data_DZD
#
_chem_comp.id DZD
_chem_comp.name "5'-O-[(R)-{[(R)-{[(3R,4R)-1-(3-carbamoylbenzyl)-4-hydroxypyrrolidin-3-yl]methoxy}(hydroxy)phosphoryl]methyl}(hydroxy)phosphoryl]adenosine"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C24 H33 N7 O11 P2"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2008-06-24
_chem_comp.pdbx_modified_date 2011-06-04
_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 657.507
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code DZD
_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 3D4B
_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
DZD O68 O68 O 0 1 N N N 1.439 23.634 9.205 -9.779 -2.111 -3.190 O68 DZD 1
DZD C66 C66 C 0 1 N N N 2.549 23.723 8.725 -10.594 -1.297 -2.803 C66 DZD 2
DZD N67 N67 N 0 1 N N N 2.855 23.324 7.484 -11.911 -1.537 -2.954 N67 DZD 3
DZD C64 C64 C 0 1 Y N N 3.628 24.284 9.582 -10.140 -0.045 -2.161 C64 DZD 4
DZD C63 C63 C 0 1 Y N N 4.787 24.815 9.007 -11.073 0.890 -1.710 C63 DZD 5
DZD C62 C62 C 0 1 Y N N 5.788 25.347 9.832 -10.642 2.056 -1.112 C62 DZD 6
DZD C61 C61 C 0 1 Y N N 5.629 25.314 11.223 -9.289 2.300 -0.958 C61 DZD 7
DZD C65 C65 C 0 1 Y N N 3.457 24.254 10.974 -8.776 0.205 -1.998 C65 DZD 8
DZD C60 C60 C 0 1 Y N N 4.471 24.765 11.785 -8.359 1.378 -1.403 C60 DZD 9
DZD C59 C59 C 0 1 N N N 4.296 24.723 13.292 -6.887 1.652 -1.232 C59 DZD 10
DZD N47 N47 N 0 1 N N N 4.876 23.520 13.920 -6.436 1.117 0.059 N47 DZD 11
DZD C48 C48 C 0 1 N N N 4.154 22.760 14.926 -6.993 1.908 1.187 C48 DZD 12
DZD C49 C49 C 0 1 N N R 5.310 22.702 15.912 -6.041 1.571 2.361 C49 DZD 13
DZD O50 O50 O 0 1 N N N 5.557 24.001 16.465 -6.055 2.612 3.339 O50 DZD 14
DZD C46 C46 C 0 1 N N N 6.250 23.045 13.716 -4.966 1.212 0.188 C46 DZD 15
DZD C45 C45 C 0 1 N N R 6.535 22.414 15.080 -4.659 1.486 1.672 C45 DZD 16
DZD C38 C38 C 0 1 N N N 6.659 20.896 15.057 -3.839 0.338 2.266 C38 DZD 17
DZD O35 O35 O 0 1 N N N 7.987 20.447 14.801 -2.549 0.308 1.653 O35 DZD 18
DZD P34 P34 P 0 1 N N R 8.299 19.864 13.348 -1.421 -0.774 2.037 P34 DZD 19
DZD O36 O36 O 0 1 N N N 7.025 19.690 12.584 -1.973 -2.139 1.881 O36 DZD 20
DZD O37 O37 O 0 1 N N N 9.219 18.746 13.569 -0.962 -0.552 3.564 O37 DZD 21
DZD C31 C31 C 0 1 N N N 9.087 21.349 12.648 0.017 -0.571 0.934 C31 DZD 22
DZD P30 P30 P 0 1 N N R 10.828 21.127 12.207 1.294 -1.796 1.370 P30 DZD 23
DZD O32 O32 O 0 1 N N N 11.689 21.050 13.461 0.694 -3.281 1.200 O32 DZD 24
DZD O33 O33 O 0 1 N N N 11.155 22.129 11.129 1.716 -1.592 2.773 O33 DZD 25
DZD O29 O29 O 0 1 N N N 10.870 19.632 11.593 2.564 -1.617 0.396 O29 DZD 26
DZD C20 C20 C 0 1 N N N 10.549 19.321 10.225 3.775 -2.361 0.550 C20 DZD 27
DZD C17 C17 C 0 1 N N R 11.371 18.080 9.914 4.770 -1.947 -0.536 C17 DZD 28
DZD C18 C18 C 0 1 N N S 12.855 18.422 9.847 6.054 -2.799 -0.442 C18 DZD 29
DZD O21 O21 O 0 1 N N N 13.540 17.397 10.579 6.017 -3.867 -1.391 O21 DZD 30
DZD C19 C19 C 0 1 N N R 13.201 18.395 8.365 7.189 -1.809 -0.785 C19 DZD 31
DZD O20 O20 O 0 1 N N N 14.511 17.907 8.126 7.889 -2.236 -1.956 O20 DZD 32
DZD C15 C15 C 0 1 N N R 12.230 17.340 7.877 6.456 -0.474 -1.046 C15 DZD 33
DZD O16 O16 O 0 1 N N N 11.026 17.528 8.643 5.210 -0.588 -0.323 O16 DZD 34
DZD N9 N9 N 0 1 Y N N 11.777 17.563 6.514 7.243 0.649 -0.534 N9 DZD 35
DZD C3 C3 C 0 1 Y N N 11.407 16.548 5.737 8.256 1.299 -1.194 C3 DZD 36
DZD C2 C2 C 0 1 Y N N 10.965 17.205 4.495 8.711 2.298 -0.317 C2 DZD 37
DZD N7 N7 N 0 1 Y N N 11.074 18.550 4.654 7.967 2.208 0.812 N7 DZD 38
DZD C8 C8 C 0 1 Y N N 11.544 18.762 5.908 7.101 1.245 0.684 C8 DZD 39
DZD C1 C1 C 0 1 Y N N 10.479 16.308 3.439 9.762 3.128 -0.745 C1 DZD 40
DZD N10 N10 N 0 1 N N N 10.081 16.856 2.267 10.253 4.128 0.075 N10 DZD 41
DZD N6 N6 N 0 1 Y N N 10.502 14.989 3.672 10.273 2.928 -1.955 N6 DZD 42
DZD C5 C5 C 0 1 Y N N 10.973 14.440 4.830 9.811 1.976 -2.744 C5 DZD 43
DZD N4 N4 N 0 1 Y N N 11.396 15.184 5.860 8.830 1.175 -2.386 N4 DZD 44
DZD HN67 HN67 H 0 0 N N N 3.816 23.470 7.250 -12.209 -2.361 -3.371 HN67 DZD 45
DZD HN6A HN6A H 0 0 N N N 2.190 22.921 6.855 -12.561 -0.887 -2.645 HN6A DZD 46
DZD H63 H63 H 0 1 N N N 4.910 24.815 7.934 -12.129 0.701 -1.829 H63 DZD 47
DZD H62 H62 H 0 1 N N N 6.677 25.780 9.397 -11.363 2.781 -0.762 H62 DZD 48
DZD H61 H61 H 0 1 N N N 6.402 25.713 11.863 -8.958 3.215 -0.490 H61 DZD 49
DZD H65 H65 H 0 1 N N N 2.558 23.843 11.410 -8.049 -0.516 -2.341 H65 DZD 50
DZD H59 H59 H 0 1 N N N 4.794 25.606 13.719 -6.332 1.171 -2.038 H59 DZD 51
DZD H59A H59A H 0 0 N N N 3.215 24.706 13.494 -6.712 2.727 -1.261 H59A DZD 52
DZD H48 H48 H 0 1 N N N 3.250 23.255 15.311 -6.963 2.973 0.961 H48 DZD 53
DZD H48A H48A H 0 0 N N N 3.709 21.804 14.613 -8.011 1.590 1.413 H48A DZD 54
DZD H49 H49 H 0 1 N N N 5.092 21.970 16.703 -6.308 0.615 2.813 H49 DZD 55
DZD HO50 HO50 H 0 0 N N N 5.612 23.938 17.411 -6.920 2.758 3.745 HO50 DZD 56
DZD H46 H46 H 0 1 N N N 6.328 22.321 12.892 -4.505 0.273 -0.119 H46 DZD 57
DZD H46A H46A H 0 0 N N N 6.962 23.829 13.421 -4.591 2.031 -0.426 H46A DZD 58
DZD H45 H45 H 0 1 N N N 7.487 22.822 15.449 -4.124 2.429 1.780 H45 DZD 59
DZD H38 H38 H 0 1 N N N 6.347 20.510 16.039 -3.728 0.489 3.340 H38 DZD 60
DZD H38A H38A H 0 0 N N N 6.022 20.525 14.240 -4.351 -0.606 2.083 H38A DZD 61
DZD HO37 HO37 H 0 0 N N N 9.418 18.330 12.738 -0.589 0.323 3.739 HO37 DZD 62
DZD H31 H31 H 0 1 N N N 8.539 21.625 11.735 -0.294 -0.721 -0.099 H31 DZD 63
DZD H31A H31A H 0 0 N N N 9.052 22.125 13.426 0.424 0.434 1.049 H31A DZD 64
DZD HO32 HO32 H 0 0 N N N 12.607 21.034 13.215 0.397 -3.485 0.303 HO32 DZD 65
DZD H20 H20 H 0 1 N N N 9.473 19.126 10.104 4.203 -2.158 1.532 H20 DZD 66
DZD H20A H20A H 0 0 N N N 10.779 20.154 9.544 3.561 -3.426 0.460 H20A DZD 67
DZD H17 H17 H 0 1 N N N 11.160 17.359 10.718 4.318 -2.049 -1.522 H17 DZD 68
DZD H18 H18 H 0 1 N N N 13.129 19.398 10.274 6.179 -3.191 0.568 H18 DZD 69
DZD HO21 HO21 H 0 0 N N N 13.692 16.650 10.012 6.800 -4.435 -1.375 HO21 DZD 70
DZD H19 H19 H 0 1 N N N 13.147 19.389 7.896 7.876 -1.709 0.055 H19 DZD 71
DZD HO20 HO20 H 0 0 N N N 14.643 17.798 7.192 8.318 -3.097 -1.865 HO20 DZD 72
DZD H15 H15 H 0 1 N N N 12.734 16.366 7.960 6.263 -0.349 -2.112 H15 DZD 73
DZD H8 H8 H 0 1 N N N 11.708 19.730 6.357 6.381 0.956 1.435 H8 DZD 74
DZD HN10 HN10 H 0 0 N N N 9.983 17.845 2.377 9.871 4.264 0.957 HN10 DZD 75
DZD HN1A HN1A H 0 0 N N N 10.763 16.666 1.561 10.978 4.695 -0.232 HN1A DZD 76
DZD H5 H5 H 0 1 N N N 11.006 13.364 4.919 10.255 1.849 -3.721 H5 DZD 77
#
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
DZD C66 O68 DOUB N N 1
DZD N67 C66 SING N N 2
DZD C66 C64 SING N N 3
DZD N67 HN67 SING N N 4
DZD N67 HN6A SING N N 5
DZD C63 C64 DOUB Y N 6
DZD C64 C65 SING Y N 7
DZD C63 C62 SING Y N 8
DZD C63 H63 SING N N 9
DZD C62 C61 DOUB Y N 10
DZD C62 H62 SING N N 11
DZD C61 C60 SING Y N 12
DZD C61 H61 SING N N 13
DZD C65 C60 DOUB Y N 14
DZD C65 H65 SING N N 15
DZD C60 C59 SING N N 16
DZD C59 N47 SING N N 17
DZD C59 H59 SING N N 18
DZD C59 H59A SING N N 19
DZD C46 N47 SING N N 20
DZD N47 C48 SING N N 21
DZD C48 C49 SING N N 22
DZD C48 H48 SING N N 23
DZD C48 H48A SING N N 24
DZD C45 C49 SING N N 25
DZD C49 O50 SING N N 26
DZD C49 H49 SING N N 27
DZD O50 HO50 SING N N 28
DZD C46 C45 SING N N 29
DZD C46 H46 SING N N 30
DZD C46 H46A SING N N 31
DZD C38 C45 SING N N 32
DZD C45 H45 SING N N 33
DZD O35 C38 SING N N 34
DZD C38 H38 SING N N 35
DZD C38 H38A SING N N 36
DZD P34 O35 SING N N 37
DZD O36 P34 DOUB N N 38
DZD C31 P34 SING N N 39
DZD P34 O37 SING N N 40
DZD O37 HO37 SING N N 41
DZD P30 C31 SING N N 42
DZD C31 H31 SING N N 43
DZD C31 H31A SING N N 44
DZD O33 P30 DOUB N N 45
DZD O29 P30 SING N N 46
DZD P30 O32 SING N N 47
DZD O32 HO32 SING N N 48
DZD C20 O29 SING N N 49
DZD C17 C20 SING N N 50
DZD C20 H20 SING N N 51
DZD C20 H20A SING N N 52
DZD O16 C17 SING N N 53
DZD C18 C17 SING N N 54
DZD C17 H17 SING N N 55
DZD C19 C18 SING N N 56
DZD C18 O21 SING N N 57
DZD C18 H18 SING N N 58
DZD O21 HO21 SING N N 59
DZD C15 C19 SING N N 60
DZD O20 C19 SING N N 61
DZD C19 H19 SING N N 62
DZD O20 HO20 SING N N 63
DZD N9 C15 SING N N 64
DZD C15 O16 SING N N 65
DZD C15 H15 SING N N 66
DZD C3 N9 SING Y N 67
DZD C8 N9 SING Y N 68
DZD C2 C3 DOUB Y N 69
DZD C3 N4 SING Y N 70
DZD C1 C2 SING Y N 71
DZD C2 N7 SING Y N 72
DZD N7 C8 DOUB Y N 73
DZD C8 H8 SING N N 74
DZD N10 C1 SING N N 75
DZD C1 N6 DOUB Y N 76
DZD N10 HN10 SING N N 77
DZD N10 HN1A SING N N 78
DZD N6 C5 SING Y N 79
DZD C5 N4 DOUB Y N 80
DZD C5 H5 SING N N 81
#
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
DZD SMILES ACDLabs 10.04 "O=C(N)c1cc(ccc1)CN2CC(O)C(C2)COP(=O)(O)CP(=O)(O)OCC5OC(n4cnc3c(ncnc34)N)C(O)C5O"
DZD SMILES_CANONICAL CACTVS 3.341 "NC(=O)c1cccc(CN2C[C@H](O)[C@@H](CO[P@@](O)(=O)C[P@](O)(=O)OC[C@H]3O[C@H]([C@H](O)[C@@H]3O)n4cnc5c(N)ncnc45)C2)c1"
DZD SMILES CACTVS 3.341 "NC(=O)c1cccc(CN2C[CH](O)[CH](CO[P](O)(=O)C[P](O)(=O)OC[CH]3O[CH]([CH](O)[CH]3O)n4cnc5c(N)ncnc45)C2)c1"
DZD SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "c1cc(cc(c1)C(=O)N)CN2C[C@@H]([C@H](C2)O)CO[P@@](=O)(C[P@@](=O)(O)OC[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4ncnc5N)O)O)O"
DZD SMILES "OpenEye OEToolkits" 1.5.0 "c1cc(cc(c1)C(=O)N)CN2CC(C(C2)O)COP(=O)(CP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)O)O)O"
DZD InChI InChI 1.03
;InChI=1S/C24H33N7O11P2/c25-21-18-23(28-10-27-21)31(11-29-18)24-20(34)19(33)17(42-24)9-41-44(38,39)12-43(36,37)40-8-15-6-30(7-16(15)32)5-13-2-1-3-14(4-13)22(26)35/h1-4,10-11,15-17,19-20,24,32-34H,5-9,12H2,(H2,26,35)(H,36,37)(H,38,39)(H2,25,27,28)/t15-,16+,17-,19-,20-,24-/m1/s1
;
DZD InChIKey InChI 1.03 IMHBNZNABRBOGP-YZOALNMRSA-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
DZD "SYSTEMATIC NAME" ACDLabs 10.04 "5'-O-[(R)-{[(R)-{[(3R,4R)-1-(3-carbamoylbenzyl)-4-hydroxypyrrolidin-3-yl]methoxy}(hydroxy)phosphoryl]methyl}(hydroxy)phosphoryl]adenosine"
DZD "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(3R,4R)-1-[(3-aminocarbonylphenyl)methyl]-4-hydroxy-pyrrolidin-3-yl]methoxy-[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl]methyl]phosphinic 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
DZD "Create component" 2008-06-24 RCSB
DZD "Modify aromatic_flag" 2011-06-04 RCSB
DZD "Modify descriptor" 2011-06-04 RCSB
#