
U2F HO2 O2B SING N N 61
#
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
U2F SMILES ACDLabs 10.04 O=P(OC1OC(C(O)C(O)C1F)CO)(O)OP(=O)(O)OCC3OC(N2C=CC(=O)NC2=O)C(O)C3O
U2F SMILES_CANONICAL CACTVS 3.341 OC[C@H]1O[C@H](O[P@](O)(=O)O[P@@](O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)N3C=CC(=O)NC3=O)[C@H](F)[C@@H](O)[C@@H]1O
U2F SMILES CACTVS 3.341 OC[CH]1O[CH](O[P](O)(=O)O[P](O)(=O)OC[CH]2O[CH]([CH](O)[CH]2O)N3C=CC(=O)NC3=O)[CH](F)[CH](O)[CH]1O
U2F SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)(O)O[P@](=O)(O)O[C@@H]3[C@@H]([C@H]([C@@H]([C@H](O3)CO)O)O)F)O)O
U2F SMILES "OpenEye OEToolkits" 1.5.0 C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)OC3C(C(C(C(O3)CO)O)O)F)O)O
U2F InChI InChI 1.03 InChI=1S/C15H23FN2O16P2/c16-8-11(23)9(21)5(3-19)32-14(8)33-36(28,29)34-35(26,27)30-4-6-10(22)12(24)13(31-6)18-2-1-7(20)17-15(18)25/h1-2,5-6,8-14,19,21-24H,3-4H2,(H,26,27)(H,28,29)(H,17,20,25)/t5-,6-,8-,9-,10-,11-,12-,13-,14-/m1/s1
U2F InChIKey InChI 1.03 NGTCPFGWXMBZEP-NQQHDEILSA-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
U2F "SYSTEMATIC NAME" ACDLabs 10.04 "[(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3R,4S,5S,6R)-3-fluoro-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl dihydrogen diphosphate (non-preferred name)"
U2F "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[[(2R,3S,4R,5R)-5-(2,4-dioxopyrimidin-1-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl] [(2R,3R,4S,5S,6R)-3-fluoro-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl] 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
U2F 'Create component' 2003-10-20 RCSB
U2F 'Modify descriptor' 2011-06-04 RCSB
#
_pdbe_chem_comp_drugbank_details.comp_id U2F
_pdbe_chem_comp_drugbank_details.drugbank_id DB03488
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name "Uridine-5'-diphosphate-2-deoxy-2-fluoro-alpha-D-galactose"
_pdbe_chem_comp_drugbank_details.description ?
_pdbe_chem_comp_drugbank_details.cas_number ?
_pdbe_chem_comp_drugbank_details.mechanism_of_action ?
#
_pdbe_chem_comp_drugbank_classification.comp_id U2F
_pdbe_chem_comp_drugbank_classification.drugbank_id DB03488
_pdbe_chem_comp_drugbank_classification.parent 'Pyrimidine nucleotide sugars'
_pdbe_chem_comp_drugbank_classification.kingdom 'Organic compounds'
_pdbe_chem_comp_drugbank_classification.class 'Pyrimidine nucleotides'
_pdbe_chem_comp_drugbank_classification.superclass 'Nucleosides, nucleotides, and analogues'
_pdbe_chem_comp_drugbank_classification.description
'This compound belongs to the class of organic compounds known as pyrimidine nucleotide sugars. These are pyrimidine nucleotides bound to a saccharide derivative through the terminal phosphate group.'
#
_pdbe_chem_comp_drugbank_targets.comp_id U2F
_pdbe_chem_comp_drugbank_targets.drugbank_id DB03488
_pdbe_chem_comp_drugbank_targets.name 'Alpha,alpha-trehalose-phosphate synthase [UDP-forming]'
_pdbe_chem_comp_drugbank_targets.organism 'Escherichia coli (strain K12)'
_pdbe_chem_comp_drugbank_targets.uniprot_id P31677
_pdbe_chem_comp_drugbank_targets.pharmacologically_active unknown
_pdbe_chem_comp_drugbank_targets.ordinal 1
#
loop_
_software.name
_software.version
_software.description
rdkit 2023.09.6 'Core functionality.'
pdbeccdutils 0.8.6 '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
U2F C1 C 7.702 -5.285 1
U2F O1 O 9.002 -4.535 2
U2F PB P 9.002 -3.035 3
U2F O1B O 10.502 -3.035 4
U2F O2B O 7.502 -3.035 5
U2F O3A O 9.002 -1.535 6
U2F PA P 10.301 -0.785 7
U2F O1A O 9.551 0.514 8
U2F O2A O 11.051 -2.084 9
U2F "O5'" O 11.600 -0.035 10
U2F "C5'" C 11.600 1.465 11
U2F "C4'" C 12.899 2.215 12
U2F "O4'" O 13.055 3.707 13
U2F "C1'" C 14.523 4.019 14
U2F "C2'" C 15.273 2.720 15
U2F "C3'" C 14.269 1.605 16
U2F "O3'" O 14.581 0.138 17
U2F "O2'" O 16.765 2.563 18
U2F N1 N 15.133 5.389 19
U2F "C6'" C 16.625 5.546 20
U2F "O6'" O 17.506 4.332 21
U2F N3 N 17.235 6.916 22
U2F "C7'" C 16.353 8.130 23
U2F "O7'" O 16.963 9.500 24
U2F "C8'" C 14.861 7.973 25
U2F "C9'" C 14.251 6.603 26
U2F C2 C 7.702 -6.785 27
U2F F1 F 9.002 -7.535 28
U2F C3 C 6.404 -7.535 29
U2F O3 O 6.404 -9.035 30
U2F C4 C 5.104 -6.785 31
U2F O4 O 3.805 -7.535 32
U2F C5 C 5.104 -5.285 33
U2F C6 C 3.805 -4.535 34
U2F O6 O 3.805 -3.035 35
U2F O5 O 6.404 -4.535 36
#
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
U2F C1 O1 SINGLE BEGINDASH 1
U2F C1 C2 SINGLE NONE 2
U2F C1 O5 SINGLE NONE 3
U2F O1 PB SINGLE NONE 4
U2F PB O1B DOUBLE NONE 5
U2F PB O2B SINGLE BEGINDASH 6
U2F PB O3A SINGLE NONE 7
U2F O3A PA SINGLE NONE 8
U2F PA O1A DOUBLE NONE 9
U2F PA O2A SINGLE BEGINDASH 10
U2F PA "O5'" SINGLE NONE 11
U2F "O5'" "C5'" SINGLE NONE 12
U2F "C4'" "C5'" SINGLE BEGINWEDGE 13
U2F "C4'" "O4'" SINGLE NONE 14
U2F "C4'" "C3'" SINGLE NONE 15
U2F "O4'" "C1'" SINGLE NONE 16
U2F "C1'" "C2'" SINGLE NONE 17
U2F "C1'" N1 SINGLE BEGINWEDGE 18
U2F "C2'" "C3'" SINGLE NONE 19
U2F "C2'" "O2'" SINGLE BEGINDASH 20
U2F "C3'" "O3'" SINGLE BEGINDASH 21
U2F N1 "C6'" SINGLE NONE 22
U2F N1 "C9'" SINGLE NONE 23
U2F "C6'" "O6'" DOUBLE NONE 24
U2F "C6'" N3 SINGLE NONE 25
U2F N3 "C7'" SINGLE NONE 26
U2F "C7'" "O7'" DOUBLE NONE 27
U2F "C7'" "C8'" SINGLE NONE 28
U2F "C8'" "C9'" DOUBLE NONE 29
U2F C2 F1 SINGLE BEGINDASH 30
U2F C2 C3 SINGLE NONE 31
U2F C3 O3 SINGLE BEGINWEDGE 32
U2F C3 C4 SINGLE NONE 33
U2F C4 O4 SINGLE BEGINDASH 34
U2F C4 C5 SINGLE NONE 35
U2F C5 C6 SINGLE BEGINWEDGE 36
U2F C5 O5 SINGLE NONE 37
U2F C6 O6 SINGLE NONE 38
#
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
U2F MurckoScaffold S1 scaffold 'O=c1ccn([C@H]2CC[C@@H](CO[PH](=O)O[PH](=O)O[C@@H]3CCCCO3)O2)c(=O)[nH]1' InChI=1S/C14H22N2O9P2/c17-11-6-7-16(14(18)15-11)12-5-4-10(23-12)9-22-26(19)25-27(20)24-13-3-1-2-8-21-13/h6-7,10,12-13,26-27H,1-5,8-9H2,(H,15,17,18)/t10-,12+,13+/m0/s1 AKKVBKIXAFLMCT-CYZMBNFOSA-N
U2F phosphate F1 fragment O=P(O)(O)O InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4) NBIIXXVUZAFLBC-UHFFFAOYSA-N
U2F pyranose F2 fragment OC1CCCCO1 InChI=1S/C5H10O2/c6-5-3-1-2-4-7-5/h5-6H,1-4H2 CELWCAITJAEQNL-UHFFFAOYSA-N
U2F pyrimidine F3 fragment c1cncnc1 InChI=1S/C4H4N2/c1-2-5-4-6-3-1/h1-4H CZPWVGJYEJSRLH-UHFFFAOYSA-N
U2F ribose F4 fragment OCC1OCC(O)C1O InChI=1S/C5H10O4/c6-1-4-5(8)3(7)2-9-4/h3-8H,1-2H2 KZVAAIRBJJYZOW-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
U2F C1 S1 1
U2F O1 S1 1
U2F PB S1 1
U2F O1B S1 1
U2F O3A S1 1
U2F PA S1 1
U2F O1A S1 1
U2F "O5'" S1 1
U2F "C5'" S1 1
U2F "C4'" S1 1
U2F "O4'" S1 1
U2F "C1'" S1 1
U2F "C2'" S1 1
U2F "C3'" S1 1
U2F N1 S1 1
U2F "C6'" S1 1
U2F "O6'" S1 1
U2F N3 S1 1
U2F "C7'" S1 1
U2F "O7'" S1 1
U2F "C8'" S1 1
U2F "C9'" S1 1
U2F C2 S1 1
U2F C3 S1 1
U2F C4 S1 1
U2F C5 S1 1
U2F O5 S1 1
U2F O1 F1 1
U2F PB F1 1
U2F O1B F1 1
U2F O2B F1 1
U2F O3A F1 1
U2F O3A F1 2
U2F PA F1 2
U2F O1A F1 2
U2F O2A F1 2
U2F "O5'" F1 2
U2F C4 F2 1
U2F C5 F2 1
U2F O5 F2 1
U2F C1 F2 1
U2F C2 F2 1
U2F C3 F2 1
U2F O1 F2 1
U2F "C8'" F3 1
U2F "C7'" F3 1
U2F N3 F3 1
U2F "C6'" F3 1
U2F N1 F3 1
U2F "C9'" F3 1
U2F "C2'" F4 1
U2F "C3'" F4 1
U2F "C4'" F4 1
U2F "O4'" F4 1
U2F "C1'" F4 1
U2F "C5'" F4 1
U2F "O5'" F4 1
U2F "O3'" F4 1
U2F "O2'" F4 1
#
_pdbe_chem_comp_rdkit_properties.comp_id U2F
_pdbe_chem_comp_rdkit_properties.exactmw 568.051
_pdbe_chem_comp_rdkit_properties.amw 568.293
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 18
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 8
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 16
_pdbe_chem_comp_rdkit_properties.NumHBD 8
_pdbe_chem_comp_rdkit_properties.NumHBA 17
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 36
_pdbe_chem_comp_rdkit_properties.NumAtoms 59
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 21
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.733
_pdbe_chem_comp_rdkit_properties.NumRings 3
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 1
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 2
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 2
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 3
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 2
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 2
_pdbe_chem_comp_rdkit_properties.NumSpiroAtoms 0
_pdbe_chem_comp_rdkit_properties.NumBridgeheadAtoms 0
_pdbe_chem_comp_rdkit_properties.NumAtomStereoCenters 11
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 231.778
_pdbe_chem_comp_rdkit_properties.tpsa 276.760
_pdbe_chem_comp_rdkit_properties.CrippenClogP -2.017
_pdbe_chem_comp_rdkit_properties.CrippenMR 107.891
_pdbe_chem_comp_rdkit_properties.chi0v 17.988
_pdbe_chem_comp_rdkit_properties.chi1v 11.092
_pdbe_chem_comp_rdkit_properties.chi2v 5.699
_pdbe_chem_comp_rdkit_properties.chi3v 5.699
_pdbe_chem_comp_rdkit_properties.chi4v 3.780
_pdbe_chem_comp_rdkit_properties.chi0n 39.199
_pdbe_chem_comp_rdkit_properties.chi1n 18.976
_pdbe_chem_comp_rdkit_properties.chi2n 3.395
_pdbe_chem_comp_rdkit_properties.chi3n 3.395
_pdbe_chem_comp_rdkit_properties.chi4n 2.018
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.410
_pdbe_chem_comp_rdkit_properties.kappa1 10.991
_pdbe_chem_comp_rdkit_properties.kappa2 11.140
_pdbe_chem_comp_rdkit_properties.kappa3 6.527
_pdbe_chem_comp_rdkit_properties.Phi 3.401
#
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
U2F UniChem ChEMBL CHEMBL593830
U2F UniChem DrugBank DB03488
U2F UniChem ZINC ZINC000016051573
U2F UniChem PubChem 448923
U2F UniChem 'Probes And Drugs' PD059736
U2F UniChem BindingDb 50304032
#
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
U2F C1 4.152 -1.177 -0.481 ETKDGv3 1
U2F O1 3.043 -1.876 0.050 ETKDGv3 2
U2F PB 1.832 -2.034 -1.145 ETKDGv3 3
U2F O1B 2.225 -3.138 -2.101 ETKDGv3 4
U2F O2B 0.390 -2.465 -0.369 ETKDGv3 5
U2F O3A 1.658 -0.572 -2.007 ETKDGv3 6
U2F PA 0.135 -0.581 -2.771 ETKDGv3 7
U2F O1A -0.092 -1.890 -3.496 ETKDGv3 8
U2F O2A 0.087 0.670 -3.911 ETKDGv3 9
U2F "O5'" -1.113 -0.348 -1.632 ETKDGv3 10
U2F "C5'" -0.810 0.798 -0.870 ETKDGv3 11
U2F "C4'" -1.936 1.078 0.131 ETKDGv3 12
U2F "O4'" -3.167 1.215 -0.538 ETKDGv3 13
U2F "C1'" -4.171 0.928 0.412 ETKDGv3 14
U2F "C2'" -3.558 0.104 1.560 ETKDGv3 15
U2F "C3'" -2.097 -0.026 1.166 ETKDGv3 16
U2F "O3'" -1.221 0.167 2.247 ETKDGv3 17
U2F "O2'" -3.730 0.745 2.803 ETKDGv3 18
U2F N1 -5.283 0.202 -0.224 ETKDGv3 19
U2F "C6'" -5.053 -0.935 -1.086 ETKDGv3 20
U2F "O6'" -3.885 -1.337 -1.330 ETKDGv3 21
U2F N3 -6.167 -1.618 -1.663 ETKDGv3 22
U2F "C7'" -7.492 -1.187 -1.348 ETKDGv3 23
U2F "O7'" -8.485 -1.778 -1.848 ETKDGv3 24
U2F "C8'" -7.689 -0.055 -0.434 ETKDGv3 25
U2F "C9'" -6.639 0.584 0.090 ETKDGv3 26
U2F C2 5.408 -1.441 0.400 ETKDGv3 27
U2F F1 5.035 -1.876 1.663 ETKDGv3 28
U2F C3 6.272 -0.173 0.535 ETKDGv3 29
U2F O3 6.836 0.146 -0.713 ETKDGv3 30
U2F C4 5.424 1.026 1.035 ETKDGv3 31
U2F O4 5.547 1.188 2.427 ETKDGv3 32
U2F C5 3.932 0.877 0.629 ETKDGv3 33
U2F C6 3.241 2.242 0.498 ETKDGv3 34
U2F O6 3.254 2.930 1.720 ETKDGv3 35
U2F O5 3.849 0.209 -0.615 ETKDGv3 36
U2F H1 4.409 -1.560 -1.496 ETKDGv3 37
U2F "H5'1" -0.712 1.693 -1.526 ETKDGv3 38
U2F "H5'2" 0.135 0.657 -0.300 ETKDGv3 39
U2F "H4'" -1.706 2.040 0.646 ETKDGv3 40
U2F "H1'" -4.541 1.904 0.800 ETKDGv3 41
U2F "H2'" -4.016 -0.908 1.625 ETKDGv3 42
U2F "H3'" -1.928 -1.026 0.702 ETKDGv3 43
U2F HB -1.260 -0.663 2.791 ETKDGv3 44
U2F HA -3.300 1.639 2.752 ETKDGv3 45
U2F H3 -6.015 -2.432 -2.300 ETKDGv3 46
U2F "H8'" -8.693 0.262 -0.181 ETKDGv3 47
U2F "H9'" -6.823 1.410 0.766 ETKDGv3 48
U2F H2 6.016 -2.253 -0.057 ETKDGv3 49
U2F HC 7.093 -0.367 1.266 ETKDGv3 50
U2F HD 7.576 -0.498 -0.868 ETKDGv3 51
U2F H4 5.838 1.946 0.566 ETKDGv3 52
U2F HE 5.219 0.358 2.860 ETKDGv3 53
U2F H5 3.374 0.305 1.408 ETKDGv3 54
U2F H6C1 2.192 2.100 0.151 ETKDGv3 55
U2F H6C2 3.761 2.857 -0.267 ETKDGv3 56
U2F H6 2.570 2.499 2.296 ETKDGv3 57
U2F HO1 0.703 1.361 -3.558 ETKDGv3 58
U2F HO2 0.380 -1.923 0.460 ETKDGv3 59
#