data_0L6 # _chem_comp.id 0L6 _chem_comp.name ;5-(5-aminopent-1-yn-1-yl)-2'-deoxycytidine 5'-(tetrahydrogen triphosphate) ; _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C14 H25 N4 O13 P3" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2012-02-08 _chem_comp.pdbx_modified_date 2012-05-11 _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 550.289 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 0L6 _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 4DFM _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 0L6 O2 O2 O 0 1 N N N 18.050 -21.118 -5.668 2.473 -2.579 1.611 O2 DCX 1 0L6 C2 C2 C 0 1 N N N 18.444 -19.944 -5.862 3.350 -1.774 1.363 C2 DCX 2 0L6 N3 N3 N 0 1 N N N 18.562 -19.090 -4.842 4.164 -1.379 2.351 N3 DCX 3 0L6 C4 C4 C 0 1 N N N 18.985 -17.840 -5.039 5.189 -0.472 2.175 C4 DCX 4 0L6 N4 N4 N 0 1 N N N 19.098 -16.992 -3.986 5.982 -0.121 3.251 N4 DCX 5 0L6 C5 C5 C 0 1 N N N 19.298 -17.399 -6.292 5.427 0.080 0.960 C5 DCX 6 0L6 C29 C29 C 0 1 N N N 19.711 -16.186 -6.401 6.489 1.022 0.771 C29 DCX 7 0L6 C30 C30 C 0 1 N N N 20.087 -15.081 -6.501 7.359 1.795 0.615 C30 DCX 8 0L6 C31 C31 C 0 1 N N N 20.495 -13.663 -6.607 8.450 2.763 0.420 C31 DCX 9 0L6 C32 C32 C 0 1 N N N 21.448 -13.348 -5.441 8.479 3.212 -1.043 C32 DCX 10 0L6 C33 C33 C 0 1 N N N 22.652 -14.295 -5.444 9.613 4.219 -1.245 C33 DCX 11 0L6 N34 N34 N 0 1 N N N 23.144 -14.472 -4.091 9.640 4.649 -2.649 N34 DCX 12 0L6 C6 C6 C 0 1 N N N 19.198 -18.268 -7.396 4.532 -0.334 -0.190 C6 DCX 13 0L6 N1 N1 N 0 1 N N N 18.769 -19.524 -7.171 3.473 -1.313 0.103 N1 DCX 14 0L6 "C1'" C1* C 0 1 N N R 18.615 -20.486 -8.268 2.563 -1.768 -0.951 C1* DCX 15 0L6 "O4'" O4* O 0 1 N N N 19.467 -20.190 -9.385 1.190 -1.618 -0.530 O4* DCX 16 0L6 "C2'" C2* C 0 1 N N N 17.182 -20.328 -8.764 2.740 -3.283 -1.196 C2* DCX 17 0L6 "C3'" C3* C 0 1 N N S 17.348 -19.456 -10.000 1.307 -3.787 -1.480 C3* DCX 18 0L6 "O3'" O3* O 0 1 N N N 16.269 -19.623 -10.924 1.223 -4.346 -2.792 O3* DCX 19 0L6 "C4'" C4* C 0 1 N N R 18.681 -19.930 -10.554 0.434 -2.515 -1.372 C4* DCX 20 0L6 "C5'" C5* C 0 1 N N N 19.347 -18.925 -11.493 -0.913 -2.846 -0.725 C5* DCX 21 0L6 "O5'" O5* O 0 1 N N N 19.652 -17.723 -10.793 -1.747 -1.686 -0.741 O5* DCX 22 0L6 PA PA P 0 1 N N N 19.427 -16.305 -11.516 -3.240 -1.672 -0.139 PA DCX 23 0L6 O1A O1A O 0 1 N N N 20.172 -15.257 -10.720 -4.175 -2.659 -1.001 O1A DCX 24 0L6 O2A O2A O 0 1 N N N 19.694 -16.388 -13.009 -3.209 -2.126 1.269 O2A DCX 25 0L6 O3A O3A O 0 1 N N N 17.854 -16.113 -11.188 -3.832 -0.176 -0.208 O3A DCX 26 0L6 PB PB P 0 1 N N N 16.648 -16.371 -12.230 -5.027 0.590 0.553 PB DCX 27 0L6 O1B O1B O 0 1 N N N 17.138 -17.120 -13.454 -6.185 -0.320 0.696 O1B DCX 28 0L6 O2B O2B O 0 1 N N N 15.525 -16.990 -11.429 -4.525 1.053 2.011 O2B DCX 29 0L6 O3B O3B O 0 1 N N N 16.168 -14.865 -12.587 -5.464 1.884 -0.300 O3B DCX 30 0L6 PG PG P 0 1 N N N 16.721 -13.960 -13.811 -6.741 2.864 -0.271 PG DCX 31 0L6 O1G O1G O 0 1 N N N 17.280 -12.733 -13.124 -6.569 3.934 0.919 O1G DCX 32 0L6 O2G O2G O 0 1 N N N 17.774 -14.796 -14.506 -6.855 3.638 -1.678 O2G DCX 33 0L6 O3G O3G O 0 1 N N N 15.489 -13.652 -14.627 -7.968 2.068 -0.045 O3G DCX 34 0L6 H1 H1 H 0 1 N N N 18.330 -19.392 -3.917 4.027 -1.751 3.236 H1 DCX 35 0L6 H2 H2 H 0 1 N N N 18.833 -17.466 -3.146 5.817 -0.513 4.123 H2 DCX 36 0L6 H3 H3 H 0 1 N N N 20.045 -16.681 -3.909 6.704 0.516 3.134 H3 DCX 37 0L6 H4 H4 H 0 1 N N N 21.010 -13.494 -7.564 8.287 3.629 1.062 H4 DCX 38 0L6 H5 H5 H 0 1 N N N 19.608 -13.015 -6.548 9.401 2.295 0.675 H5 DCX 39 0L6 H6 H6 H 0 1 N N N 21.805 -12.312 -5.538 8.642 2.346 -1.685 H6 DCX 40 0L6 H7 H7 H 0 1 N N N 20.904 -13.461 -4.492 7.528 3.680 -1.298 H7 DCX 41 0L6 H8 H8 H 0 1 N N N 22.348 -15.270 -5.852 9.450 5.084 -0.603 H8 DCX 42 0L6 H9 H9 H 0 1 N N N 23.450 -13.868 -6.069 10.564 3.751 -0.990 H9 DCX 43 0L6 H10 H10 H 0 1 N N N 23.929 -15.091 -4.100 8.748 5.028 -2.929 H10 DCX 44 0L6 H11 H11 H 0 1 N N N 23.422 -13.586 -3.719 10.382 5.315 -2.809 H11 DCX 45 0L6 H13 H13 H 0 1 N N N 20.198 -18.339 -7.849 4.060 0.561 -0.595 H13 DCX 46 0L6 H14 H14 H 0 1 N N N 18.503 -17.808 -8.113 5.170 -0.753 -0.968 H14 DCX 47 0L6 H15 H15 H 0 1 N N N 18.775 -21.513 -7.909 2.741 -1.211 -1.871 H15 DCX 48 0L6 H16 H16 H 0 1 N N N 16.554 -19.831 -8.010 3.384 -3.458 -2.058 H16 DCX 49 0L6 H17 H17 H 0 1 N N N 16.742 -21.303 -9.023 3.150 -3.768 -0.310 H17 DCX 50 0L6 H18 H18 H 0 1 N N N 17.435 -18.403 -9.693 1.006 -4.522 -0.733 H18 DCX 51 0L6 H19 H19 H 0 1 N N N 15.463 -19.312 -10.529 1.798 -5.111 -2.931 H19 DCX 52 0L6 H20 H20 H 0 1 N N N 18.517 -20.867 -11.107 0.283 -2.073 -2.358 H20 DCX 53 0L6 H21 H21 H 0 1 N N N 18.664 -18.697 -12.325 -1.396 -3.649 -1.281 H21 DCX 54 0L6 H22 H22 H 0 1 N N N 20.276 -19.360 -11.890 -0.752 -3.164 0.306 H22 DCX 55 0L6 H23 H23 H 0 1 N N N 20.740 -14.763 -11.299 -4.242 -2.421 -1.936 H23 DCX 56 0L6 H24 H24 H 0 1 N N N 15.267 -17.812 -11.828 -3.766 1.653 1.994 H24 DCX 57 0L6 H25 H25 H 0 1 N N N 16.743 -11.979 -13.336 -5.783 4.492 0.836 H25 DCX 58 0L6 H26 H26 H 0 1 N N N 17.483 -15.006 -15.386 -7.604 4.248 -1.731 H26 DCX 59 # 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 0L6 O3G PG DOUB N N 1 0L6 O2G PG SING N N 2 0L6 PG O1G SING N N 3 0L6 PG O3B SING N N 4 0L6 O1B PB DOUB N N 5 0L6 O2A PA DOUB N N 6 0L6 O3B PB SING N N 7 0L6 PB O2B SING N N 8 0L6 PB O3A SING N N 9 0L6 PA O3A SING N N 10 0L6 PA "O5'" SING N N 11 0L6 PA O1A SING N N 12 0L6 "C5'" "O5'" SING N N 13 0L6 "C5'" "C4'" SING N N 14 0L6 "O3'" "C3'" SING N N 15 0L6 "C4'" "C3'" SING N N 16 0L6 "C4'" "O4'" SING N N 17 0L6 "C3'" "C2'" SING N N 18 0L6 "O4'" "C1'" SING N N 19 0L6 "C2'" "C1'" SING N N 20 0L6 "C1'" N1 SING N N 21 0L6 C6 N1 SING N N 22 0L6 C6 C5 SING N N 23 0L6 N1 C2 SING N N 24 0L6 C31 C30 SING N N 25 0L6 C31 C32 SING N N 26 0L6 C30 C29 TRIP N N 27 0L6 C29 C5 SING N N 28 0L6 C5 C4 DOUB N N 29 0L6 C2 O2 DOUB N N 30 0L6 C2 N3 SING N N 31 0L6 C33 C32 SING N N 32 0L6 C33 N34 SING N N 33 0L6 C4 N3 SING N N 34 0L6 C4 N4 SING N N 35 0L6 N3 H1 SING N N 36 0L6 N4 H2 SING N N 37 0L6 N4 H3 SING N N 38 0L6 C31 H4 SING N N 39 0L6 C31 H5 SING N N 40 0L6 C32 H6 SING N N 41 0L6 C32 H7 SING N N 42 0L6 C33 H8 SING N N 43 0L6 C33 H9 SING N N 44 0L6 N34 H10 SING N N 45 0L6 N34 H11 SING N N 46 0L6 C6 H13 SING N N 47 0L6 C6 H14 SING N N 48 0L6 "C1'" H15 SING N N 49 0L6 "C2'" H16 SING N N 50 0L6 "C2'" H17 SING N N 51 0L6 "C3'" H18 SING N N 52 0L6 "O3'" H19 SING N N 53 0L6 "C4'" H20 SING N N 54 0L6 "C5'" H21 SING N N 55 0L6 "C5'" H22 SING N N 56 0L6 O1A H23 SING N N 57 0L6 O2B H24 SING N N 58 0L6 O1G H25 SING N N 59 0L6 O2G H26 SING N N 60 # 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 0L6 SMILES ACDLabs 12.01 "O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC2OC(N1C(=O)NC(=C(C#CCCCN)C1)N)CC2O" 0L6 InChI InChI 1.03 "InChI=1S/C14H25N4O13P3/c15-5-3-1-2-4-9-7-18(14(20)17-13(9)16)12-6-10(19)11(29-12)8-28-33(24,25)31-34(26,27)30-32(21,22)23/h10-12,19H,1,3,5-8,15-16H2,(H,17,20)(H,24,25)(H,26,27)(H2,21,22,23)/t10-,11+,12+/m0/s1" 0L6 InChIKey InChI 1.03 QDKMIMUSGQEUSC-QJPTWQEYSA-N 0L6 SMILES_CANONICAL CACTVS 3.370 "NCCCC#CC1=C(N)NC(=O)N(C1)[C@H]2C[C@H](O)[C@@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O2" 0L6 SMILES CACTVS 3.370 "NCCCC#CC1=C(N)NC(=O)N(C1)[CH]2C[CH](O)[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O2" 0L6 SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "C1[C@@H]([C@H](O[C@H]1N2CC(=C(NC2=O)N)C#CCCCN)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O" 0L6 SMILES "OpenEye OEToolkits" 1.7.6 "C1C(C(OC1N2CC(=C(NC2=O)N)C#CCCCN)COP(=O)(O)OP(=O)(O)OP(=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 0L6 "SYSTEMATIC NAME" ACDLabs 12.01 ;5-(5-aminopent-1-yn-1-yl)-2'-deoxycytidine 5'-(tetrahydrogen triphosphate) ; 0L6 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "[[(2R,3S,5R)-5-[6-azanyl-5-(5-azanylpent-1-ynyl)-2-oxidanylidene-1,4-dihydropyrimidin-3-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site 0L6 "Create component" 2012-02-08 RCSB #