data_4BD
#
_chem_comp.id 4BD
_chem_comp.name "5'-O-[(S)-{difluoro[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}(hydroxy)phosphoryl]thymidine"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C11 H17 F2 N2 O13 P3"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2009-03-20
_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 516.176
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code 4BD
_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 3GDX
_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
4BD PA PA P 0 1 N N S 5.188 5.440 14.944 1.242 -1.081 -0.575 PA 4BD 1
4BD O1A O1A O 0 1 N N N 4.011 5.447 15.857 1.028 -0.290 -1.960 O1A 4BD 2
4BD O2A O2A O 0 1 N N N 6.451 6.054 15.428 1.777 -2.432 -0.855 O2A 4BD 3
4BD C3A C3A C 0 1 N N N 5.517 3.763 14.364 2.421 -0.166 0.472 C3A 4BD 4
4BD F1A F1A F 0 1 N N N 6.343 3.831 13.327 1.915 1.111 0.737 F1A 4BD 5
4BD F2A F2A F 0 1 N N N 6.162 3.123 15.344 2.607 -0.853 1.676 F2A 4BD 6
4BD "O5'" "O5'" O 0 1 N N N 4.723 6.377 13.733 -0.168 -1.211 0.192 "O5'" 4BD 7
4BD PB PB P 0 1 N N S 4.116 2.756 13.879 4.017 -0.019 -0.396 PB 4BD 8
4BD O1B O1B O 0 1 N N N 4.281 2.314 12.471 3.820 0.708 -1.670 O1B 4BD 9
4BD O2B O2B O 0 1 N N N 2.841 3.387 14.282 4.599 -1.489 -0.702 O2B 4BD 10
4BD O3B O3B O 0 1 N N N 4.232 1.484 14.684 5.058 0.789 0.528 O3B 4BD 11
4BD PG PG P 0 1 N N N 4.000 1.277 16.169 6.593 1.244 0.350 PG 4BD 12
4BD O1G O1G O 0 1 N N N 5.193 0.557 16.685 7.231 1.556 1.794 O1G 4BD 13
4BD O2G O2G O 0 1 N N N 2.662 0.674 16.372 7.357 0.158 -0.303 O2G 4BD 14
4BD O3G O3G O 0 1 N N N 4.002 2.615 16.825 6.657 2.569 -0.563 O3G 4BD 15
4BD "C5'" "C5'" C 0 1 N N N 3.512 6.143 13.017 -1.267 -1.965 -0.322 "C5'" 4BD 16
4BD "C4'" "C4'" C 0 1 N N R 3.713 6.378 11.538 -2.445 -1.878 0.651 "C4'" 4BD 17
4BD "O4'" "O4'" O 0 1 N N N 4.547 7.541 11.279 -2.989 -0.541 0.673 "O4'" 4BD 18
4BD "C1'" "C1'" C 0 1 N N R 5.290 7.337 10.088 -4.333 -0.643 1.171 "C1'" 4BD 19
4BD N1 N1 N 0 1 N N N 6.737 7.470 10.390 -5.182 0.358 0.520 N1 4BD 20
4BD C6 C6 C 0 1 N N N 7.219 7.163 11.645 -5.921 1.220 1.284 C6 4BD 21
4BD C2 C2 C 0 1 N N N 7.594 7.874 9.378 -5.223 0.426 -0.823 C2 4BD 22
4BD O2 O2 O 0 1 N N N 7.218 8.202 8.265 -4.555 -0.346 -1.483 O2 4BD 23
4BD N3 N3 N 0 1 N N N 8.923 7.877 9.724 -5.995 1.336 -1.447 N3 4BD 24
4BD C4 C4 C 0 1 N N N 9.471 7.531 10.942 -6.742 2.199 -0.729 C4 4BD 25
4BD O4 O4 O 0 1 N N N 10.688 7.526 11.079 -7.440 3.023 -1.293 O4 4BD 26
4BD C5 C5 C 0 1 N N N 8.517 7.174 11.973 -6.703 2.143 0.685 C5 4BD 27
4BD C5M C5M C 0 1 N N N 9.022 6.573 13.247 -7.525 3.100 1.510 C5M 4BD 28
4BD "C2'" "C2'" C 0 1 N N N 4.921 5.943 9.563 -4.840 -2.059 0.833 "C2'" 4BD 29
4BD "C3'" "C3'" C 0 1 N N S 4.436 5.252 10.837 -3.629 -2.746 0.153 "C3'" 4BD 30
4BD "O3'" "O3'" O 0 1 N N N 3.492 4.222 10.594 -3.497 -4.099 0.594 "O3'" 4BD 31
4BD HO1A HO1A H 0 0 N N N 4.309 5.448 16.759 0.678 0.605 -1.852 HO1A 4BD 32
4BD HO2B HO2B H 0 0 N N N 2.837 3.522 15.222 4.753 -2.023 0.090 HO2B 4BD 33
4BD HO1G HO1G H 0 0 N N N 5.803 0.403 15.973 8.156 1.836 1.763 HO1G 4BD 34
4BD HO3G HO3G H 0 0 N N N 4.002 2.506 17.769 6.176 3.323 -0.195 HO3G 4BD 35
4BD "H5'" "H5'" H 0 1 N N N 3.196 5.101 13.176 -1.565 -1.561 -1.289 "H5'" 4BD 36
4BD "H5'A" "H5'A" H 0 0 N N N 2.743 6.838 13.385 -0.970 -3.007 -0.440 "H5'A" 4BD 37
4BD "H4'" "H4'" H 0 1 N N N 2.686 6.491 11.162 -2.138 -2.185 1.651 "H4'" 4BD 38
4BD "H1'" "H1'" H 0 1 N N N 5.057 8.083 9.314 -4.342 -0.491 2.250 "H1'" 4BD 39
4BD H6 H6 H 0 1 N N N 6.505 6.897 12.411 -5.879 1.162 2.362 H6 4BD 40
4BD HN3 HN3 H 0 1 N N N 9.566 8.162 9.013 -6.013 1.370 -2.416 HN3 4BD 41
4BD H5M H5M H 0 1 N N N 9.146 5.488 13.117 -6.941 3.997 1.714 H5M 4BD 42
4BD H5MA H5MA H 0 0 N N N 9.991 7.024 13.506 -8.427 3.371 0.961 H5MA 4BD 43
4BD H5MB H5MB H 0 0 N N N 8.300 6.765 14.054 -7.801 2.624 2.451 H5MB 4BD 44
4BD "H2'" "H2'" H 0 1 N N N 4.140 5.984 8.790 -5.117 -2.592 1.743 "H2'" 4BD 45
4BD "H2'A" "H2'A" H 0 0 N N N 5.752 5.422 9.064 -5.686 -2.007 0.148 "H2'A" 4BD 46
4BD "H3'" "H3'" H 0 1 N N N 5.267 4.779 11.381 -3.714 -2.698 -0.932 "H3'" 4BD 47
4BD "HO3'" "HO3'" H 0 0 N N N 3.281 4.197 9.668 -4.258 -4.657 0.382 "HO3'" 4BD 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
4BD "O5'" PA SING N N 1
4BD C3A PA SING N N 2
4BD PA O2A DOUB N N 3
4BD PA O1A SING N N 4
4BD O1A HO1A SING N N 5
4BD F1A C3A SING N N 6
4BD PB C3A SING N N 7
4BD C3A F2A SING N N 8
4BD "C5'" "O5'" SING N N 9
4BD O1B PB DOUB N N 10
4BD PB O2B SING N N 11
4BD PB O3B SING N N 12
4BD O2B HO2B SING N N 13
4BD O3B PG SING N N 14
4BD PG O2G DOUB N N 15
4BD PG O1G SING N N 16
4BD PG O3G SING N N 17
4BD O1G HO1G SING N N 18
4BD O3G HO3G SING N N 19
4BD "C4'" "C5'" SING N N 20
4BD "C5'" "H5'" SING N N 21
4BD "C5'" "H5'A" SING N N 22
4BD "C3'" "C4'" SING N N 23
4BD "O4'" "C4'" SING N N 24
4BD "C4'" "H4'" SING N N 25
4BD "C1'" "O4'" SING N N 26
4BD "C2'" "C1'" SING N N 27
4BD "C1'" N1 SING N N 28
4BD "C1'" "H1'" SING N N 29
4BD C2 N1 SING N N 30
4BD N1 C6 SING N N 31
4BD C6 C5 DOUB N N 32
4BD C6 H6 SING N N 33
4BD O2 C2 DOUB N N 34
4BD C2 N3 SING N N 35
4BD N3 C4 SING N N 36
4BD N3 HN3 SING N N 37
4BD C4 O4 DOUB N N 38
4BD C4 C5 SING N N 39
4BD C5 C5M SING N N 40
4BD C5M H5M SING N N 41
4BD C5M H5MA SING N N 42
4BD C5M H5MB SING N N 43
4BD "C2'" "C3'" SING N N 44
4BD "C2'" "H2'" SING N N 45
4BD "C2'" "H2'A" SING N N 46
4BD "O3'" "C3'" SING N N 47
4BD "C3'" "H3'" SING N N 48
4BD "O3'" "HO3'" 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
4BD SMILES ACDLabs 10.04 "O=P(O)(O)OP(=O)(O)C(F)(F)P(=O)(O)OCC2OC(N1C(=O)NC(=O)C(=C1)C)CC2O"
4BD SMILES_CANONICAL CACTVS 3.341 "CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P@](O)(=O)C(F)(F)[P@@](O)(=O)O[P](O)(O)=O)O2)C(=O)NC1=O"
4BD SMILES CACTVS 3.341 "CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(=O)C(F)(F)[P](O)(=O)O[P](O)(O)=O)O2)C(=O)NC1=O"
4BD SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)CO[P@](=O)(C(F)(F)[P@](=O)(O)OP(=O)(O)O)O)O"
4BD SMILES "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(C(F)(F)P(=O)(O)OP(=O)(O)O)O)O"
4BD InChI InChI 1.03 "InChI=1S/C11H17F2N2O13P3/c1-5-3-15(10(18)14-9(5)17)8-2-6(16)7(27-8)4-26-29(19,20)11(12,13)30(21,22)28-31(23,24)25/h3,6-8,16H,2,4H2,1H3,(H,19,20)(H,21,22)(H,14,17,18)(H2,23,24,25)/t6-,7+,8+/m0/s1"
4BD InChIKey InChI 1.03 WQZXQECPJNOPSV-XLPZGREQSA-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
4BD "SYSTEMATIC NAME" ACDLabs 10.04 "5'-O-[(S)-{difluoro[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}(hydroxy)phosphoryl]thymidine"
4BD "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[difluoro-(hydroxy-phosphonooxy-phosphoryl)methyl]-[[(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-pyrimidin-1-yl)oxolan-2-yl]methoxy]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
4BD "Create component" 2009-03-20 RCSB
4BD "Modify descriptor" 2011-06-04 RCSB
#