data_9GM
#
_chem_comp.id 9GM
_chem_comp.name "2-amino-9-{5-O-[(S)-hydroxy{[(R)-hydroxy(phosphonoamino)phosphoryl]oxy}phosphoryl]-alpha-L-xylofuranosyl}-1,9-dihydro-6H-purin-6-one"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C10 H17 N6 O13 P3"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2017-05-10
_chem_comp.pdbx_modified_date 2017-12-01
_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 522.196
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code 9GM
_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 5VPY
_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
9GM C1 C1 C 0 1 N N N 16.890 -7.382 10.668 7.241 -1.314 0.880 C1 9GM 1
9GM C2 C2 C 0 1 Y N N 17.140 -6.101 12.472 5.073 -0.801 0.271 C2 9GM 2
9GM C3 C3 C 0 1 Y N N 17.747 -5.059 11.817 4.946 -2.038 -0.371 C3 9GM 3
9GM C4 C4 C 0 1 Y N N 17.594 -4.467 13.871 3.062 -0.993 -0.612 C4 9GM 4
9GM C5 C5 C 0 1 N N R 16.305 -6.523 14.749 3.525 1.170 0.605 C5 9GM 5
9GM C6 C6 C 0 1 N N S 16.238 -5.402 16.620 1.608 1.851 -0.501 C6 9GM 6
9GM N2 N1 N 0 1 N N N 16.671 -7.268 11.969 6.223 -0.483 0.876 N2 9GM 7
9GM O1 O1 O 0 1 N N N 15.453 -5.638 15.443 2.098 1.286 0.734 O1 9GM 8
9GM O4 O2 O 0 1 N N N 18.652 -1.950 17.522 -2.819 2.633 -0.932 O4 9GM 9
9GM O5 O3 O 0 1 N N N 16.240 -1.260 17.995 -3.127 0.415 0.233 O5 9GM 10
9GM O6 O4 O 0 1 N N N 17.517 0.456 19.091 -5.556 0.809 1.160 O6 9GM 11
9GM P1 P1 P 0 1 N N N 17.363 -2.412 18.119 -2.300 1.795 0.172 P1 9GM 12
9GM O7 O5 O 0 1 N N N 15.521 1.106 17.603 -5.133 0.430 -1.300 O7 9GM 13
9GM O8 O6 O 0 1 N N N 14.236 0.159 22.296 -6.998 -1.657 -1.407 O8 9GM 14
9GM O9 O7 O 0 1 N N N 14.491 2.231 21.003 -7.310 -1.373 1.082 O9 9GM 15
9GM P2 P2 P 0 1 N N N 16.124 0.187 18.640 -4.681 0.033 0.053 P2 9GM 16
9GM O10 O8 O 0 1 N N N 16.506 0.953 21.737 -6.636 -3.661 0.255 O10 9GM 17
9GM O11 O9 O 0 1 N N N 15.512 -7.631 17.541 2.439 4.129 -0.116 O11 9GM 18
9GM O12 O10 O 0 1 N N N 18.488 -7.198 15.792 4.640 1.638 -1.516 O12 9GM 19
9GM N1 N2 N 0 1 N N N 16.503 -8.492 10.021 8.401 -0.945 1.514 N1 9GM 20
9GM N3 N3 N 0 1 Y N N 18.035 -4.029 12.709 3.695 -2.095 -0.891 N3 9GM 21
9GM N4 N4 N 0 1 Y N N 17.044 -5.734 13.779 3.874 -0.162 0.105 N4 9GM 22
9GM C7 C7 C 0 1 N N N 15.655 -4.328 17.472 0.236 2.496 -0.290 C7 9GM 23
9GM O2 O11 O 0 1 N N N 16.574 -3.304 17.114 -0.743 1.476 -0.083 O2 9GM 24
9GM O3 O12 O 0 1 N N N 17.338 -2.998 19.486 -2.466 2.582 1.567 O3 9GM 25
9GM N5 N5 N 0 1 N N N 15.090 -0.053 19.863 -4.877 -1.627 0.245 N5 9GM 26
9GM P3 P3 P 0 1 N N N 15.075 0.844 21.234 -6.491 -2.069 0.064 P3 9GM 27
9GM C8 C8 C 0 1 N N S 16.579 -6.792 17.136 2.668 2.926 -0.853 C8 9GM 28
9GM C9 C9 C 0 1 N N S 17.093 -7.335 15.802 3.983 2.244 -0.401 C9 9GM 29
9GM C10 C10 C 0 1 N N N 17.974 -5.180 10.424 6.046 -2.927 -0.351 C10 9GM 30
9GM O13 O13 O 0 1 N N N 18.477 -4.361 9.648 5.979 -4.015 -0.898 O13 9GM 31
9GM N6 N6 N 0 1 N N N 17.475 -6.386 9.924 7.176 -2.535 0.276 N6 9GM 32
9GM H1 H1 H 0 1 N N N 17.655 -3.902 14.790 2.047 -0.768 -0.905 H1 9GM 33
9GM H2 H2 H 0 1 N N N 15.683 -7.242 14.195 4.000 1.341 1.571 H2 9GM 34
9GM H3 H3 H 0 1 N N N 17.195 -4.994 16.262 1.558 1.091 -1.280 H3 9GM 35
9GM H4 H4 H 0 1 N N N 17.856 1.217 18.635 -5.314 0.597 2.071 H4 9GM 36
9GM H5 H5 H 0 1 N N N 13.541 0.743 22.576 -6.505 -2.076 -2.125 H5 9GM 37
9GM H6 H6 H 0 1 N N N 16.749 1.869 21.806 -7.542 -3.987 0.164 H6 9GM 38
9GM H7 H7 H 0 1 N N N 15.165 -7.324 18.370 3.077 4.831 -0.302 H7 9GM 39
9GM H8 H8 H 0 1 N N N 18.865 -7.738 16.477 4.949 2.268 -2.181 H8 9GM 40
9GM H9 H9 H 0 1 N N N 16.051 -9.230 10.521 8.460 -0.081 1.951 H9 9GM 41
9GM H10 H10 H 0 1 N N N 16.667 -8.581 9.039 9.160 -1.548 1.525 H10 9GM 42
9GM H11 H11 H 0 1 N N N 14.621 -4.082 17.190 0.272 3.149 0.582 H11 9GM 43
9GM H12 H12 H 0 1 N N N 15.695 -4.573 18.544 -0.029 3.081 -1.171 H12 9GM 44
9GM H13 H13 H 0 1 N N N 18.218 -3.008 19.843 -2.145 2.091 2.336 H13 9GM 45
9GM H14 H14 H 0 1 N N N 14.176 0.039 19.468 -4.288 -2.137 -0.395 H14 9GM 46
9GM H15 H15 H 0 1 N N N 17.389 -6.749 17.879 2.680 3.124 -1.924 H15 9GM 47
9GM H16 H16 H 0 1 N N N 16.807 -8.394 15.716 4.642 2.965 0.083 H16 9GM 48
9GM H17 H17 H 0 1 N N N 17.550 -6.537 8.938 7.946 -3.125 0.297 H17 9GM 49
#
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
9GM O13 C10 DOUB N N 1
9GM N6 C10 SING N N 2
9GM N6 C1 SING N N 3
9GM N1 C1 SING N N 4
9GM C10 C3 SING N N 5
9GM C1 N2 DOUB N N 6
9GM C3 C2 DOUB Y N 7
9GM C3 N3 SING Y N 8
9GM N2 C2 SING N N 9
9GM C2 N4 SING Y N 10
9GM N3 C4 DOUB Y N 11
9GM N4 C4 SING Y N 12
9GM N4 C5 SING N N 13
9GM C5 O1 SING N N 14
9GM C5 C9 SING N N 15
9GM O1 C6 SING N N 16
9GM O12 C9 SING N N 17
9GM C9 C8 SING N N 18
9GM C6 C8 SING N N 19
9GM C6 C7 SING N N 20
9GM O2 C7 SING N N 21
9GM O2 P1 SING N N 22
9GM C8 O11 SING N N 23
9GM O4 P1 DOUB N N 24
9GM O7 P2 DOUB N N 25
9GM O5 P1 SING N N 26
9GM O5 P2 SING N N 27
9GM P1 O3 SING N N 28
9GM P2 O6 SING N N 29
9GM P2 N5 SING N N 30
9GM N5 P3 SING N N 31
9GM O9 P3 DOUB N N 32
9GM P3 O10 SING N N 33
9GM P3 O8 SING N N 34
9GM C4 H1 SING N N 35
9GM C5 H2 SING N N 36
9GM C6 H3 SING N N 37
9GM O6 H4 SING N N 38
9GM O8 H5 SING N N 39
9GM O10 H6 SING N N 40
9GM O11 H7 SING N N 41
9GM O12 H8 SING N N 42
9GM N1 H9 SING N N 43
9GM N1 H10 SING N N 44
9GM C7 H11 SING N N 45
9GM C7 H12 SING N N 46
9GM O3 H13 SING N N 47
9GM N5 H14 SING N N 48
9GM C8 H15 SING N N 49
9GM C9 H16 SING N N 50
9GM N6 H17 SING N N 51
#
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
9GM SMILES ACDLabs 12.01 "C2(=Nc1n(cnc1C(=O)N2)C3OC(C(O)C3O)COP(=O)(OP(O)(=O)NP(O)(=O)O)O)N"
9GM InChI InChI 1.03
"InChI=1S/C10H17N6O13P3/c11-10-13-7-4(8(19)14-10)12-2-16(7)9-6(18)5(17)3(28-9)1-27-32(25,26)29-31(23,24)15-30(20,21)22/h2-3,5-6,9,17-18H,1H2,(H,25,26)(H3,11,13,14,19)(H4,15,20,21,22,23,24)/t3-,5+,6-,9+/m0/s1"
9GM InChIKey InChI 1.03 UQABYHGXWYXDTK-FULWYAMNSA-N
9GM SMILES_CANONICAL CACTVS 3.385 "NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@@H](CO[P](O)(=O)O[P](O)(=O)N[P](O)(O)=O)[C@@H](O)[C@@H]3O"
9GM SMILES CACTVS 3.385 "NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)N[P](O)(O)=O)[CH](O)[CH]3O"
9GM SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "c1nc2c(n1[C@H]3[C@H]([C@@H]([C@@H](O3)COP(=O)(O)OP(=O)(NP(=O)(O)O)O)O)O)N=C(NC2=O)N"
9GM SMILES "OpenEye OEToolkits" 2.0.6 "c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(NP(=O)(O)O)O)O)O)N=C(NC2=O)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
9GM "SYSTEMATIC NAME" ACDLabs 12.01 "2-amino-9-{5-O-[(S)-hydroxy{[(R)-hydroxy(phosphonoamino)phosphoryl]oxy}phosphoryl]-alpha-L-xylofuranosyl}-1,9-dihydro-6H-purin-6-one"
9GM "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "[[[[(2~{S},3~{S},4~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]amino]phosphonic acid"
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
9GM "Create component" 2017-05-10 RCSB
9GM "Initial release" 2017-12-06 RCSB
#