data_FDV
#
_chem_comp.id FDV
_chem_comp.name "5'-O-[(R)-hydroxy({(R)-hydroxy[(1S)-1-phosphonoethyl]phosphoryl}oxy)phosphoryl]thymidine"
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C12 H21 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 2018-03-26
_chem_comp.pdbx_modified_date 2018-06-15
_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 494.222
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code FDV
_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 6CTJ
_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
FDV N1 N1 N 0 1 N N N 54.622 8.446 9.765 5.003 -0.443 0.471 N1 FDV 1
FDV C2 C1 C 0 1 N N N 55.369 8.867 8.760 5.206 -0.319 -0.853 C2 FDV 2
FDV O2 O1 O 0 1 N N N 54.840 9.159 7.732 4.635 0.562 -1.467 O2 FDV 3
FDV N3 N2 N 0 1 N N N 56.690 8.984 8.859 6.034 -1.155 -1.508 N3 FDV 4
FDV C4 C2 C 0 1 N N N 57.304 8.667 9.991 6.675 -2.136 -0.841 C4 FDV 5
FDV O4 O2 O 0 1 N N N 58.501 8.769 10.084 7.424 -2.893 -1.433 O4 FDV 6
FDV C5 C3 C 0 1 N N N 56.567 8.206 11.105 6.469 -2.279 0.552 C5 FDV 7
FDV C7 C4 C 0 1 N N N 57.238 7.816 12.447 7.173 -3.368 1.320 C7 FDV 8
FDV C6 C5 C 0 1 N N N 55.184 8.115 10.937 5.634 -1.426 1.183 C6 FDV 9
FDV PA P1 P 0 1 N N N 53.285 6.070 14.193 -1.351 1.360 -0.807 PA FDV 10
FDV PB P2 P 0 1 N N N 52.208 3.457 13.540 -4.001 0.063 -0.523 PB FDV 11
FDV PG P3 P 0 1 N N N 52.429 2.095 16.204 -6.373 -1.415 0.501 PG FDV 12
FDV "C1'" C6 C 0 1 N N R 53.296 8.342 9.586 4.101 0.486 1.157 "C1'" FDV 13
FDV O1A O3 O 0 1 N N N 52.264 6.151 15.263 -1.005 1.091 -2.356 O1A FDV 14
FDV O2B O4 O 0 1 N N N 51.985 2.965 12.114 -4.277 -0.104 -1.968 O2B FDV 15
FDV O1G O5 O 0 1 N N N 51.980 3.472 16.624 -7.012 -1.414 -0.977 O1G FDV 16
FDV "C2'" C7 C 0 1 N N N 52.892 6.892 9.190 4.627 1.933 1.036 "C2'" FDV 17
FDV O2A O6 O 0 1 N N N 54.674 6.305 14.732 -1.922 2.717 -0.657 O2A FDV 18
FDV O1B O7 O 0 1 N N N 50.918 3.944 14.194 -4.793 1.351 0.029 O1B FDV 19
FDV C4B C8 C 0 1 N N N 54.369 1.928 14.260 -3.947 -1.424 1.781 C4B FDV 20
FDV O2G O8 O 0 1 N N N 53.633 1.690 17.065 -6.862 -2.727 1.296 O2G FDV 21
FDV "C3'" C9 C 0 1 N N S 52.580 6.340 10.305 3.348 2.785 0.872 "C3'" FDV 22
FDV "O3'" O9 O 0 1 N N N 51.745 5.126 10.171 3.224 3.714 1.950 "O3'" FDV 23
FDV O3A O10 O 0 1 N N N 53.276 4.675 13.416 -2.420 0.268 -0.299 O3A FDV 24
FDV C3B C10 C 0 1 N N S 52.883 2.011 14.443 -4.555 -1.423 0.377 C3B FDV 25
FDV O3G O11 O 0 1 N N N 51.320 1.066 16.397 -6.813 -0.204 1.230 O3G FDV 26
FDV "C4'" C11 C 0 1 N N R 51.789 7.549 11.077 2.201 1.751 0.913 "C4'" FDV 27
FDV "O4'" O12 O 0 1 N N N 52.470 8.606 10.876 2.811 0.506 0.508 "O4'" FDV 28
FDV "C5'" C12 C 0 1 N N N 51.678 7.224 12.551 1.093 2.145 -0.066 "C5'" FDV 29
FDV "O5'" O13 O 0 1 N N N 52.973 7.228 13.142 -0.007 1.243 0.071 "O5'" FDV 30
FDV H1 H1 H 0 1 N N N 57.222 9.312 8.078 6.169 -1.051 -2.463 H1 FDV 31
FDV H2 H2 H 0 1 N N N 56.468 7.489 13.161 7.797 -3.947 0.640 H2 FDV 32
FDV H3 H3 H 0 1 N N N 57.951 6.996 12.276 7.796 -2.921 2.095 H3 FDV 33
FDV H4 H4 H 0 1 N N N 57.772 8.686 12.857 6.433 -4.023 1.781 H4 FDV 34
FDV H5 H5 H 0 1 N N N 54.564 7.777 11.754 5.465 -1.519 2.246 H5 FDV 35
FDV H6 H6 H 0 1 N N N 52.942 9.027 8.801 3.994 0.205 2.205 H6 FDV 36
FDV H7 H7 H 0 1 N N N 52.688 6.338 16.092 -0.626 0.219 -2.529 H7 FDV 37
FDV H8 H8 H 0 1 N N N 51.082 3.433 16.932 -6.766 -2.180 -1.512 H8 FDV 38
FDV H9 H9 H 0 1 N N N 52.032 6.900 8.504 5.164 2.221 1.939 H9 FDV 39
FDV H10 H10 H 0 1 N N N 53.735 6.367 8.716 5.268 2.035 0.160 H10 FDV 40
FDV H11 H11 H 0 1 N N N 50.197 3.850 13.582 -4.658 1.522 0.971 H11 FDV 41
FDV H12 H12 H 0 1 N N N 54.758 1.057 14.807 -2.860 -1.429 1.706 H12 FDV 42
FDV H13 H13 H 0 1 N N N 54.601 1.823 13.190 -4.271 -0.532 2.318 H13 FDV 43
FDV H14 H14 H 0 1 N N N 54.838 2.844 14.649 -4.278 -2.312 2.319 H14 FDV 44
FDV H15 H15 H 0 1 N N N 53.433 0.888 17.533 -7.822 -2.789 1.400 H15 FDV 45
FDV H16 H16 H 0 1 N N N 53.468 6.098 10.908 3.357 3.307 -0.085 H16 FDV 46
FDV H17 H17 H 0 1 N N N 51.944 4.525 10.879 3.950 4.349 2.008 H17 FDV 47
FDV H18 H18 H 0 1 N N N 52.390 1.119 14.028 -4.231 -2.314 -0.160 H18 FDV 48
FDV H19 H19 H 0 1 N N N 50.778 7.608 10.648 1.801 1.668 1.924 H19 FDV 49
FDV H20 H20 H 0 1 N N N 51.048 7.978 13.045 0.760 3.160 0.151 H20 FDV 50
FDV H21 H21 H 0 1 N N N 51.223 6.230 12.673 1.476 2.099 -1.085 H21 FDV 51
#
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
FDV O2 C2 DOUB N N 1
FDV C2 N3 SING N N 2
FDV C2 N1 SING N N 3
FDV N3 C4 SING N N 4
FDV "C2'" "C1'" SING N N 5
FDV "C2'" "C3'" SING N N 6
FDV "C1'" N1 SING N N 7
FDV "C1'" "O4'" SING N N 8
FDV N1 C6 SING N N 9
FDV C4 O4 DOUB N N 10
FDV C4 C5 SING N N 11
FDV "O3'" "C3'" SING N N 12
FDV "C3'" "C4'" SING N N 13
FDV "O4'" "C4'" SING N N 14
FDV C6 C5 DOUB N N 15
FDV "C4'" "C5'" SING N N 16
FDV C5 C7 SING N N 17
FDV O2B PB DOUB N N 18
FDV "C5'" "O5'" SING N N 19
FDV "O5'" PA SING N N 20
FDV O3A PB SING N N 21
FDV O3A PA SING N N 22
FDV PB O1B SING N N 23
FDV PB C3B SING N N 24
FDV PA O2A DOUB N N 25
FDV PA O1A SING N N 26
FDV C4B C3B SING N N 27
FDV C3B PG SING N N 28
FDV PG O3G DOUB N N 29
FDV PG O1G SING N N 30
FDV PG O2G SING N N 31
FDV N3 H1 SING N N 32
FDV C7 H2 SING N N 33
FDV C7 H3 SING N N 34
FDV C7 H4 SING N N 35
FDV C6 H5 SING N N 36
FDV "C1'" H6 SING N N 37
FDV O1A H7 SING N N 38
FDV O1G H8 SING N N 39
FDV "C2'" H9 SING N N 40
FDV "C2'" H10 SING N N 41
FDV O1B H11 SING N N 42
FDV C4B H12 SING N N 43
FDV C4B H13 SING N N 44
FDV C4B H14 SING N N 45
FDV O2G H15 SING N N 46
FDV "C3'" H16 SING N N 47
FDV "O3'" H17 SING N N 48
FDV C3B H18 SING N N 49
FDV "C4'" H19 SING N N 50
FDV "C5'" H20 SING N N 51
FDV "C5'" H21 SING N N 52
#
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
FDV SMILES ACDLabs 12.01 "N1(C=C(C(NC1=O)=O)C)C2OC(C(C2)O)COP(=O)(O)OP(O)(C(P(=O)(O)O)C)=O"
FDV InChI InChI 1.03 "InChI=1S/C12H21N2O13P3/c1-6-4-14(12(17)13-11(6)16)10-3-8(15)9(26-10)5-25-30(23,24)27-29(21,22)7(2)28(18,19)20/h4,7-10,15H,3,5H2,1-2H3,(H,21,22)(H,23,24)(H,13,16,17)(H2,18,19,20)/t7-,8-,9+,10+/m0/s1"
FDV InChIKey InChI 1.03 UWVKVMOYWXUGRK-AXTSPUMRSA-N
FDV SMILES_CANONICAL CACTVS 3.385 "C[C@@H]([P](O)(O)=O)[P](O)(=O)O[P](O)(=O)OC[C@H]1O[C@H](C[C@@H]1O)N2C=C(C)C(=O)NC2=O"
FDV SMILES CACTVS 3.385 "C[CH]([P](O)(O)=O)[P](O)(=O)O[P](O)(=O)OC[CH]1O[CH](C[CH]1O)N2C=C(C)C(=O)NC2=O"
FDV SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)OP(=O)([C@@H](C)P(=O)(O)O)O)O"
FDV SMILES "OpenEye OEToolkits" 2.0.6 "CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(O)OP(=O)(C(C)P(=O)(O)O)O)O"
#
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
FDV "SYSTEMATIC NAME" ACDLabs 12.01 "5'-O-[(R)-hydroxy({(R)-hydroxy[(1S)-1-phosphonoethyl]phosphoryl}oxy)phosphoryl]thymidine"
FDV "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "[(1~{S})-1-[[[(2~{R},3~{S},5~{R})-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]ethyl]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
FDV "Create component" 2018-03-26 RCSB
FDV "Initial release" 2018-06-20 RCSB
#