data_DZ4
#
_chem_comp.id DZ4
_chem_comp.name "2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C10 H17 N6 O11 P3"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2010-04-29
_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 490.197
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code DZ4
_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 3MR2
_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
DZ4 N1 N1 N 0 1 Y N N -24.207 49.699 6.436 7.821 -2.008 0.572 N1 DZ4 1
DZ4 C2 C2 C 0 1 Y N N -23.086 49.961 5.755 7.744 -0.731 0.899 C2 DZ4 2
DZ4 N3 N3 N 0 1 Y N N -22.252 49.002 5.385 6.634 -0.035 0.773 N3 DZ4 3
DZ4 C4 C4 C 0 1 Y N N -22.520 47.721 5.673 5.529 -0.603 0.301 C4 DZ4 4
DZ4 C5 C5 C 0 1 Y N N -23.691 47.371 6.410 5.560 -1.960 -0.062 C5 DZ4 5
DZ4 C6 C6 C 0 1 Y N N -24.546 48.427 6.771 6.768 -2.660 0.091 C6 DZ4 6
DZ4 N6 N6 N 0 1 N N N -25.712 48.181 7.472 6.858 -3.999 -0.250 N6 DZ4 7
DZ4 N7 N7 N 0 1 Y N N -23.682 46.024 6.550 4.320 -2.282 -0.505 N7 DZ4 8
DZ4 C8 C8 C 0 1 Y N N -22.612 45.551 5.982 3.550 -1.236 -0.438 C8 DZ4 9
DZ4 N9 N9 N 0 1 Y N N -21.868 46.581 5.431 4.249 -0.174 0.053 N9 DZ4 10
DZ4 PA PA P 0 1 N N N -21.547 41.518 5.831 -2.084 1.944 0.630 PA DZ4 11
DZ4 PB PB P 0 1 N N N -18.921 41.227 7.203 -4.136 0.125 0.207 PB DZ4 12
DZ4 PG PG P 0 1 N N N -19.161 38.687 8.258 -5.823 -2.246 -0.358 PG DZ4 13
DZ4 "C1'" C1* C 0 1 N N R -20.634 46.513 4.692 3.730 1.178 0.276 C1* DZ4 14
DZ4 O1A O1A O 0 1 N N N -21.270 40.509 5.100 -2.667 2.854 -0.382 O1A DZ4 15
DZ4 O1B O1B O 0 1 N N N -18.540 40.869 6.041 -4.704 0.439 1.537 O1B DZ4 16
DZ4 O1G O1G O 0 1 N N N -19.818 38.448 7.133 -6.780 -1.458 -1.167 O1G DZ4 17
DZ4 "C2'" C2* C 0 1 N N N -19.472 46.346 5.687 4.041 2.067 -0.944 C2* DZ4 18
DZ4 O2A O2A O 0 1 N N N -22.845 41.639 6.332 -2.683 2.301 2.081 O2A DZ4 19
DZ4 O2B O2B O 0 1 N N N -18.331 42.292 7.586 -4.788 1.099 -0.898 O2B DZ4 20
DZ4 O2G O2G O 0 1 N N N -18.124 37.875 8.468 -5.497 -3.631 -1.111 O2G DZ4 21
DZ4 "C3'" C3* C 0 1 N N S -19.044 44.905 5.607 2.651 2.550 -1.425 C3* DZ4 22
DZ4 "O3'" O3* O 0 1 N N N -17.768 44.571 5.830 2.693 3.927 -1.804 O3* DZ4 23
DZ4 N3A N3A N 0 1 N N N -20.543 41.569 7.067 -2.469 0.352 0.241 N3A DZ4 24
DZ4 O3B O3B O 0 1 N N N -18.688 40.142 8.262 -4.462 -1.406 -0.168 O3B DZ4 25
DZ4 O3G O3G O 0 1 N N N -20.022 38.534 9.299 -6.467 -2.557 1.084 O3G DZ4 26
DZ4 "C4'" C4* C 0 1 N N R -19.672 44.527 4.259 1.781 2.352 -0.157 C4* DZ4 27
DZ4 "O4'" O4* O 0 1 N N N -20.600 45.461 3.871 2.300 1.135 0.420 O4* DZ4 28
DZ4 "C5'" C5* C 0 1 N N N -20.181 43.084 4.336 0.308 2.183 -0.536 C5* DZ4 29
DZ4 "O5'" O5* O 0 1 N N N -21.364 42.799 5.021 -0.484 2.119 0.652 O5* DZ4 30
DZ4 H2 H2 H 0 1 N N N -22.855 50.985 5.500 8.625 -0.240 1.286 H2 DZ4 31
DZ4 HN6 HN6 H 0 1 N N N -26.183 49.045 7.650 7.698 -4.471 -0.139 HN6 DZ4 32
DZ4 HN6A HN6A H 0 0 N N N -26.305 47.583 6.933 6.082 -4.464 -0.599 HN6A DZ4 33
DZ4 H8 H8 H 0 1 N N N -22.342 44.506 5.945 2.510 -1.212 -0.729 H8 DZ4 34
DZ4 "H1'" H1* H 0 1 N N N -20.551 47.436 4.100 4.182 1.606 1.171 H1* DZ4 35
DZ4 "H2'" H2* H 0 1 N N N -18.637 47.011 5.419 4.659 2.915 -0.650 H2* DZ4 36
DZ4 "H2'A" H2*A H 0 0 N N N -19.801 46.594 6.707 4.536 1.486 -1.722 H2*A DZ4 37
DZ4 HO2A HO2A H 0 0 N N N -23.369 40.904 6.036 -2.345 1.743 2.795 HO2A DZ4 38
DZ4 HO2B HO2B H 0 0 N N N -17.731 42.583 6.909 -4.461 0.950 -1.795 HO2B DZ4 39
DZ4 HO2G HO2G H 0 0 N N N -18.052 37.260 7.747 -6.273 -4.190 -1.259 HO2G DZ4 40
DZ4 "H3'" H3* H 0 1 N N N -19.383 44.305 6.464 2.288 1.933 -2.247 H3* DZ4 41
DZ4 "HO3'" HO3* H 0 0 N N N -17.666 43.631 5.741 3.295 4.115 -2.537 HO3* DZ4 42
DZ4 HN3A HN3A H 0 0 N N N -20.585 42.530 7.341 -2.049 0.083 -0.637 HN3A DZ4 43
DZ4 HO3G HO3G H 0 0 N N N -20.880 38.294 8.968 -5.893 -3.071 1.668 HO3G DZ4 44
DZ4 "H4'" H4* H 0 1 N N N -18.924 44.546 3.452 1.907 3.189 0.529 H4* DZ4 45
DZ4 "H5'" H5* H 0 1 N N N -20.344 42.761 3.297 -0.011 3.033 -1.140 H5* DZ4 46
DZ4 "H5'A" H5*A H 0 0 N N N -19.390 42.507 4.838 0.183 1.263 -1.106 H5*A DZ4 47
#
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
DZ4 C2 N1 DOUB Y N 1
DZ4 N1 C6 SING Y N 2
DZ4 N3 C2 SING Y N 3
DZ4 C2 H2 SING N N 4
DZ4 N3 C4 DOUB Y N 5
DZ4 N9 C4 SING Y N 6
DZ4 C4 C5 SING Y N 7
DZ4 C5 N7 SING Y N 8
DZ4 C5 C6 DOUB Y N 9
DZ4 C6 N6 SING N N 10
DZ4 N6 HN6 SING N N 11
DZ4 N6 HN6A SING N N 12
DZ4 C8 N7 DOUB Y N 13
DZ4 N9 C8 SING Y N 14
DZ4 C8 H8 SING N N 15
DZ4 "C1'" N9 SING N N 16
DZ4 "O5'" PA SING N N 17
DZ4 O1A PA DOUB N N 18
DZ4 PA O2A SING N N 19
DZ4 PA N3A SING N N 20
DZ4 O1B PB DOUB N N 21
DZ4 N3A PB SING N N 22
DZ4 PB O2B SING N N 23
DZ4 PB O3B SING N N 24
DZ4 O1G PG DOUB N N 25
DZ4 PG O3B SING N N 26
DZ4 PG O2G SING N N 27
DZ4 PG O3G SING N N 28
DZ4 "O4'" "C1'" SING N N 29
DZ4 "C1'" "C2'" SING N N 30
DZ4 "C1'" "H1'" SING N N 31
DZ4 "C3'" "C2'" SING N N 32
DZ4 "C2'" "H2'" SING N N 33
DZ4 "C2'" "H2'A" SING N N 34
DZ4 O2A HO2A SING N N 35
DZ4 O2B HO2B SING N N 36
DZ4 O2G HO2G SING N N 37
DZ4 "C4'" "C3'" SING N N 38
DZ4 "C3'" "O3'" SING N N 39
DZ4 "C3'" "H3'" SING N N 40
DZ4 "O3'" "HO3'" SING N N 41
DZ4 N3A HN3A SING N N 42
DZ4 O3G HO3G SING N N 43
DZ4 "O4'" "C4'" SING N N 44
DZ4 "C4'" "C5'" SING N N 45
DZ4 "C4'" "H4'" SING N N 46
DZ4 "C5'" "O5'" SING N N 47
DZ4 "C5'" "H5'" SING N N 48
DZ4 "C5'" "H5'A" SING N N 49
#
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
DZ4 SMILES ACDLabs 12.01 "O=P(O)(O)OP(=O)(O)NP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)CC3O"
DZ4 SMILES_CANONICAL CACTVS 3.370 "Nc1ncnc2n(cnc12)[C@H]3C[C@H](O)[C@@H](CO[P](O)(=O)N[P](O)(=O)O[P](O)(O)=O)O3"
DZ4 SMILES CACTVS 3.370 "Nc1ncnc2n(cnc12)[CH]3C[CH](O)[CH](CO[P](O)(=O)N[P](O)(=O)O[P](O)(O)=O)O3"
DZ4 SMILES_CANONICAL "OpenEye OEToolkits" 1.7.0 "c1nc(c2c(n1)n(cn2)[C@H]3C[C@@H]([C@H](O3)CO[P@@](=O)(N[P@@](=O)(O)OP(=O)(O)O)O)O)N"
DZ4 SMILES "OpenEye OEToolkits" 1.7.0 "c1nc(c2c(n1)n(cn2)C3CC(C(O3)COP(=O)(NP(=O)(O)OP(=O)(O)O)O)O)N"
DZ4 InChI InChI 1.03 "InChI=1S/C10H17N6O11P3/c11-9-8-10(13-3-12-9)16(4-14-8)7-1-5(17)6(26-7)2-25-28(18,19)15-29(20,21)27-30(22,23)24/h3-7,17H,1-2H2,(H2,11,12,13)(H2,22,23,24)(H3,15,18,19,20,21)/t5-,6+,7+/m0/s1"
DZ4 InChIKey InChI 1.03 WKIPJDSLGCBQCU-RRKCRQDMSA-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
DZ4 "SYSTEMATIC NAME" ACDLabs 12.01 "2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine"
DZ4 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.0 "[(2R,3S,5R)-5-(6-aminopurin-9-yl)-3-hydroxy-oxolan-2-yl]methoxy-N-[hydroxy(phosphonooxy)phosphoryl]phosphonamidic 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
DZ4 "Create component" 2010-04-29 RCSB
DZ4 "Modify aromatic_flag" 2011-06-04 RCSB
DZ4 "Modify descriptor" 2011-06-04 RCSB
#