data_N6T
#
_chem_comp.id N6T
_chem_comp.name "2'-deoxy-5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonoamino)phosphoryl]methyl}phosphoryl]-3,4-dihydrothymidine"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C11 H20 N3 O12 P3"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2014-11-13
_chem_comp.pdbx_modified_date 2015-06-26
_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 479.211
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code N6T
_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 4RT2
_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
N6T O4 O4 O 0 1 N N N 10.837 7.640 10.877 -7.279 -3.222 0.971 O4 N6T 1
N6T C4 C4 C 0 1 N N N 9.432 7.627 10.697 -6.593 -2.314 0.538 C4 N6T 2
N6T C5 C5 C 0 1 N N N 8.621 7.197 11.769 -6.607 -2.003 -0.843 C5 N6T 3
N6T C7 C7 C 0 1 N N N 9.208 6.765 13.062 -7.470 -2.792 -1.794 C7 N6T 4
N6T C6 C6 C 0 1 N N N 7.238 7.185 11.553 -5.838 -0.991 -1.297 C6 N6T 5
N6T N3 N3 N 0 1 N N N 8.872 8.013 9.518 -5.817 -1.591 1.371 N3 N6T 6
N6T C2 C2 C 0 1 N N N 7.577 7.979 9.386 -5.060 -0.587 0.891 C2 N6T 7
N6T O2 O2 O 0 1 N N N 7.117 8.312 8.335 -4.365 0.057 1.654 O2 N6T 8
N6T N1 N1 N 0 1 N N N 6.738 7.586 10.377 -5.060 -0.285 -0.420 N1 N6T 9
N6T "C1'" "C1'" C 0 1 N N R 5.304 7.539 10.166 -4.225 0.813 -0.912 "C1'" N6T 10
N6T "C2'" "C2'" C 0 1 N N N 4.993 6.090 9.666 -4.659 2.149 -0.269 "C2'" N6T 11
N6T "C3'" "C3'" C 0 1 N N S 4.488 5.377 10.929 -3.332 2.907 -0.045 "C3'" N6T 12
N6T "O3'" "O3'" O 0 1 N N N 3.660 4.205 10.520 -3.321 4.128 -0.787 "O3'" N6T 13
N6T "O4'" "O4'" O 0 1 N N N 4.605 7.671 11.267 -2.855 0.630 -0.493 "O4'" N6T 14
N6T "C4'" "C4'" C 0 1 N N R 3.771 6.315 11.534 -2.252 1.939 -0.579 "C4'" N6T 15
N6T "C5'" "C5'" C 0 1 N N N 3.635 6.065 13.021 -0.998 2.007 0.293 "C5'" N6T 16
N6T "O5'" "O5'" O 0 1 N N N 4.910 6.112 13.593 0.028 1.195 -0.283 "O5'" N6T 17
N6T PA PA P 0 1 N N N 5.277 5.176 14.877 1.489 1.031 0.373 PA N6T 18
N6T O1A O1A O 0 1 N N N 4.163 5.214 15.900 1.358 0.289 1.796 O1A N6T 19
N6T O2A O2A O 0 1 N N N 6.637 5.647 15.485 2.095 2.367 0.567 O2A N6T 20
N6T C3A C3A C 0 1 N N N 5.534 3.433 14.292 2.544 0.040 -0.734 C3A N6T 21
N6T PB PB P 0 1 N N N 4.040 2.524 13.802 4.199 -0.146 0.008 PB N6T 22
N6T O1B O1B O 0 1 N N N 4.099 2.316 12.245 4.079 -0.827 1.316 O1B N6T 23
N6T O2B O2B O 0 1 N N N 2.806 3.223 14.208 4.858 1.308 0.219 O2B N6T 24
N6T N3B N3B N 0 1 N N N 4.123 1.053 14.594 5.173 -1.061 -1.014 N3B N6T 25
N6T PG PG P 0 1 N N N 4.012 0.992 16.245 6.713 -1.256 -0.364 PG N6T 26
N6T O2G O2G O 0 1 N N N 2.913 0.023 16.596 6.614 -1.947 0.941 O2G N6T 27
N6T O1G O1G O 0 1 N N N 5.238 0.513 16.817 7.613 -2.135 -1.370 O1G N6T 28
N6T O3G O3G O 0 1 N N N 3.716 2.405 16.772 7.395 0.187 -0.156 O3G N6T 29
N6T H1 H1 H 0 1 N N N 8.402 6.473 13.752 -8.013 -3.559 -1.241 H1 N6T 30
N6T H2 H2 H 0 1 N N N 9.875 5.907 12.893 -8.181 -2.123 -2.279 H2 N6T 31
N6T H3 H3 H 0 1 N N N 9.782 7.595 13.500 -6.842 -3.264 -2.549 H3 N6T 32
N6T H4 H4 H 0 1 N N N 6.573 6.852 12.336 -5.835 -0.740 -2.347 H4 N6T 33
N6T H5 H5 H 0 1 N N N 9.449 8.320 8.761 -5.805 -1.795 2.319 H5 N6T 34
N6T H6 H6 H 0 1 N N N 5.007 8.256 9.386 -4.284 0.876 -1.998 H6 N6T 35
N6T H7 H7 H 0 1 N N N 4.219 6.101 8.884 -5.308 2.705 -0.946 H7 N6T 36
N6T H8 H8 H 0 1 N N N 5.900 5.605 9.277 -5.162 1.969 0.682 H8 N6T 37
N6T H9 H9 H 0 1 N N N 5.346 5.043 11.531 -3.178 3.102 1.016 H9 N6T 38
N6T H10 H10 H 0 1 N N N 3.796 3.491 11.132 -4.018 4.749 -0.533 H10 N6T 39
N6T H11 H11 H 0 1 N N N 2.772 6.432 11.088 -2.009 2.177 -1.615 H11 N6T 40
N6T H12 H12 H 0 1 N N N 2.997 6.839 13.471 -0.652 3.039 0.354 H12 N6T 41
N6T H13 H13 H 0 1 N N N 3.187 5.075 13.192 -1.231 1.643 1.294 H13 N6T 42
N6T H14 H14 H 0 1 N N N 4.506 5.522 16.731 0.968 -0.594 1.745 H14 N6T 43
N6T H15 H15 H 0 1 N N N 6.016 2.873 15.107 2.098 -0.944 -0.877 H15 N6T 44
N6T H16 H16 H 0 1 N N N 6.207 3.466 13.423 2.633 0.542 -1.698 H16 N6T 45
N6T H17 H17 H 0 1 N N N 2.282 3.413 13.439 4.968 1.813 -0.598 H17 N6T 46
N6T H18 H18 H 0 1 N N N 3.380 0.489 14.234 4.749 -1.954 -1.214 H18 N6T 47
N6T H19 H19 H 0 1 N N N 5.075 -0.299 17.282 8.515 -2.288 -1.058 H19 N6T 48
N6T H20 H20 H 0 1 N N N 2.883 2.405 17.228 7.493 0.697 -0.972 H20 N6T 49
#
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
N6T O2 C2 DOUB N N 1
N6T C2 N3 SING N N 2
N6T C2 N1 SING N N 3
N6T N3 C4 SING N N 4
N6T "C2'" "C1'" SING N N 5
N6T "C2'" "C3'" SING N N 6
N6T "C1'" N1 SING N N 7
N6T "C1'" "O4'" SING N N 8
N6T N1 C6 SING N N 9
N6T "O3'" "C3'" SING N N 10
N6T C4 O4 DOUB N N 11
N6T C4 C5 SING N N 12
N6T "C3'" "C4'" SING N N 13
N6T "O4'" "C4'" SING N N 14
N6T "C4'" "C5'" SING N N 15
N6T C6 C5 DOUB N N 16
N6T C5 C7 SING N N 17
N6T O1B PB DOUB N N 18
N6T "C5'" "O5'" SING N N 19
N6T "O5'" PA SING N N 20
N6T PB O2B SING N N 21
N6T PB C3A SING N N 22
N6T PB N3B SING N N 23
N6T C3A PA SING N N 24
N6T N3B PG SING N N 25
N6T PA O2A DOUB N N 26
N6T PA O1A SING N N 27
N6T PG O2G DOUB N N 28
N6T PG O3G SING N N 29
N6T PG O1G SING N N 30
N6T C7 H1 SING N N 31
N6T C7 H2 SING N N 32
N6T C7 H3 SING N N 33
N6T C6 H4 SING N N 34
N6T N3 H5 SING N N 35
N6T "C1'" H6 SING N N 36
N6T "C2'" H7 SING N N 37
N6T "C2'" H8 SING N N 38
N6T "C3'" H9 SING N N 39
N6T "O3'" H10 SING N N 40
N6T "C4'" H11 SING N N 41
N6T "C5'" H12 SING N N 42
N6T "C5'" H13 SING N N 43
N6T O1A H14 SING N N 44
N6T C3A H15 SING N N 45
N6T C3A H16 SING N N 46
N6T O2B H17 SING N N 47
N6T N3B H18 SING N N 48
N6T O1G H19 SING N N 49
N6T O3G H20 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
N6T SMILES ACDLabs 12.01 "O=P(O)(O)NP(=O)(O)CP(=O)(O)OCC2OC(N1C(=O)NC(=O)C(=C1)C)CC2O"
N6T InChI InChI 1.03 "InChI=1S/C11H20N3O12P3/c1-6-3-14(11(17)12-10(6)16)9-2-7(15)8(26-9)4-25-28(20,21)5-27(18,19)13-29(22,23)24/h3,7-9,15H,2,4-5H2,1H3,(H,20,21)(H,12,16,17)(H4,13,18,19,22,23,24)/t7-,8+,9+/m0/s1"
N6T InChIKey InChI 1.03 FTYKINXQGSFHAF-DJLDLDEBSA-N
N6T SMILES_CANONICAL CACTVS 3.385 "CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P](O)(=O)C[P](O)(=O)N[P](O)(O)=O)O2)C(=O)NC1=O"
N6T SMILES CACTVS 3.385 "CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(=O)C[P](O)(=O)N[P](O)(O)=O)O2)C(=O)NC1=O"
N6T SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)COP(=O)(CP(=O)(NP(=O)(O)O)O)O)O"
N6T SMILES "OpenEye OEToolkits" 1.7.6 "CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(CP(=O)(NP(=O)(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
N6T "SYSTEMATIC NAME" ACDLabs 12.01 "2'-deoxy-5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonoamino)phosphoryl]methyl}phosphoryl]-3,4-dihydrothymidine"
N6T "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "[[[[(2R,3S,5R)-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]methyl-oxidanyl-phosphoryl]amino]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
N6T "Create component" 2014-11-13 RCSB
N6T "Initial release" 2015-07-01 RCSB
#