data_H84
#
_chem_comp.id H84
_chem_comp.name "2'-deoxy-5'-O-[(R)-{[(R)-[dibromo(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]adenosine"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C11 H16 Br2 N5 O11 P3"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms "beta, gamma dATP analogue"
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2018-06-14
_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 647.001
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code H84
_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 6CR3
_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
H84 N1 N1 N 0 1 Y N N 9.773 8.526 8.319 -8.865 -2.414 -0.748 N1 H84 1
H84 C2 C1 C 0 1 Y N N 8.637 8.528 7.641 -8.387 -1.671 -1.730 C2 H84 2
H84 N3 N2 N 0 1 Y N N 7.475 8.237 8.228 -7.339 -0.889 -1.579 N3 H84 3
H84 C4 C2 C 0 1 Y N N 7.474 7.935 9.585 -6.711 -0.817 -0.410 C4 H84 4
H84 C5 C3 C 0 1 Y N N 8.649 7.929 10.316 -7.180 -1.589 0.667 C5 H84 5
H84 C6 C4 C 0 1 Y N N 9.849 8.241 9.642 -8.302 -2.408 0.456 C6 H84 6
H84 N6 N3 N 0 1 N N N 11.158 8.238 10.355 -8.810 -3.190 1.478 N6 H84 7
H84 N7 N4 N 0 1 Y N N 8.347 7.605 11.610 -6.373 -1.332 1.724 N7 H84 8
H84 C8 C5 C 0 1 Y N N 7.042 7.410 11.675 -5.460 -0.474 1.373 C8 H84 9
H84 N9 N5 N 0 1 Y N N 6.493 7.622 10.458 -5.626 -0.125 0.066 N9 H84 10
H84 PA P1 P 0 1 N N N 4.832 5.371 14.938 0.676 2.028 1.015 PA H84 11
H84 PB P2 P 0 1 N N N 3.792 2.714 14.043 3.374 0.847 0.676 PB H84 12
H84 PG P3 P 0 1 N N N 3.716 1.423 16.839 5.773 -0.783 0.004 PG H84 13
H84 "C1'" C6 C 0 1 N N R 5.107 7.483 10.088 -4.798 0.816 -0.692 "C1'" H84 14
H84 O1A O1 O 0 1 N N N 3.696 5.457 15.961 0.403 1.808 2.586 O1A H84 15
H84 O2B O2 O 0 1 N N N 3.737 2.215 12.657 3.713 0.754 2.114 O2B H84 16
H84 O1G O3 O 0 1 N N N 3.670 2.901 17.237 6.141 -0.885 1.568 O1G H84 17
H84 "C2'" C7 C 0 1 N N N 4.881 6.223 9.775 -5.389 2.241 -0.607 "C2'" H84 18
H84 O2A O4 O 0 1 N N N 6.195 5.538 15.574 1.174 3.403 0.788 O2A H84 19
H84 O1B O5 O 0 1 N N N 2.381 3.200 14.527 4.080 2.148 0.042 O1B H84 20
H84 O2G O6 O 0 1 N N N 4.635 0.644 17.736 6.294 -2.102 -0.757 O2G H84 21
H84 "C3'" C8 C 0 1 N N S 4.371 5.606 10.996 -4.148 3.158 -0.529 "C3'" H84 22
H84 "O3'" O7 O 0 1 N N N 3.567 4.444 10.781 -4.110 4.047 -1.647 "O3'" H84 23
H84 O3A O8 O 0 1 N N N 4.891 3.951 14.067 1.777 0.968 0.508 O3A H84 24
H84 C3B C9 C 0 1 N N N 4.540 1.440 15.173 3.965 -0.646 -0.186 C3B H84 25
H84 BR1 BR1 BR 0 0 N N N 4.660 -0.306 14.438 3.102 -2.234 0.589 BR1 H84 26
H84 BR2 BR2 BR 0 0 N N N 6.414 1.861 15.425 3.514 -0.522 -2.096 BR2 H84 27
H84 O3G O9 O 0 1 N N N 2.371 0.758 16.672 6.422 0.412 -0.579 O3G H84 28
H84 "C4'" C10 C 0 1 N N R 3.540 6.810 11.603 -2.954 2.179 -0.575 "C4'" H84 29
H84 "O4'" O10 O 0 1 N N N 4.183 7.818 11.345 -3.486 0.925 -0.097 "O4'" H84 30
H84 "C5'" C11 C 0 1 N N N 3.357 6.639 13.212 -1.830 2.665 0.342 "C5'" H84 31
H84 "O5'" O11 O 0 1 N N N 4.627 6.561 13.801 -0.693 1.811 0.197 "O5'" H84 32
H84 H1 H1 H 0 1 N N N 8.651 8.771 6.589 -8.875 -1.706 -2.693 H1 H84 33
H84 H2 H2 H 0 1 N N N 11.889 8.468 9.712 -9.585 -3.752 1.321 H2 H84 34
H84 H3 H3 H 0 1 N N N 11.138 8.914 11.092 -8.391 -3.177 2.353 H3 H84 35
H84 H4 H4 H 0 1 N N N 6.498 7.125 12.563 -4.685 -0.093 2.023 H4 H84 36
H84 H5 H5 H 0 1 N N N 4.852 8.175 9.272 -4.718 0.498 -1.731 H5 H84 37
H84 H6 H6 H 0 1 N N N 4.059 5.602 16.827 0.074 0.926 2.809 H6 H84 38
H84 H7 H7 H 0 1 N N N 2.765 3.179 17.320 5.749 -1.647 2.016 H7 H84 39
H84 H8 H8 H 0 1 N N N 4.136 6.154 8.969 -5.974 2.466 -1.499 H8 H84 40
H84 H9 H9 H 0 1 N N N 5.813 5.733 9.456 -6.000 2.348 0.289 H9 H84 41
H84 H10 H10 H 0 1 N N N 1.748 3.081 13.829 3.901 2.272 -0.900 H10 H84 42
H84 H11 H11 H 0 1 N N N 4.192 -0.140 18.040 7.250 -2.239 -0.697 H11 H84 43
H84 H12 H12 H 0 1 N N N 5.203 5.378 11.679 -4.146 3.719 0.406 H12 H84 44
H84 H13 H13 H 0 1 N N N 3.733 3.812 11.470 -4.869 4.644 -1.701 H13 H84 45
H84 H14 H14 H 0 1 N N N 2.537 6.796 11.151 -2.589 2.073 -1.597 H14 H84 46
H84 H15 H15 H 0 1 N N N 2.813 7.505 13.617 -1.556 3.685 0.072 H15 H84 47
H84 H16 H16 H 0 1 N N N 2.793 5.719 13.425 -2.171 2.643 1.377 H16 H84 48
# #
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
H84 C2 N3 DOUB Y N 1
H84 C2 N1 SING Y N 2
H84 N3 C4 SING Y N 3
H84 N1 C6 DOUB Y N 4
H84 C4 C5 DOUB Y N 5
H84 C4 N9 SING Y N 6
H84 C6 C5 SING Y N 7
H84 C6 N6 SING N N 8
H84 "C2'" "C1'" SING N N 9
H84 "C2'" "C3'" SING N N 10
H84 "C1'" N9 SING N N 11
H84 "C1'" "O4'" SING N N 12
H84 C5 N7 SING Y N 13
H84 N9 C8 SING Y N 14
H84 "O3'" "C3'" SING N N 15
H84 "C3'" "C4'" SING N N 16
H84 "O4'" "C4'" SING N N 17
H84 "C4'" "C5'" SING N N 18
H84 N7 C8 DOUB Y N 19
H84 O2B PB DOUB N N 20
H84 "C5'" "O5'" SING N N 21
H84 "O5'" PA SING N N 22
H84 PB O3A SING N N 23
H84 PB O1B SING N N 24
H84 PB C3B SING N N 25
H84 O3A PA SING N N 26
H84 BR1 C3B SING N N 27
H84 PA O2A DOUB N N 28
H84 PA O1A SING N N 29
H84 C3B BR2 SING N N 30
H84 C3B PG SING N N 31
H84 O3G PG DOUB N N 32
H84 PG O1G SING N N 33
H84 PG O2G SING N N 34
H84 C2 H1 SING N N 35
H84 N6 H2 SING N N 36
H84 N6 H3 SING N N 37
H84 C8 H4 SING N N 38
H84 "C1'" H5 SING N N 39
H84 O1A H6 SING N N 40
H84 O1G H7 SING N N 41
H84 "C2'" H8 SING N N 42
H84 "C2'" H9 SING N N 43
H84 O1B H10 SING N N 44
H84 O2G H11 SING N N 45
H84 "C3'" H12 SING N N 46
H84 "O3'" H13 SING N N 47
H84 "C4'" H14 SING N N 48
H84 "C5'" H15 SING N N 49
H84 "C5'" H16 SING N N 50
# #
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
H84 SMILES ACDLabs 12.01 "n1c(c2c(nc1)n(cn2)C3OC(C(C3)O)COP(=O)(O)OP(O)(C(P(O)(O)=O)(Br)Br)=O)N"
H84 InChI InChI 1.03 "InChI=1S/C11H16Br2N5O11P3/c12-11(13,30(20,21)22)31(23,24)29-32(25,26)27-2-6-5(19)1-7(28-6)18-4-17-8-9(14)15-3-16-10(8)18/h3-7,19H,1-2H2,(H,23,24)(H,25,26)(H2,14,15,16)(H2,20,21,22)/t5-,6+,7+/m0/s1"
H84 InChIKey InChI 1.03 QNLUNEAMUQCVKG-RRKCRQDMSA-N
H84 SMILES_CANONICAL CACTVS 3.385 "Nc1ncnc2n(cnc12)[C@H]3C[C@H](O)[C@@H](CO[P](O)(=O)O[P](O)(=O)C(Br)(Br)[P](O)(O)=O)O3"
H84 SMILES CACTVS 3.385 "Nc1ncnc2n(cnc12)[CH]3C[CH](O)[CH](CO[P](O)(=O)O[P](O)(=O)C(Br)(Br)[P](O)(O)=O)O3"
H84 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "c1nc(c2c(n1)n(cn2)[C@H]3C[C@@H]([C@H](O3)COP(=O)(O)OP(=O)(C(P(=O)(O)O)(Br)Br)O)O)N"
H84 SMILES "OpenEye OEToolkits" 2.0.6 "c1nc(c2c(n1)n(cn2)C3CC(C(O3)COP(=O)(O)OP(=O)(C(P(=O)(O)O)(Br)Br)O)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
H84 "SYSTEMATIC NAME" ACDLabs 12.01 "2'-deoxy-5'-O-[(R)-{[(R)-[dibromo(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]adenosine"
H84 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "[[[[(2~{R},3~{S},5~{R})-5-(6-aminopurin-9-yl)-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]-bis(bromanyl)methyl]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
H84 "Create component" 2018-06-14 RCSB
H84 "Initial release" 2018-06-27 RCSB
H84 "Modify synonyms" 2021-03-13 RCSB
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id H84
_pdbx_chem_comp_synonyms.name "beta, gamma dATP analogue"
_pdbx_chem_comp_synonyms.provenance PDB
_pdbx_chem_comp_synonyms.type ?
##