data_C6T
#
_chem_comp.id C6T
_chem_comp.name "2'-deoxy-5'-O-[(S)-hydroxy{[(R)-hydroxy(phosphonomethyl)phosphoryl]amino}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 C6T
_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 4RT3
_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
C6T O4 O4 O 0 1 N N N 10.754 7.723 11.003 -8.155 2.112 -0.957 O4 C6T 1
C6T C4 C4 C 0 1 N N N 9.384 7.705 10.780 -7.258 1.376 -0.589 C4 C6T 2
C6T C5 C5 C 0 1 N N N 8.547 7.268 11.820 -7.322 0.750 0.679 C5 C6T 3
C6T C7 C7 C 0 1 N N N 9.110 6.812 13.164 -8.501 0.986 1.588 C7 C6T 4
C6T C6 C6 C 0 1 N N N 7.164 7.233 11.554 -6.314 -0.062 1.063 C6 C6T 5
C6T N3 N3 N 0 1 N N N 8.882 8.098 9.590 -6.196 1.145 -1.388 N3 C6T 6
C6T C2 C2 C 0 1 N N N 7.569 8.049 9.417 -5.205 0.331 -0.980 C2 C6T 7
C6T O2 O2 O 0 1 N N N 7.123 8.389 8.343 -4.254 0.131 -1.711 O2 C6T 8
C6T N1 N1 N 0 1 N N N 6.715 7.640 10.355 -5.252 -0.266 0.225 N1 C6T 9
C6T "C1'" "C1'" C 0 1 N N R 5.290 7.559 10.078 -4.158 -1.148 0.641 "C1'" C6T 10
C6T "C2'" "C2'" C 0 1 N N N 5.002 6.340 9.705 -4.045 -2.354 -0.318 "C2'" C6T 11
C6T "C3'" "C3'" C 0 1 N N S 4.459 5.606 10.934 -2.524 -2.599 -0.435 "C3'" C6T 12
C6T "O3'" "O3'" O 0 1 N N N 3.689 4.474 10.648 -2.188 -3.902 0.046 "O3'" C6T 13
C6T "O4'" "O4'" O 0 1 N N N 4.464 7.784 11.413 -2.891 -0.465 0.526 "O4'" C6T 14
C6T "C4'" "C4'" C 0 1 N N R 3.688 6.764 11.583 -1.898 -1.512 0.467 "C4'" C6T 15
C6T "C5'" "C5'" C 0 1 N N N 3.441 6.503 13.113 -0.603 -0.985 -0.155 "C5'" C6T 16
C6T "O5'" "O5'" O 0 1 N N N 4.709 6.516 13.769 0.019 -0.067 0.747 "O5'" C6T 17
C6T PA PA P 0 1 N N N 5.045 5.344 14.797 1.405 0.683 0.417 PA C6T 18
C6T O1A O1A O 0 1 N N N 3.908 5.301 15.811 1.674 1.823 1.521 O1A C6T 19
C6T O2A O2A O 0 1 N N N 6.359 5.684 15.458 1.323 1.304 -0.924 O2A C6T 20
C6T N3A N3A N 0 1 N N N 5.154 3.920 13.908 2.666 -0.431 0.443 N3A C6T 21
C6T PB PB P 0 1 N N N 4.004 2.684 13.800 4.136 0.313 0.103 PB C6T 22
C6T O1B O1B O 0 1 N N N 3.959 2.232 12.267 4.406 1.359 1.115 O1B C6T 23
C6T O2B O2B O 0 1 N N N 2.611 3.117 14.379 4.071 0.985 -1.359 O2B C6T 24
C6T C3B C3B C 0 1 N N N 4.634 1.243 14.744 5.470 -0.929 0.142 C3B C6T 25
C6T PG PG P 0 1 N N N 4.129 1.154 16.500 7.062 -0.122 -0.227 PG C6T 26
C6T O2G O2G O 0 1 N N N 2.892 0.309 16.573 7.003 0.496 -1.571 O2G C6T 27
C6T O1G O1G O 0 1 N N N 5.205 0.547 17.365 7.356 1.016 0.874 O1G C6T 28
C6T O3G O3G O 0 1 N N N 3.808 2.583 16.904 8.241 -1.219 -0.193 O3G C6T 29
C6T H1 H1 H 0 1 N N N 8.284 6.514 13.826 -9.203 1.665 1.104 H1 C6T 30
C6T H2 H2 H 0 1 N N N 9.782 5.955 13.008 -8.996 0.037 1.795 H2 C6T 31
C6T H3 H3 H 0 1 N N N 9.671 7.638 13.626 -8.155 1.426 2.524 H3 C6T 32
C6T H4 H4 H 0 1 N N N 6.472 6.883 12.306 -6.346 -0.549 2.027 H4 C6T 33
C6T H5 H5 H 0 1 N N N 9.485 8.417 8.859 -6.147 1.568 -2.259 H5 C6T 34
C6T H6 H6 H 0 1 N N N 4.992 8.320 9.341 -4.314 -1.488 1.664 H6 C6T 35
C6T H7 H7 H 0 1 N N N 4.241 6.359 8.911 -4.541 -3.227 0.106 H7 C6T 36
C6T H8 H8 H 0 1 N N N 5.907 5.836 9.334 -4.468 -2.108 -1.292 H8 C6T 37
C6T H9 H9 H 0 1 N N N 5.305 5.340 11.586 -2.195 -2.475 -1.467 H9 C6T 38
C6T H10 H10 H 0 1 N N N 3.884 3.790 11.278 -2.604 -4.622 -0.448 H10 C6T 39
C6T H11 H11 H 0 1 N N N 2.715 6.876 11.082 -1.707 -1.910 1.464 H11 C6T 40
C6T H12 H12 H 0 1 N N N 2.797 7.292 13.528 0.072 -1.818 -0.349 H12 C6T 41
C6T H13 H13 H 0 1 N N N 2.958 5.525 13.252 -0.831 -0.475 -1.091 H13 C6T 42
C6T H14 H14 H 0 1 N N N 4.247 5.499 16.676 1.739 1.488 2.426 H14 C6T 43
C6T H15 H15 H 0 1 N N N 5.981 3.471 14.246 2.489 -1.192 -0.195 H15 C6T 44
C6T H16 H16 H 0 1 N N N 1.948 3.037 13.703 3.897 0.357 -2.073 H16 C6T 45
C6T H17 H17 H 0 1 N N N 4.277 0.331 14.244 5.514 -1.384 1.131 H17 C6T 46
C6T H18 H18 H 0 1 N N N 5.733 1.273 14.711 5.271 -1.699 -0.604 H18 C6T 47
C6T H19 H19 H 0 1 N N N 4.874 -0.243 17.775 7.408 0.682 1.780 H19 C6T 48
C6T H20 H20 H 0 1 N N N 2.886 2.651 17.122 9.118 -0.859 -0.381 H20 C6T 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
C6T O2 C2 DOUB N N 1
C6T C2 N3 SING N N 2
C6T C2 N1 SING N N 3
C6T N3 C4 SING N N 4
C6T "C2'" "C1'" SING N N 5
C6T "C2'" "C3'" SING N N 6
C6T "C1'" N1 SING N N 7
C6T "C1'" "O4'" SING N N 8
C6T N1 C6 SING N N 9
C6T "O3'" "C3'" SING N N 10
C6T C4 O4 DOUB N N 11
C6T C4 C5 SING N N 12
C6T "C3'" "C4'" SING N N 13
C6T "O4'" "C4'" SING N N 14
C6T C6 C5 DOUB N N 15
C6T "C4'" "C5'" SING N N 16
C6T C5 C7 SING N N 17
C6T O1B PB DOUB N N 18
C6T "C5'" "O5'" SING N N 19
C6T "O5'" PA SING N N 20
C6T PB N3A SING N N 21
C6T PB O2B SING N N 22
C6T PB C3B SING N N 23
C6T N3A PA SING N N 24
C6T C3B PG SING N N 25
C6T PA O2A DOUB N N 26
C6T PA O1A SING N N 27
C6T PG O2G DOUB N N 28
C6T PG O3G SING N N 29
C6T PG O1G SING N N 30
C6T C7 H1 SING N N 31
C6T C7 H2 SING N N 32
C6T C7 H3 SING N N 33
C6T C6 H4 SING N N 34
C6T N3 H5 SING N N 35
C6T "C1'" H6 SING N N 36
C6T "C2'" H7 SING N N 37
C6T "C2'" H8 SING N N 38
C6T "C3'" H9 SING N N 39
C6T "O3'" H10 SING N N 40
C6T "C4'" H11 SING N N 41
C6T "C5'" H12 SING N N 42
C6T "C5'" H13 SING N N 43
C6T O1A H14 SING N N 44
C6T N3A H15 SING N N 45
C6T O2B H16 SING N N 46
C6T C3B H17 SING N N 47
C6T C3B H18 SING N N 48
C6T O1G H19 SING N N 49
C6T 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
C6T SMILES ACDLabs 12.01 "O=P(O)(O)CP(=O)(O)NP(=O)(O)OCC2OC(N1C(=O)NC(=O)C(=C1)C)CC2O"
C6T InChI InChI 1.03 "InChI=1S/C11H20N3O12P3/c1-6-3-14(11(17)12-10(6)16)9-2-7(15)8(26-9)4-25-29(23,24)13-27(18,19)5-28(20,21)22/h3,7-9,15H,2,4-5H2,1H3,(H,12,16,17)(H2,20,21,22)(H3,13,18,19,23,24)/t7-,8+,9+/m0/s1"
C6T InChIKey InChI 1.03 ARKIPWDBYLJBIH-DJLDLDEBSA-N
C6T SMILES_CANONICAL CACTVS 3.385 "CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P](O)(=O)N[P](O)(=O)C[P](O)(O)=O)O2)C(=O)NC1=O"
C6T SMILES CACTVS 3.385 "CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(=O)N[P](O)(=O)C[P](O)(O)=O)O2)C(=O)NC1=O"
C6T SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)COP(=O)(NP(=O)(CP(=O)(O)O)O)O)O"
C6T SMILES "OpenEye OEToolkits" 1.7.6 "CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(NP(=O)(CP(=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
C6T "SYSTEMATIC NAME" ACDLabs 12.01 "2'-deoxy-5'-O-[(S)-hydroxy{[(R)-hydroxy(phosphonomethyl)phosphoryl]amino}phosphoryl]-3,4-dihydrothymidine"
C6T "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]amino]-oxidanyl-phosphoryl]methylphosphonic 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
C6T "Create component" 2014-11-13 RCSB
C6T "Initial release" 2015-07-01 RCSB
#