data_OI3
#
_chem_comp.id OI3
_chem_comp.name
;2'-deoxyadenosine 5'-fluoro-diphosphoribose
;
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C15 H22 F N5 O13 P2"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms
;[[(2~{R},3~{R},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-fluoranyl-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{R})-3,4,5-tris(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate; [[(2R,3R,4R,5R)-5-(6-aminopurin-9-yl)-4-fluoranyl-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2R,3S,4R,5R)-3,4,5-tris(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate; 2'-deoxy-2'-fluoro-ADPR
;
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2022-09-07
_chem_comp.pdbx_modified_date 2024-03-15
_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 561.307
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code OI3
_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 8AZL
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site PDBE
#
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
OI3 "C4'" C1 C 0 1 N N R N N N 19.869 -6.555 -8.155 2.726 1.873 0.777 "C4'" OI3 1
OI3 "C1'" C2 C 0 1 N N R N N N 21.695 -5.094 -8.153 4.435 0.340 0.823 "C1'" OI3 2
OI3 C5 C3 C 0 1 Y N N N N N 22.524 -2.271 -6.083 6.635 -2.153 -0.678 C5 OI3 3
OI3 C6 C4 C 0 1 Y N N N N N 22.400 -0.880 -5.904 7.707 -3.048 -0.523 C6 OI3 4
OI3 "C2'" C5 C 0 1 N N R N N N 22.256 -6.270 -8.111 5.156 1.707 0.844 "C2'" OI3 5
OI3 C3D C6 C 0 1 N N S N N N 18.585 -10.718 0.409 -7.596 -2.022 -0.164 C3D OI3 6
OI3 C4D C7 C 0 1 N N R N N N 19.184 -10.886 -0.734 -6.241 -1.442 0.286 C4D OI3 7
OI3 C5D C8 C 0 1 N N N N N N 18.251 -10.684 -1.884 -5.596 -0.672 -0.868 C5D OI3 8
OI3 "C5'" C9 C 0 1 N N N N N N 19.342 -7.349 -6.916 1.669 2.522 -0.118 "C5'" OI3 9
OI3 C8 C10 C 0 1 Y N N N N N 22.900 -4.417 -6.084 4.975 -0.906 -1.304 C8 OI3 10
OI3 C2 C11 C 0 1 Y N N N N N 21.145 -0.748 -7.805 7.881 -2.403 1.687 C2 OI3 11
OI3 C4 C12 C 0 1 Y N N N N N 21.916 -2.834 -7.181 6.236 -1.396 0.437 C4 OI3 12
OI3 "C3'" C13 C 0 1 N N R N N N 21.189 -7.178 -8.680 4.005 2.738 0.813 "C3'" OI3 13
OI3 C1D C14 C 0 1 N N R N N N 20.517 -9.295 0.367 -7.715 -1.006 2.017 C1D OI3 14
OI3 C2D C15 C 0 1 N N R N N N 19.031 -9.294 0.861 -8.618 -1.407 0.823 C2D OI3 15
OI3 F1 F1 F 0 1 N N N N N N 23.398 -6.367 -9.022 5.908 1.846 2.014 F1 OI3 16
OI3 N9 N1 N 0 1 Y N N N N N 22.176 -4.155 -7.161 5.188 -0.620 0.012 N9 OI3 17
OI3 N7 N2 N 0 1 Y N N N N N 23.114 -3.283 -5.425 5.828 -1.802 -1.708 N7 OI3 18
OI3 N6 N3 N 0 1 N N N N N N 23.002 -0.208 -4.774 8.145 -3.819 -1.585 N6 OI3 19
OI3 N1 N4 N 0 1 Y N N N N N 21.709 -0.157 -6.758 8.291 -3.136 0.668 N1 OI3 20
OI3 N3 N5 N 0 1 Y N N N N N 21.227 -2.051 -8.017 6.881 -1.553 1.588 N3 OI3 21
OI3 O3D O1 O 0 1 N N N N N N 19.119 -11.755 1.331 -7.591 -3.447 -0.056 O3D OI3 22
OI3 O5D O2 O 0 1 N N N N N N 18.922 -11.132 -3.027 -4.291 -0.238 -0.481 O5D OI3 23
OI3 O1B O3 O 0 1 N N N N N N 17.138 -10.433 -4.737 -4.027 1.818 -1.921 O1B OI3 24
OI3 O2B O4 O 0 1 N N N N N N 19.417 -11.096 -5.518 -2.913 -0.301 -2.719 O2B OI3 25
OI3 O3A O5 O 0 1 N N N N N N 19.044 -8.812 -4.313 -1.994 1.032 -0.648 O3A OI3 26
OI3 O1A O6 O 0 1 N N N N N N 20.587 -6.783 -4.182 -0.551 2.274 -2.304 O1A OI3 27
OI3 O2A O7 O 0 1 N N N N N N 21.638 -9.066 -4.368 -1.428 3.580 -0.331 O2A OI3 28
OI3 "O5'" O8 O 0 1 N N N N N N 20.424 -8.058 -6.394 0.456 1.769 -0.046 "O5'" OI3 29
OI3 "O4'" O9 O 0 1 N N N N N N 20.139 -5.345 -7.819 3.151 0.610 0.220 "O4'" OI3 30
OI3 "O3'" O10 O 0 1 N N N N N N 21.201 -7.103 -10.049 4.029 3.549 1.990 "O3'" OI3 31
OI3 O4D O11 O 0 1 N N N N N N 20.414 -9.767 -0.826 -6.500 -0.551 1.383 O4D OI3 32
OI3 O1D O12 O 0 1 N N N N N N 21.001 -7.968 0.309 -8.315 0.050 2.770 O1D OI3 33
OI3 O2D O13 O 0 1 N N N N N N 18.981 -9.116 2.178 -9.589 -2.376 1.221 O2D OI3 34
OI3 PB P1 P 0 1 N N N N N N 18.615 -10.387 -4.466 -3.322 0.604 -1.452 PB OI3 35
OI3 PA P2 P 0 1 N N N N N N 20.486 -8.174 -4.775 -0.872 2.166 -0.864 PA OI3 36
OI3 "H'4" H1 H 0 1 N N N N N N 19.113 -6.614 -8.952 2.335 1.732 1.785 "H'4" OI3 37
OI3 "H'1" H2 H 0 1 N N N N N N 21.754 -4.642 -9.154 4.309 -0.037 1.837 "H'1" OI3 38
OI3 "H'2" H3 H 0 1 N N N N N N 22.532 -6.594 -7.096 5.791 1.817 -0.035 "H'2" OI3 39
OI3 "HR'3" H4 H 0 0 N N N N N N 17.488 -10.768 0.353 -7.821 -1.717 -1.186 "HR'3" OI3 40
OI3 "HR'4" H5 H 0 0 N N N N N N 19.646 -11.881 -0.816 -5.581 -2.248 0.608 "HR'4" OI3 41
OI3 H5R1 H7 H 0 0 N N N N N N 17.330 -11.266 -1.732 -5.518 -1.321 -1.740 H5R1 OI3 42
OI3 H5R2 H8 H 0 0 N N N N N N 17.999 -9.618 -1.985 -6.209 0.195 -1.114 H5R2 OI3 43
OI3 "H5'1" H9 H 0 0 N N N N N N 18.947 -6.653 -6.161 1.484 3.542 0.219 "H5'1" OI3 44
OI3 "H5'2" H10 H 0 0 N N N N N N 18.548 -8.045 -7.224 2.026 2.538 -1.148 "H5'2" OI3 45
OI3 H8 H11 H 0 1 N N N N N N 23.258 -5.392 -5.789 4.213 -0.454 -1.921 H8 OI3 46
OI3 H2 H12 H 0 1 N N N N N N 20.598 -0.141 -8.511 8.384 -2.506 2.637 H2 OI3 47
OI3 "H'3" H13 H 0 1 N N N N N N 21.305 -8.204 -8.302 4.072 3.358 -0.081 "H'3" OI3 48
OI3 "HR'2" H14 H 0 0 N N N N N N 18.461 -8.537 0.303 -9.099 -0.531 0.388 "HR'2" OI3 49
OI3 H61 H15 H 0 1 N N N N N N 22.789 0.768 -4.814 7.711 -3.745 -2.449 H61 OI3 50
OI3 H62 H16 H 0 1 N N N N N N 22.640 -0.594 -3.925 8.886 -4.433 -1.465 H62 OI3 51
OI3 HOR3 H17 H 0 0 N N N N N N 18.705 -11.667 2.182 -8.420 -3.864 -0.326 HOR3 OI3 52
OI3 HOB2 H18 H 0 0 N N N N N N 18.832 -11.452 -6.177 -2.446 -1.115 -2.487 HOB2 OI3 53
OI3 HOA2 H19 H 0 0 N N N N N N 22.229 -8.583 -3.802 -1.660 3.583 0.608 HOA2 OI3 54
OI3 "HO'3" H20 H 0 0 N N N N N N 22.006 -7.482 -10.380 4.811 4.113 2.063 "HO'3" OI3 55
OI3 HOR1 H22 H 0 0 N N N N N N 21.902 -7.972 0.009 -7.791 0.340 3.529 HOR1 OI3 56
OI3 HOR2 H23 H 0 0 N N N N N N 19.263 -8.234 2.390 -10.252 -2.038 1.839 HOR2 OI3 57
OI3 "HR'1" H6 H 0 0 N N N N N N 21.125 -9.918 1.040 -7.516 -1.867 2.655 "HR'1" OI3 58
#
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
OI3 "C4'" "C5'" SING N N 1
OI3 "C4'" "C3'" SING N N 2
OI3 "C4'" "O4'" SING N N 3
OI3 "C1'" "C2'" SING N N 4
OI3 "C1'" N9 SING N N 5
OI3 "C1'" "O4'" SING N N 6
OI3 C5 C6 DOUB Y N 7
OI3 C5 C4 SING Y N 8
OI3 C5 N7 SING Y N 9
OI3 C6 N6 SING N N 10
OI3 C6 N1 SING Y N 11
OI3 "C2'" "C3'" SING N N 12
OI3 "C2'" F1 SING N N 13
OI3 C3D C4D SING N N 14
OI3 C3D C2D SING N N 15
OI3 C3D O3D SING N N 16
OI3 C4D C5D SING N N 17
OI3 C5D O5D SING N N 18
OI3 "C5'" "O5'" SING N N 19
OI3 C8 N9 SING Y N 20
OI3 C8 N7 DOUB Y N 21
OI3 C2 N1 DOUB Y N 22
OI3 C2 N3 SING Y N 23
OI3 C4 N9 SING Y N 24
OI3 C4 N3 DOUB Y N 25
OI3 "C3'" "O3'" SING N N 26
OI3 C1D C2D SING N N 27
OI3 C1D O4D SING N N 28
OI3 C1D O1D SING N N 29
OI3 C2D O2D SING N N 30
OI3 O5D PB SING N N 31
OI3 O1B PB DOUB N N 32
OI3 O2B PB SING N N 33
OI3 O3A PB SING N N 34
OI3 O3A PA SING N N 35
OI3 O1A PA DOUB N N 36
OI3 O2A PA SING N N 37
OI3 "O5'" PA SING N N 38
OI3 "C4'" "H'4" SING N N 39
OI3 "C1'" "H'1" SING N N 40
OI3 "C2'" "H'2" SING N N 41
OI3 C3D "HR'3" SING N N 42
OI3 C4D "HR'4" SING N N 43
OI3 C5D H5R1 SING N N 44
OI3 C5D H5R2 SING N N 45
OI3 "C5'" "H5'1" SING N N 46
OI3 "C5'" "H5'2" SING N N 47
OI3 C8 H8 SING N N 48
OI3 C2 H2 SING N N 49
OI3 "C3'" "H'3" SING N N 50
OI3 C2D "HR'2" SING N N 51
OI3 N6 H61 SING N N 52
OI3 N6 H62 SING N N 53
OI3 O3D HOR3 SING N N 54
OI3 O2B HOB2 SING N N 55
OI3 O2A HOA2 SING N N 56
OI3 "O3'" "HO'3" SING N N 57
OI3 O1D HOR1 SING N N 58
OI3 O2D HOR2 SING N N 59
OI3 C4D O4D SING N N 60
OI3 C1D "HR'1" 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
OI3 InChI InChI 1.06 "InChI=1S/C15H22FN5O13P2/c16-7-9(22)5(32-14(7)21-4-20-8-12(17)18-3-19-13(8)21)1-30-35(26,27)34-36(28,29)31-2-6-10(23)11(24)15(25)33-6/h3-7,9-11,14-15,22-25H,1-2H2,(H,26,27)(H,28,29)(H2,17,18,19)/t5-,6-,7-,9-,10-,11-,14-,15-/m1/s1"
OI3 InChIKey InChI 1.06 DGMUNKKEZYJBEL-IUNVFAKASA-N
OI3 SMILES_CANONICAL CACTVS 3.385 "Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)OC[C@H]4O[C@@H](O)[C@H](O)[C@@H]4O)[C@@H](O)[C@H]3F"
OI3 SMILES CACTVS 3.385 "Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]4O[CH](O)[CH](O)[CH]4O)[CH](O)[CH]3F"
OI3 SMILES_CANONICAL "OpenEye OEToolkits" 3.1.0.0 "c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)OP(=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)O)O)O)O)F)N"
OI3 SMILES "OpenEye OEToolkits" 3.1.0.0 "c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)O)O)O)O)F)N"
#
_pdbx_chem_comp_identifier.comp_id OI3
_pdbx_chem_comp_identifier.type "SYSTEMATIC NAME"
_pdbx_chem_comp_identifier.program "OpenEye OEToolkits"
_pdbx_chem_comp_identifier.program_version 3.1.0.0
_pdbx_chem_comp_identifier.identifier
"[[(2~{R},3~{R},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-fluoranyl-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{R})-3,4,5-tris(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate"
#
loop_
_pdbx_chem_comp_synonyms.ordinal
_pdbx_chem_comp_synonyms.comp_id
_pdbx_chem_comp_synonyms.name
_pdbx_chem_comp_synonyms.provenance
_pdbx_chem_comp_synonyms.type
1 OI3 "[[(2~{R},3~{R},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-fluoranyl-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{R})-3,4,5-tris(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate" PDB ?
2 OI3 "[[(2R,3R,4R,5R)-5-(6-aminopurin-9-yl)-4-fluoranyl-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2R,3S,4R,5R)-3,4,5-tris(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate" PDB ?
3 OI3 "2'-deoxy-2'-fluoro-ADPR" AUTHOR ?
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
OI3 'Create component' 2022-09-08 PDBE
OI3 'Initial release' 2024-03-20 RCSB
#
loop_
_pdbe_chem_comp_synonyms.comp_id
_pdbe_chem_comp_synonyms.name
_pdbe_chem_comp_synonyms.provenance
_pdbe_chem_comp_synonyms.type
OI3 '[[(2~{R},3~{R},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-fluoranyl-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{R})-3,4,5-tris(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate' wwPDB ?
OI3 '[[(2R,3R,4R,5R)-5-(6-aminopurin-9-yl)-4-fluoranyl-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2R,3S,4R,5R)-3,4,5-tris(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate' wwPDB ?
OI3 "2'-deoxy-2'-fluoro-ADPR" wwPDB ?
#
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
OI3 "C4'" C 6.475 0.800 1
OI3 "C1'" C 6.728 3.214 2
OI3 C5 C 7.598 6.988 3
OI3 C6 C 7.136 8.415 4
OI3 "C2'" C 5.261 2.902 5
OI3 C3D C 13.892 -8.350 6
OI3 C4D C 13.429 -6.923 7
OI3 C5D C 12.002 -6.460 8
OI3 "C5'" C 6.787 -0.667 9
OI3 C8 C 8.797 4.893 10
OI3 C2 C 4.664 7.616 11
OI3 C4 C 6.592 5.875 12
OI3 "C3'" C 5.104 1.410 13
OI3 C1D C 15.856 -6.923 14
OI3 C2D C 15.392 -8.350 15
OI3 F1 F 4.146 3.905 16
OI3 N9 N 7.339 4.584 17
OI3 N7 N 8.957 6.375 18
OI3 N6 N 8.142 9.528 19
OI3 N1 N 5.670 8.729 20
OI3 N3 N 5.125 6.189 21
OI3 O3D O 13.010 -9.563 22
OI3 O5D O 11.690 -4.992 23
OI3 O1B O 10.727 -3.102 24
OI3 O2B O 9.800 -5.955 25
OI3 O3A O 8.837 -4.066 26
OI3 O1A O 7.058 -2.910 27
OI3 O2A O 9.992 -2.286 28
OI3 "O5'" O 8.213 -1.131 29
OI3 "O4'" O 7.478 1.914 30
OI3 "O3'" O 3.805 0.660 31
OI3 O4D O 14.642 -6.042 32
OI3 O1D O 17.282 -6.460 33
OI3 O2D O 16.274 -9.563 34
OI3 PB P 10.264 -4.529 35
OI3 PA P 8.525 -2.598 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
OI3 "C4'" "C5'" SINGLE BEGINDASH 1
OI3 "C4'" "C3'" SINGLE NONE 2
OI3 "C4'" "O4'" SINGLE NONE 3
OI3 "C1'" "C2'" SINGLE NONE 4
OI3 "C1'" N9 SINGLE BEGINDASH 5
OI3 "C1'" "O4'" SINGLE NONE 6
OI3 C5 C6 DOUBLE NONE 7
OI3 C5 C4 SINGLE NONE 8
OI3 C5 N7 SINGLE NONE 9
OI3 C6 N6 SINGLE NONE 10
OI3 C6 N1 SINGLE NONE 11
OI3 "C2'" "C3'" SINGLE NONE 12
OI3 "C2'" F1 SINGLE BEGINWEDGE 13
OI3 C3D C4D SINGLE NONE 14
OI3 C3D C2D SINGLE NONE 15
OI3 C3D O3D SINGLE BEGINDASH 16
OI3 C4D C5D SINGLE BEGINWEDGE 17
OI3 C5D O5D SINGLE NONE 18
OI3 "C5'" "O5'" SINGLE NONE 19
OI3 C8 N9 SINGLE NONE 20
OI3 C8 N7 DOUBLE NONE 21
OI3 C2 N1 DOUBLE NONE 22
OI3 C2 N3 SINGLE NONE 23
OI3 C4 N9 SINGLE NONE 24
OI3 C4 N3 DOUBLE NONE 25
OI3 "C3'" "O3'" SINGLE BEGINWEDGE 26
OI3 C1D C2D SINGLE NONE 27
OI3 C1D O4D SINGLE NONE 28
OI3 C1D O1D SINGLE BEGINWEDGE 29
OI3 C2D O2D SINGLE BEGINDASH 30
OI3 O5D PB SINGLE NONE 31
OI3 O1B PB DOUBLE NONE 32
OI3 PB O2B SINGLE BEGINWEDGE 33
OI3 O3A PB SINGLE NONE 34
OI3 O3A PA SINGLE NONE 35
OI3 O1A PA DOUBLE NONE 36
OI3 PA O2A SINGLE BEGINWEDGE 37
OI3 "O5'" PA SINGLE NONE 38
OI3 C4D O4D SINGLE NONE 39
#
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
OI3 MurckoScaffold S1 scaffold 'O=[PH](OC[C@@H]1CCCO1)O[PH](=O)OC[C@@H]1CC[C@H](n2cnc3cncnc32)O1' InChI=1S/C15H22N4O7P2/c20-27(23-7-11-2-1-5-22-11)26-28(21)24-8-12-3-4-14(25-12)19-10-18-13-6-16-9-17-15(13)19/h6,9-12,14,27-28H,1-5,7-8H2/t11-,12-,14+/m0/s1 UJUHCPFOMLEXIT-SGMGOOAPSA-N
OI3 adenine F1 fragment 'Nc1ncnc2nc[nH]c12' InChI=1S/C5H5N5/c6-4-3-5(9-1-7-3)10-2-8-4/h1-2H,(H3,6,7,8,9,10) GFFGJBXGBJISGV-UHFFFAOYSA-N
OI3 furanose F2 fragment OC1CCCO1 InChI=1S/C4H8O2/c5-4-2-1-3-6-4/h4-5H,1-3H2 JNODDICFTDYODH-UHFFFAOYSA-N
OI3 imidazole F3 fragment 'c1c[nH]cn1' InChI=1S/C3H4N2/c1-2-5-3-4-1/h1-3H,(H,4,5) RAXXELZNTBOGNW-UHFFFAOYSA-N
OI3 phosphate F4 fragment O=P(O)(O)O InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4) NBIIXXVUZAFLBC-UHFFFAOYSA-N
OI3 purine F5 fragment 'c1ncc2[nH]cnc2n1' InChI=1S/C5H4N4/c1-4-5(8-2-6-1)9-3-7-4/h1-3H,(H,6,7,8,9) KDCGOANMDULRCW-UHFFFAOYSA-N
OI3 pyrimidine F6 fragment c1cncnc1 InChI=1S/C4H4N2/c1-2-5-4-6-3-1/h1-4H CZPWVGJYEJSRLH-UHFFFAOYSA-N
OI3 ribose F7 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
OI3 "C4'" S1 1
OI3 "C1'" S1 1
OI3 C5 S1 1
OI3 C6 S1 1
OI3 "C2'" S1 1
OI3 C3D S1 1
OI3 C4D S1 1
OI3 C5D S1 1
OI3 "C5'" S1 1
OI3 C8 S1 1
OI3 C2 S1 1
OI3 C4 S1 1
OI3 "C3'" S1 1
OI3 C1D S1 1
OI3 C2D S1 1
OI3 N9 S1 1
OI3 N7 S1 1
OI3 N1 S1 1
OI3 N3 S1 1
OI3 O5D S1 1
OI3 O1B S1 1
OI3 O3A S1 1
OI3 O1A S1 1
OI3 "O5'" S1 1
OI3 "O4'" S1 1
OI3 O4D S1 1
OI3 PB S1 1
OI3 PA S1 1
OI3 N1 F1 1
OI3 C6 F1 1
OI3 C5 F1 1
OI3 C4 F1 1
OI3 N3 F1 1
OI3 C2 F1 1
OI3 N9 F1 1
OI3 C8 F1 1
OI3 N7 F1 1
OI3 N6 F1 1
OI3 C3D F2 1
OI3 C4D F2 1
OI3 O4D F2 1
OI3 C1D F2 1
OI3 C2D F2 1
OI3 O1D F2 1
OI3 C5 F3 1
OI3 C4 F3 1
OI3 N9 F3 1
OI3 C8 F3 1
OI3 N7 F3 1
OI3 O5D F4 1
OI3 PB F4 1
OI3 O1B F4 1
OI3 O2B F4 1
OI3 O3A F4 1
OI3 O3A F4 2
OI3 PA F4 2
OI3 O1A F4 2
OI3 O2A F4 2
OI3 "O5'" F4 2
OI3 N7 F5 1
OI3 C8 F5 1
OI3 N9 F5 1
OI3 C4 F5 1
OI3 C5 F5 1
OI3 C6 F5 1
OI3 N1 F5 1
OI3 C2 F5 1
OI3 N3 F5 1
OI3 C5 F6 1
OI3 C6 F6 1
OI3 N1 F6 1
OI3 C2 F6 1
OI3 N3 F6 1
OI3 C4 F6 1
OI3 C2D F7 1
OI3 C3D F7 1
OI3 C4D F7 1
OI3 O4D F7 1
OI3 C1D F7 1
OI3 C5D F7 1
OI3 O5D F7 1
OI3 O3D F7 1
OI3 O2D F7 1
#
_pdbe_chem_comp_rdkit_properties.comp_id OI3
_pdbe_chem_comp_rdkit_properties.exactmw 561.067
_pdbe_chem_comp_rdkit_properties.amw 561.309
_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 7
_pdbe_chem_comp_rdkit_properties.NumHBA 18
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 36
_pdbe_chem_comp_rdkit_properties.NumAtoms 58
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 21
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.667
_pdbe_chem_comp_rdkit_properties.NumRings 4
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 2
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 2
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 2
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 4
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 2
_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 10
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 231.312
_pdbe_chem_comp_rdkit_properties.tpsa 271.290
_pdbe_chem_comp_rdkit_properties.CrippenClogP -3.115
_pdbe_chem_comp_rdkit_properties.CrippenMR 107.051
_pdbe_chem_comp_rdkit_properties.chi0v 18.105
_pdbe_chem_comp_rdkit_properties.chi1v 11.348
_pdbe_chem_comp_rdkit_properties.chi2v 5.927
_pdbe_chem_comp_rdkit_properties.chi3v 5.927
_pdbe_chem_comp_rdkit_properties.chi4v 3.901
_pdbe_chem_comp_rdkit_properties.chi0n 38.316
_pdbe_chem_comp_rdkit_properties.chi1n 18.771
_pdbe_chem_comp_rdkit_properties.chi2n 3.697
_pdbe_chem_comp_rdkit_properties.chi3n 3.697
_pdbe_chem_comp_rdkit_properties.chi4n 2.265
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.700
_pdbe_chem_comp_rdkit_properties.kappa1 10.816
_pdbe_chem_comp_rdkit_properties.kappa2 10.221
_pdbe_chem_comp_rdkit_properties.kappa3 5.581
_pdbe_chem_comp_rdkit_properties.Phi 3.071
#
#
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
OI3 "C4'" 2.580 3.115 -0.440 ETKDGv3 1
OI3 "C1'" 4.542 1.947 -0.480 ETKDGv3 2
OI3 C5 5.438 -1.609 -0.029 ETKDGv3 3
OI3 C6 6.279 -2.610 -0.285 ETKDGv3 4
OI3 "C2'" 4.197 2.261 -1.935 ETKDGv3 5
OI3 C3D -5.888 -0.473 0.068 ETKDGv3 6
OI3 C4D -4.955 -1.692 -0.002 ETKDGv3 7
OI3 C5D -3.968 -1.726 1.171 ETKDGv3 8
OI3 "C5'" 1.365 2.176 -0.470 ETKDGv3 9
OI3 C8 4.068 -0.210 0.904 ETKDGv3 10
OI3 C2 7.194 -1.345 -2.116 ETKDGv3 11
OI3 C4 5.466 -0.432 -0.816 ETKDGv3 12
OI3 "C3'" 3.160 3.347 -1.832 ETKDGv3 13
OI3 C1D -7.091 -2.509 0.074 ETKDGv3 14
OI3 C2D -7.188 -1.069 0.552 ETKDGv3 15
OI3 F1 5.315 2.676 -2.642 ETKDGv3 16
OI3 N9 4.565 0.500 -0.253 ETKDGv3 17
OI3 N7 4.540 -1.421 1.055 ETKDGv3 18
OI3 N6 6.321 -3.787 0.522 ETKDGv3 19
OI3 N1 7.180 -2.449 -1.405 ETKDGv3 20
OI3 N3 6.302 -0.252 -1.792 ETKDGv3 21
OI3 O3D -6.021 0.141 -1.195 ETKDGv3 22
OI3 O5D -3.099 -0.621 1.082 ETKDGv3 23
OI3 O1B -1.227 -1.938 2.408 ETKDGv3 24
OI3 O2B -2.928 -0.587 3.852 ETKDGv3 25
OI3 O3A -0.983 0.681 2.379 ETKDGv3 26
OI3 O1A 0.357 -0.568 0.470 ETKDGv3 27
OI3 O2A -1.469 1.143 -0.322 ETKDGv3 28
OI3 "O5'" 0.912 1.970 0.848 ETKDGv3 29
OI3 "O4'" 3.589 2.555 0.369 ETKDGv3 30
OI3 "O3'" 3.774 4.609 -1.895 ETKDGv3 31
OI3 O4D -5.731 -2.875 0.019 ETKDGv3 32
OI3 O1D -7.766 -3.368 0.953 ETKDGv3 33
OI3 O2D -8.312 -0.430 0.004 ETKDGv3 34
OI3 PB -2.035 -0.658 2.416 ETKDGv3 35
OI3 PA -0.285 0.756 0.827 ETKDGv3 36
OI3 "H'4" 2.258 4.082 0.004 ETKDGv3 37
OI3 "H'1" 5.541 2.365 -0.229 ETKDGv3 38
OI3 "H'2" 3.754 1.374 -2.443 ETKDGv3 39
OI3 "HR'3" -5.533 0.296 0.790 ETKDGv3 40
OI3 "HR'4" -4.366 -1.674 -0.946 ETKDGv3 41
OI3 H5R1 -3.391 -2.677 1.107 ETKDGv3 42
OI3 H5R2 -4.546 -1.711 2.123 ETKDGv3 43
OI3 "H5'1" 1.671 1.216 -0.947 ETKDGv3 44
OI3 "H5'2" 0.564 2.652 -1.077 ETKDGv3 45
OI3 H8 3.367 0.223 1.605 ETKDGv3 46
OI3 H2 7.883 -1.247 -2.943 ETKDGv3 47
OI3 "H'3" 2.399 3.246 -2.642 ETKDGv3 48
OI3 "HR'2" -7.225 -1.043 1.667 ETKDGv3 49
OI3 H61 7.001 -4.547 0.299 ETKDGv3 50
OI3 H62 5.678 -3.909 1.336 ETKDGv3 51
OI3 HOR3 -6.331 -0.545 -1.843 ETKDGv3 52
OI3 HOB2 -3.448 0.253 3.782 ETKDGv3 53
OI3 HOA2 -1.881 1.978 0.014 ETKDGv3 54
OI3 "HO'3" 3.047 5.270 -2.033 ETKDGv3 55
OI3 HOR1 -8.736 -3.231 0.794 ETKDGv3 56
OI3 HOR2 -8.391 0.443 0.471 ETKDGv3 57
OI3 "HR'1" -7.516 -2.608 -0.953 ETKDGv3 58
#