data_85T
#
_chem_comp.id 85T
_chem_comp.name "4-amino-1-{2-cyano-2-deoxy-5-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-arabinofuranosyl}pyrimidin-2(1H)-one"
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C10 H15 N4 O13 P3"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2021-09-08
_chem_comp.pdbx_modified_date 2021-10-22
_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 492.166
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code 85T
_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 7S2Y
_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
85T PA P1 P 0 1 N N N -20.538 5.852 43.571 -1.516 1.482 -0.662 PA 85T 1
85T O1A O1 O 0 1 N N N -19.219 6.468 43.879 -1.241 1.093 -2.063 O1A 85T 2
85T O2A O2 O 0 1 N N N -21.624 5.782 44.642 -2.098 2.982 -0.625 O2A 85T 3
85T O3B O3 O 0 1 N N N -22.897 5.511 40.978 -4.846 -0.705 0.655 O3B 85T 4
85T O2B O4 O 0 1 N N N -23.370 7.066 42.938 -4.689 0.734 -1.412 O2B 85T 5
85T N01 N1 N 0 1 N N N -21.153 1.027 41.326 4.853 1.143 -2.226 N01 85T 6
85T C02 C1 C 0 1 N N N -20.084 0.940 41.768 4.703 1.363 -1.122 C02 85T 7
85T "C2'" C2 C 0 1 N N S -18.801 0.865 42.418 4.509 1.648 0.309 "C2'" 85T 8
85T "C3'" C3 C 0 1 N N S -18.002 2.153 41.990 3.381 2.688 0.517 "C3'" 85T 9
85T "O3'" O5 O 0 1 N N N -16.568 1.774 41.990 3.694 3.552 1.612 "O3'" 85T 10
85T "C4'" C4 C 0 1 N N R -18.112 2.982 42.931 2.138 1.837 0.840 "C4'" 85T 11
85T "C5'" C5 C 0 1 N N N -18.809 4.207 42.513 1.035 2.118 -0.182 "C5'" 85T 12
85T "O5'" O6 O 0 1 N N N -20.172 4.254 43.062 -0.152 1.415 0.191 "O5'" 85T 13
85T O3A O7 O 0 1 N N N -20.982 6.785 42.262 -2.596 0.471 -0.026 O3A 85T 14
85T PB P2 P 0 1 N N N -22.467 6.890 41.749 -3.933 -0.231 -0.583 PB 85T 15
85T O1B O8 O 0 1 N N N -22.518 7.954 40.740 -3.536 -1.510 -1.477 O1B 85T 16
85T PG P3 P 0 1 N N N -23.430 5.438 39.380 -6.381 -1.170 0.800 PG 85T 17
85T O1G O9 O 0 1 N N N -24.918 5.318 39.437 -6.713 -2.120 -0.285 O1G 85T 18
85T O2G O10 O 0 1 N N N -22.943 4.137 38.723 -6.592 -1.889 2.225 O2G 85T 19
85T O3G O11 O 0 1 N N N -22.921 6.729 38.656 -7.343 0.117 0.701 O3G 85T 20
85T "O4'" O12 O 0 1 N N N -19.198 2.335 44.007 2.533 0.457 0.764 "O4'" 85T 21
85T "C1'" C6 C 0 1 N N R -18.943 1.091 43.965 3.948 0.407 1.049 "C1'" 85T 22
85T N1 N2 N 0 1 N N N -20.161 0.460 44.586 4.539 -0.823 0.516 N1 85T 23
85T C6 C7 C 0 1 N N N -21.381 1.077 44.556 3.877 -1.534 -0.439 C6 85T 24
85T C5 C8 C 0 1 N N N -22.480 0.444 45.079 4.433 -2.669 -0.924 C5 85T 25
85T C4 C9 C 0 1 N N N -22.229 -0.776 45.664 5.685 -3.083 -0.425 C4 85T 26
85T N4 N3 N 0 1 N N N -23.271 -1.534 46.294 6.274 -4.233 -0.900 N4 85T 27
85T N3 N4 N 0 1 N N N -20.981 -1.328 45.691 6.293 -2.359 0.505 N3 85T 28
85T C2 C10 C 0 1 N N N -19.944 -0.702 45.145 5.735 -1.241 0.969 C2 85T 29
85T O2 O13 O 0 1 N N N -18.804 -1.191 45.149 6.316 -0.590 1.820 O2 85T 30
85T H1 H1 H 0 1 N N N -21.302 6.173 45.446 -2.301 3.304 0.264 H1 85T 31
85T H2 H2 H 0 1 N N N -18.241 -0.054 42.190 5.439 1.986 0.766 H2 85T 32
85T H3 H3 H 0 1 N N N -18.333 2.501 41.000 3.224 3.267 -0.392 H3 85T 33
85T H4 H4 H 0 1 N N N -16.042 2.523 41.736 4.501 4.069 1.486 H4 85T 34
85T H5 H5 H 0 1 N N N -17.178 3.213 43.464 1.781 2.068 1.844 H5 85T 35
85T H7 H7 H 0 1 N N N -18.246 5.081 42.873 0.829 3.188 -0.209 H7 85T 36
85T H8 H8 H 0 1 N N N -18.863 4.233 41.415 1.360 1.786 -1.168 H8 85T 37
85T H9 H9 H 0 1 N N N -23.143 8.617 41.010 -3.037 -2.185 -0.998 H9 85T 38
85T H10 H10 H 0 1 N N N -23.690 3.586 38.518 -7.495 -2.196 2.381 H10 85T 39
85T H11 H11 H 0 1 N N N -23.665 7.242 38.362 -7.181 0.783 1.383 H11 85T 40
85T H13 H13 H 0 1 N N N -18.024 0.779 44.483 4.127 0.487 2.122 H13 85T 41
85T H14 H14 H 0 1 N N N -21.479 2.061 44.121 2.919 -1.196 -0.805 H14 85T 42
85T H15 H15 H 0 1 N N N -23.471 0.872 45.035 3.926 -3.249 -1.681 H15 85T 43
85T H16 H16 H 0 1 N N N -23.061 -2.414 46.720 5.827 -4.760 -1.581 H16 85T 44
85T H17 H17 H 0 1 N N N -24.207 -1.182 46.307 7.135 -4.515 -0.555 H17 85T 45
# #
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
85T PA O1A DOUB N N 1
85T PA O2A SING N N 2
85T PA "O5'" SING N N 3
85T PA O3A SING N N 4
85T O3B PB SING N N 5
85T O3B PG SING N N 6
85T O2B PB DOUB N N 7
85T N01 C02 TRIP N N 8
85T C02 "C2'" SING N N 9
85T "C2'" "C3'" SING N N 10
85T "C2'" "C1'" SING N N 11
85T "C3'" "O3'" SING N N 12
85T "C3'" "C4'" SING N N 13
85T "C4'" "C5'" SING N N 14
85T "C5'" "O5'" SING N N 15
85T O3A PB SING N N 16
85T PB O1B SING N N 17
85T PG O1G DOUB N N 18
85T PG O2G SING N N 19
85T PG O3G SING N N 20
85T "O4'" "C1'" SING N N 21
85T "C1'" N1 SING N N 22
85T N1 C6 SING N N 23
85T N1 C2 SING N N 24
85T C6 C5 DOUB N N 25
85T C5 C4 SING N N 26
85T C4 N4 SING N N 27
85T C4 N3 DOUB N N 28
85T N3 C2 SING N N 29
85T C2 O2 DOUB N N 30
85T O2A H1 SING N N 31
85T "C2'" H2 SING N N 32
85T "C3'" H3 SING N N 33
85T "O3'" H4 SING N N 34
85T "C4'" H5 SING N N 35
85T "C5'" H7 SING N N 36
85T "C5'" H8 SING N N 37
85T O1B H9 SING N N 38
85T O2G H10 SING N N 39
85T O3G H11 SING N N 40
85T "C1'" H13 SING N N 41
85T C6 H14 SING N N 42
85T C5 H15 SING N N 43
85T N4 H16 SING N N 44
85T N4 H17 SING N N 45
85T "C4'" "O4'" SING N N 46
# #
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
85T SMILES ACDLabs 12.01 "O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC1OC(N2C=CC(N)=NC2=O)C(C#N)C1O"
85T InChI InChI 1.03 "InChI=1S/C10H15N4O13P3/c11-3-5-8(15)6(25-9(5)14-2-1-7(12)13-10(14)16)4-24-29(20,21)27-30(22,23)26-28(17,18)19/h1-2,5-6,8-9,15H,4H2,(H,20,21)(H,22,23)(H2,12,13,16)(H2,17,18,19)/t5-,6+,8-,9+/m0/s1"
85T InChIKey InChI 1.03 DZFZBFCEJVKCLY-JWIUVKOKSA-N
85T SMILES_CANONICAL CACTVS 3.385 "NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@@H]2C#N"
85T SMILES CACTVS 3.385 "NC1=NC(=O)N(C=C1)[CH]2O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]2C#N"
85T SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C1=CN(C(=O)N=C1N)[C@H]2[C@H]([C@@H](C(O2)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)C#N"
85T SMILES "OpenEye OEToolkits" 2.0.7 "C1=CN(C(=O)N=C1N)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)C#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
85T "SYSTEMATIC NAME" ACDLabs 12.01 "4-amino-1-{2-cyano-2-deoxy-5-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-arabinofuranosyl}pyrimidin-2(1H)-one"
85T "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "[[(3~{S},4~{S},5~{R})-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-4-cyano-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono 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
85T "Create component" 2021-09-08 RCSB
85T "Initial release" 2021-10-27 RCSB
##