data_JYP
#
_chem_comp.id JYP
_chem_comp.name "Adenophostin A"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C16 H26 N5 O18 P3"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms "[(2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-(hydroxymethyl)-4-[(2~{R},3~{S},4~{R},5~{S},6~{S})-6-(hydroxymethyl)-3-oxidanyl-4,5-diphosphonooxy-oxan-2-yl]oxy-oxolan-3-yl] dihydrogen phosphate"
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2018-10-23
_chem_comp.pdbx_modified_date 2021-03-13
_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 669.322
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code JYP
_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 6MU1
_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.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
JYP C1 C1 C 0 1 Y N N 181.515 139.482 87.801 7.494 -0.910 -0.448 C1 JYP 1
JYP N1 N1 N 0 1 Y N N 181.775 140.819 87.672 6.304 -0.424 -0.729 N1 JYP 2
JYP C2 C2 C 0 1 Y N N 180.826 141.696 88.010 5.751 0.505 0.045 C2 JYP 3
JYP C3 C3 C 0 1 Y N N 179.573 141.257 88.502 6.457 0.963 1.171 C3 JYP 4
JYP C4 C4 C 0 1 Y N N 179.362 139.924 88.618 7.724 0.414 1.428 C4 JYP 5
JYP N2 N2 N 0 1 Y N N 180.321 139.066 88.286 8.194 -0.511 0.598 N2 JYP 6
JYP N3 N3 N 0 1 N N N 178.142 139.435 89.262 8.466 0.826 2.522 N3 JYP 7
JYP N4 N4 N 0 1 Y N N 178.676 142.512 88.575 5.680 1.893 1.777 N4 JYP 8
JYP C5 C5 C 0 1 Y N N 179.528 143.501 88.124 4.571 2.032 1.111 C5 JYP 9
JYP N5 N5 N 0 1 Y N N 180.663 142.950 87.840 4.567 1.197 0.034 N5 JYP 10
JYP C6 C6 C 0 1 N N R 181.524 143.623 86.892 3.494 1.062 -0.955 C6 JYP 11
JYP C7 C7 C 0 1 N N R 181.540 145.085 87.179 2.513 -0.054 -0.535 C7 JYP 12
JYP C8 C8 C 0 1 N N S 182.915 145.475 87.453 1.128 0.484 -0.958 C8 JYP 13
JYP C9 C9 C 0 1 N N R 183.768 144.256 87.353 1.436 1.863 -1.583 C9 JYP 14
JYP O1 O1 O 0 1 N N N 182.899 143.111 87.018 2.692 2.263 -0.993 O1 JYP 15
JYP C10 C10 C 0 1 N N N 184.450 144.005 88.667 0.337 2.867 -1.228 C10 JYP 16
JYP O2 O2 O 0 1 N N N 185.060 142.723 88.646 0.580 4.099 -1.909 O2 JYP 17
JYP O3 O3 O 0 1 N N N 183.007 146.031 88.801 0.278 0.630 0.182 O3 JYP 18
JYP C11 C11 C 0 1 N N R 182.980 147.455 88.733 -1.112 0.456 -0.103 C11 JYP 19
JYP C12 C12 C 0 1 N N S 184.260 148.010 89.329 -1.939 0.874 1.115 C12 JYP 20
JYP C13 C13 C 0 1 N N R 184.025 148.394 90.807 -3.422 0.628 0.824 C13 JYP 21
JYP C14 C14 C 0 1 N N S 182.985 149.503 90.892 -3.623 -0.847 0.464 C14 JYP 22
JYP C15 C15 C 0 1 N N S 181.929 149.297 89.812 -2.730 -1.200 -0.729 C15 JYP 23
JYP O4 O4 O 0 1 N N N 181.879 147.933 89.449 -1.368 -0.918 -0.402 O4 JYP 24
JYP C16 C16 C 0 1 N N N 180.558 149.730 90.350 -2.880 -2.687 -1.056 C16 JYP 25
JYP O5 O5 O 0 1 N N N 180.272 151.030 89.913 -2.138 -2.991 -2.239 O5 JYP 26
JYP O6 O6 O 0 1 N N N 183.613 150.746 90.701 -4.991 -1.074 0.122 O6 JYP 27
JYP P1 P1 P 0 1 N N N 183.504 151.889 91.921 -5.936 -2.105 0.919 P1 JYP 28
JYP O7 O7 O 0 1 N N N 183.324 151.193 93.249 -7.365 -2.203 0.184 O7 JYP 29
JYP O8 O8 O 0 1 N N N 182.317 152.793 91.662 -5.300 -3.441 0.942 O8 JYP 30
JYP O9 O9 O 0 1 N N N 184.771 152.717 91.953 -6.144 -1.584 2.429 O9 JYP 31
JYP O10 O10 O 0 1 N N N 185.221 148.841 91.364 -3.837 1.447 -0.271 O10 JYP 32
JYP P2 P2 P 0 1 N N N 185.316 148.991 93.006 -5.004 2.550 -0.149 P2 JYP 33
JYP O11 O11 O 0 1 N N N 185.970 147.761 93.586 -5.115 3.370 -1.530 O11 JYP 34
JYP O12 O12 O 0 1 N N N 183.930 149.141 93.580 -6.405 1.817 0.154 O12 JYP 35
JYP O13 O13 O 0 1 N N N 186.139 150.212 93.354 -4.687 3.483 0.955 O13 JYP 36
JYP O14 O14 O 0 1 N N N 184.650 149.142 88.614 -1.729 2.263 1.380 O14 JYP 37
JYP O15 O15 O 0 1 N N N 181.041 145.823 86.018 2.810 -1.269 -1.227 O15 JYP 38
JYP P3 P3 P 0 1 N N N 182.102 146.817 85.186 3.174 -2.642 -0.471 P3 JYP 39
JYP O16 O16 O 0 1 N N N 183.110 147.404 86.151 4.564 -2.466 0.323 O16 JYP 40
JYP O17 O17 O 0 1 N N N 182.825 146.012 84.131 2.098 -2.979 0.487 O17 JYP 41
JYP O18 O18 O 0 1 N N N 181.325 147.940 84.521 3.321 -3.827 -1.552 O18 JYP 42
JYP H1 H1 H 0 1 N N N 182.263 138.757 87.516 7.912 -1.667 -1.096 H1 JYP 43
JYP H2 H2 H 0 1 N N N 178.199 138.443 89.374 8.111 1.502 3.121 H2 JYP 44
JYP H3 H3 H 0 1 N N N 178.042 139.867 90.158 9.340 0.440 2.689 H3 JYP 45
JYP H4 H4 H 0 1 N N N 179.289 144.550 88.026 3.771 2.709 1.373 H4 JYP 46
JYP H5 H5 H 0 1 N N N 181.160 143.456 85.868 3.909 0.852 -1.940 H5 JYP 47
JYP H6 H6 H 0 1 N N N 180.908 145.294 88.055 2.549 -0.210 0.543 H6 JYP 48
JYP H7 H7 H 0 1 N N N 183.250 146.220 86.716 0.669 -0.177 -1.693 H7 JYP 49
JYP H8 H8 H 0 1 N N N 184.524 144.396 86.566 1.534 1.776 -2.665 H8 JYP 50
JYP H9 H9 H 0 1 N N N 185.218 144.774 88.834 -0.631 2.468 -1.531 H9 JYP 51
JYP H10 H10 H 0 1 N N N 183.709 144.045 89.479 0.338 3.040 -0.152 H10 JYP 52
JYP H11 H11 H 0 1 N N N 185.492 142.564 89.477 -0.079 4.784 -1.730 H11 JYP 53
JYP H12 H12 H 0 1 N N N 182.917 147.775 87.683 -1.387 1.072 -0.959 H12 JYP 54
JYP H13 H13 H 0 1 N N N 185.040 147.235 89.287 -1.635 0.287 1.981 H13 JYP 55
JYP H14 H14 H 0 1 N N N 183.650 147.511 91.345 -4.013 0.872 1.707 H14 JYP 56
JYP H15 H15 H 0 1 N N N 182.499 149.462 91.878 -3.353 -1.470 1.317 H15 JYP 57
JYP H16 H16 H 0 1 N N N 182.182 149.919 88.941 -3.027 -0.606 -1.593 H16 JYP 58
JYP H17 H17 H 0 1 N N N 179.785 149.041 89.980 -2.499 -3.282 -0.226 H17 JYP 59
JYP H18 H18 H 0 1 N N N 180.572 149.708 91.450 -3.932 -2.920 -1.217 H18 JYP 60
JYP H19 H19 H 0 1 N N N 179.423 151.297 90.246 -2.187 -3.919 -2.507 H19 JYP 61
JYP H20 H20 H 0 1 N N N 182.504 151.468 93.643 -7.987 -2.807 0.612 H20 JYP 62
JYP H21 H21 H 0 1 N N N 184.557 153.630 91.804 -6.557 -0.712 2.491 H21 JYP 63
JYP H22 H22 H 0 1 N N N 186.762 148.011 94.048 -5.800 4.052 -1.528 H22 JYP 64
JYP H23 H23 H 0 1 N N N 183.865 149.970 94.039 -6.677 1.189 -0.529 H23 JYP 65
JYP H24 H24 H 0 1 N N N 185.452 149.491 88.986 -0.808 2.492 1.569 H24 JYP 66
JYP H25 H25 H 0 1 N N N 183.986 147.144 85.892 5.315 -2.244 -0.244 H25 JYP 67
JYP H26 H26 H 0 1 N N N 181.455 147.902 83.581 3.540 -4.686 -1.166 H26 JYP 68
# #
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
JYP O17 P3 DOUB N N 1
JYP O18 P3 SING N N 2
JYP P3 O15 SING N N 3
JYP P3 O16 SING N N 4
JYP O15 C7 SING N N 5
JYP C6 O1 SING N N 6
JYP C6 C7 SING N N 7
JYP C6 N5 SING N N 8
JYP O1 C9 SING N N 9
JYP C7 C8 SING N N 10
JYP C9 C8 SING N N 11
JYP C9 C10 SING N N 12
JYP C8 O3 SING N N 13
JYP N1 C1 DOUB Y N 14
JYP N1 C2 SING Y N 15
JYP C1 N2 SING Y N 16
JYP N5 C2 SING Y N 17
JYP N5 C5 SING Y N 18
JYP C2 C3 DOUB Y N 19
JYP C5 N4 DOUB Y N 20
JYP N2 C4 DOUB Y N 21
JYP C3 N4 SING Y N 22
JYP C3 C4 SING Y N 23
JYP O14 C12 SING N N 24
JYP C4 N3 SING N N 25
JYP O2 C10 SING N N 26
JYP C11 O3 SING N N 27
JYP C11 C12 SING N N 28
JYP C11 O4 SING N N 29
JYP C12 C13 SING N N 30
JYP O4 C15 SING N N 31
JYP C15 C16 SING N N 32
JYP C15 C14 SING N N 33
JYP O5 C16 SING N N 34
JYP O6 C14 SING N N 35
JYP O6 P1 SING N N 36
JYP C13 C14 SING N N 37
JYP C13 O10 SING N N 38
JYP O10 P2 SING N N 39
JYP O8 P1 DOUB N N 40
JYP P1 O9 SING N N 41
JYP P1 O7 SING N N 42
JYP P2 O13 DOUB N N 43
JYP P2 O12 SING N N 44
JYP P2 O11 SING N N 45
JYP C1 H1 SING N N 46
JYP N3 H2 SING N N 47
JYP N3 H3 SING N N 48
JYP C5 H4 SING N N 49
JYP C6 H5 SING N N 50
JYP C7 H6 SING N N 51
JYP C8 H7 SING N N 52
JYP C9 H8 SING N N 53
JYP C10 H9 SING N N 54
JYP C10 H10 SING N N 55
JYP O2 H11 SING N N 56
JYP C11 H12 SING N N 57
JYP C12 H13 SING N N 58
JYP C13 H14 SING N N 59
JYP C14 H15 SING N N 60
JYP C15 H16 SING N N 61
JYP C16 H17 SING N N 62
JYP C16 H18 SING N N 63
JYP O5 H19 SING N N 64
JYP O7 H20 SING N N 65
JYP O9 H21 SING N N 66
JYP O11 H22 SING N N 67
JYP O12 H23 SING N N 68
JYP O14 H24 SING N N 69
JYP O16 H25 SING N N 70
JYP O18 H26 SING N N 71
# #
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
JYP InChI InChI 1.03 "InChI=1S/C16H26N5O18P3/c17-13-7-14(19-3-18-13)21(4-20-7)15-12(39-42(31,32)33)9(5(1-22)34-15)36-16-8(24)11(38-41(28,29)30)10(6(2-23)35-16)37-40(25,26)27/h3-6,8-12,15-16,22-24H,1-2H2,(H2,17,18,19)(H2,25,26,27)(H2,28,29,30)(H2,31,32,33)/t5-,6+,8+,9+,10+,11-,12-,15-,16-/m1/s1"
JYP InChIKey InChI 1.03 RENVITLQVBEFDT-YFPOSXHWSA-N
JYP SMILES_CANONICAL CACTVS 3.385 "Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO)[C@H](O[C@H]4O[C@@H](CO)[C@H](O[P](O)(O)=O)[C@H](O[P](O)(O)=O)[C@@H]4O)[C@H]3O[P](O)(O)=O"
JYP SMILES CACTVS 3.385 "Nc1ncnc2n(cnc12)[CH]3O[CH](CO)[CH](O[CH]4O[CH](CO)[CH](O[P](O)(O)=O)[CH](O[P](O)(O)=O)[CH]4O)[CH]3O[P](O)(O)=O"
JYP SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@H]([C@H](O3)CO)O[C@@H]4[C@H]([C@H]([C@H]([C@@H](O4)CO)OP(=O)(O)O)OP(=O)(O)O)O)OP(=O)(O)O)N"
JYP SMILES "OpenEye OEToolkits" 2.0.6 "c1nc(c2c(n1)n(cn2)C3C(C(C(O3)CO)OC4C(C(C(C(O4)CO)OP(=O)(O)O)OP(=O)(O)O)O)OP(=O)(O)O)N"
#
_pdbx_chem_comp_identifier.comp_id JYP
_pdbx_chem_comp_identifier.type "SYSTEMATIC NAME"
_pdbx_chem_comp_identifier.program "OpenEye OEToolkits"
_pdbx_chem_comp_identifier.program_version 2.0.6
_pdbx_chem_comp_identifier.identifier "[(2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-(hydroxymethyl)-4-[(2~{R},3~{S},4~{R},5~{S},6~{S})-6-(hydroxymethyl)-3-oxidanyl-4,5-diphosphonooxy-oxan-2-yl]oxy-oxolan-3-yl] dihydrogen 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
JYP "Create component" 2018-10-23 RCSB
JYP "Initial release" 2018-12-05 RCSB
JYP "Modify synonyms" 2021-03-13 RCSB
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id JYP
_pdbx_chem_comp_synonyms.name "[(2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-(hydroxymethyl)-4-[(2~{R},3~{S},4~{R},5~{S},6~{S})-6-(hydroxymethyl)-3-oxidanyl-4,5-diphosphonooxy-oxan-2-yl]oxy-oxolan-3-yl] dihydrogen phosphate"
_pdbx_chem_comp_synonyms.provenance PDB
_pdbx_chem_comp_synonyms.type ?
##