data_KGV # _chem_comp.id KGV _chem_comp.name ;3'-deoxy-3'-(D-phenylalanylamino)adenosine 5'-(dihydrogen phosphate) ; _chem_comp.type "RNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C19 H24 N7 O7 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2018-12-04 _chem_comp.pdbx_modified_date 2018-12-07 _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 493.410 _chem_comp.one_letter_code ? _chem_comp.three_letter_code KGV _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 6N9F _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 KGV C2 C1 C 0 1 Y N N 87.963 -45.987 3.301 0.949 -5.307 -0.600 C2 KGV 1 KGV C4 C2 C 0 1 Y N N 89.307 -46.755 1.553 1.971 -3.274 -0.275 C4 KGV 2 KGV C5 C3 C 0 1 Y N N 89.849 -45.399 1.401 3.184 -3.936 -0.021 C5 KGV 3 KGV C6 C4 C 0 1 Y N N 89.336 -44.360 2.314 3.196 -5.341 -0.072 C6 KGV 4 KGV N7 N1 N 0 1 Y N N 90.740 -45.444 0.400 4.112 -2.984 0.236 N7 KGV 5 KGV O O1 O 0 1 N N N 91.297 -50.046 -4.264 -2.100 1.024 2.397 O KGV 6 KGV C C5 C 0 1 N N N 90.418 -50.806 -3.901 -2.320 1.045 1.204 C KGV 7 KGV CA C6 C 0 1 N N R 90.104 -52.025 -4.704 -3.739 1.132 0.702 CA KGV 8 KGV CB C7 C 0 1 N N N 90.381 -53.227 -3.818 -4.219 -0.260 0.287 CB KGV 9 KGV CG C8 C 0 1 Y N N 90.206 -54.505 -4.597 -5.590 -0.154 -0.329 CG KGV 10 KGV CD2 C9 C 0 1 Y N N 91.232 -54.961 -5.412 -6.716 -0.251 0.468 CD2 KGV 11 KGV CE2 C10 C 0 1 Y N N 91.074 -56.142 -6.126 -7.973 -0.149 -0.096 CE2 KGV 12 KGV CZ C11 C 0 1 Y N N 89.892 -56.866 -6.021 -8.106 0.049 -1.458 CZ KGV 13 KGV CE1 C12 C 0 1 Y N N 88.865 -56.412 -5.203 -6.981 0.147 -2.255 CE1 KGV 14 KGV CD1 C13 C 0 1 Y N N 89.027 -55.232 -4.490 -5.723 0.044 -1.691 CD1 KGV 15 KGV N N2 N 0 1 N N N 88.706 -51.988 -5.080 -4.605 1.652 1.768 N KGV 16 KGV "N3'" N3 N 0 1 N N N 89.710 -50.621 -2.790 -1.297 0.989 0.329 "N3'" KGV 17 KGV "C3'" C14 C 0 1 N N S 90.103 -49.584 -1.862 0.081 0.904 0.817 "C3'" KGV 18 KGV "C4'" C15 C 0 1 N N S 91.239 -50.059 -0.980 1.061 1.464 -0.232 "C4'" KGV 19 KGV "C5'" C16 C 0 1 N N N 92.541 -49.459 -1.487 1.833 2.647 0.355 "C5'" KGV 20 KGV "O5'" O2 O 0 1 N N N 93.401 -49.143 -0.400 2.652 3.232 -0.659 "O5'" KGV 21 KGV P P1 P 0 1 N N N 94.850 -48.521 -0.704 3.604 4.503 -0.393 P KGV 22 KGV OP2 O3 O 0 1 N N N 95.865 -49.612 -0.460 2.698 5.786 -0.039 OP2 KGV 23 KGV OP1 O4 O 0 1 N N N 94.816 -47.823 -2.042 4.511 4.212 0.739 OP1 KGV 24 KGV "C2'" C17 C 0 1 N N R 88.998 -49.189 -0.908 0.507 -0.575 0.984 "C2'" KGV 25 KGV "O2'" O5 O 0 1 N N N 88.083 -50.272 -0.769 -0.636 -1.426 1.082 "O2'" KGV 26 KGV "C1'" C18 C 0 1 N N R 89.686 -48.965 0.422 1.282 -0.839 -0.332 "C1'" KGV 27 KGV "O4'" O6 O 0 1 N N N 90.963 -49.602 0.343 1.973 0.406 -0.572 "O4'" KGV 28 KGV N9 N4 N 0 1 Y N N 89.908 -47.511 0.640 2.240 -1.934 -0.156 N9 KGV 29 KGV C8 C19 C 0 1 Y N N 90.762 -46.725 -0.047 3.560 -1.808 0.157 C8 KGV 30 KGV N3 N5 N 0 1 Y N N 88.383 -46.982 2.506 0.889 -3.993 -0.558 N3 KGV 31 KGV N1 N6 N 0 1 Y N N 88.411 -44.725 3.222 2.065 -5.974 -0.363 N1 KGV 32 KGV N6 N7 N 0 1 N N N 89.794 -43.037 2.242 4.361 -6.048 0.169 N6 KGV 33 KGV OP3 O7 O 0 1 N Y N 93.843 -48.478 0.484 4.474 4.808 -1.713 O1 KGV 34 KGV H1 H1 H 0 1 N N N 87.219 -46.215 4.050 0.052 -5.861 -0.833 H1 KGV 35 KGV H2 H2 H 0 1 N N N 90.746 -52.065 -5.596 -3.779 1.802 -0.157 H2 KGV 36 KGV H3 H3 H 0 1 N N N 91.413 -53.170 -3.442 -3.526 -0.682 -0.440 H3 KGV 37 KGV H4 H4 H 0 1 N N N 89.681 -53.221 -2.970 -4.264 -0.905 1.164 H4 KGV 38 KGV H5 H5 H 0 1 N N N 92.151 -54.399 -5.491 -6.612 -0.406 1.532 H5 KGV 39 KGV H6 H6 H 0 1 N N N 91.870 -56.498 -6.763 -8.852 -0.225 0.527 H6 KGV 40 KGV H7 H7 H 0 1 N N N 89.772 -57.784 -6.577 -9.089 0.128 -1.899 H7 KGV 41 KGV H8 H8 H 0 1 N N N 87.946 -56.974 -5.122 -7.085 0.302 -3.319 H8 KGV 42 KGV H9 H9 H 0 1 N N N 88.233 -54.878 -3.849 -4.844 0.124 -2.313 H9 KGV 43 KGV H10 H10 H 0 1 N N N 88.484 -52.800 -5.619 -4.585 1.048 2.577 H10 KGV 44 KGV H11 H11 H 0 1 N N N 88.140 -51.969 -4.256 -4.348 2.596 2.016 H11 KGV 45 KGV H13 H13 H 0 1 N N N 88.913 -51.194 -2.598 -1.474 1.006 -0.625 H13 KGV 46 KGV H14 H14 H 0 1 N N N 90.431 -48.692 -2.416 0.185 1.441 1.760 H14 KGV 47 KGV H15 H15 H 0 1 N N N 91.300 -51.157 -1.013 0.513 1.780 -1.120 H15 KGV 48 KGV H16 H16 H 0 1 N N N 93.041 -50.184 -2.145 1.129 3.391 0.727 H16 KGV 49 KGV H17 H17 H 0 1 N N N 92.321 -48.542 -2.053 2.461 2.300 1.175 H17 KGV 50 KGV HOP2 H18 H 0 0 N N N 96.396 -49.731 -1.239 2.079 6.035 -0.738 H18 KGV 51 KGV H19 H19 H 0 1 N N N 88.501 -48.269 -1.248 1.157 -0.697 1.850 H19 KGV 52 KGV H20 H20 H 0 1 N N N 87.388 -50.025 -0.170 -0.421 -2.363 1.187 H20 KGV 53 KGV H21 H21 H 0 1 N N N 89.079 -49.387 1.236 0.592 -1.061 -1.146 H21 KGV 54 KGV H22 H22 H 0 1 N N N 91.388 -47.073 -0.855 4.073 -0.871 0.317 H22 KGV 55 KGV H23 H23 H 0 1 N N N 89.333 -42.486 2.937 5.182 -5.574 0.376 H23 KGV 56 KGV H24 H24 H 0 1 N N N 90.781 -43.017 2.402 4.357 -7.017 0.131 H24 KGV 57 KGV HOP3 H25 H 0 0 N Y N 93.118 -47.904 0.265 5.071 5.563 -1.624 H25 KGV 58 # 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 KGV CE2 CZ DOUB Y N 1 KGV CE2 CD2 SING Y N 2 KGV CZ CE1 SING Y N 3 KGV CD2 CG DOUB Y N 4 KGV CE1 CD1 DOUB Y N 5 KGV N CA SING N N 6 KGV CA C SING N N 7 KGV CA CB SING N N 8 KGV CG CD1 SING Y N 9 KGV CG CB SING N N 10 KGV O C DOUB N N 11 KGV C "N3'" SING N N 12 KGV "N3'" "C3'" SING N N 13 KGV OP1 P DOUB N N 14 KGV "C3'" "C4'" SING N N 15 KGV "C3'" "C2'" SING N N 16 KGV "C5'" "C4'" SING N N 17 KGV "C5'" "O5'" SING N N 18 KGV "C4'" "O4'" SING N N 19 KGV "C2'" "O2'" SING N N 20 KGV "C2'" "C1'" SING N N 21 KGV P OP2 SING N N 22 KGV P "O5'" SING N N 23 KGV C8 N7 DOUB Y N 24 KGV C8 N9 SING Y N 25 KGV "O4'" "C1'" SING N N 26 KGV N7 C5 SING Y N 27 KGV "C1'" N9 SING N N 28 KGV N9 C4 SING Y N 29 KGV C5 C4 DOUB Y N 30 KGV C5 C6 SING Y N 31 KGV C4 N3 SING Y N 32 KGV N6 C6 SING N N 33 KGV C6 N1 DOUB Y N 34 KGV N3 C2 DOUB Y N 35 KGV N1 C2 SING Y N 36 KGV P OP3 SING N N 37 KGV C2 H1 SING N N 38 KGV CA H2 SING N N 39 KGV CB H3 SING N N 40 KGV CB H4 SING N N 41 KGV CD2 H5 SING N N 42 KGV CE2 H6 SING N N 43 KGV CZ H7 SING N N 44 KGV CE1 H8 SING N N 45 KGV CD1 H9 SING N N 46 KGV N H10 SING N N 47 KGV N H11 SING N N 48 KGV "N3'" H13 SING N N 49 KGV "C3'" H14 SING N N 50 KGV "C4'" H15 SING N N 51 KGV "C5'" H16 SING N N 52 KGV "C5'" H17 SING N N 53 KGV OP2 HOP2 SING N N 54 KGV "C2'" H19 SING N N 55 KGV "O2'" H20 SING N N 56 KGV "C1'" H21 SING N N 57 KGV C8 H22 SING N N 58 KGV N6 H23 SING N N 59 KGV N6 H24 SING N N 60 KGV OP3 HOP3 SING N N 61 # 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 KGV SMILES ACDLabs 12.01 "c1nc2c(c(n1)N)ncn2C4C(C(NC(=O)C(Cc3ccccc3)N)C(O4)COP(O)(O)=O)O" KGV InChI InChI 1.03 "InChI=1S/C19H24N7O7P/c20-11(6-10-4-2-1-3-5-10)18(28)25-13-12(7-32-34(29,30)31)33-19(15(13)27)26-9-24-14-16(21)22-8-23-17(14)26/h1-5,8-9,11-13,15,19,27H,6-7,20H2,(H,25,28)(H2,21,22,23)(H2,29,30,31)/t11-,12-,13-,15-,19-/m1/s1" KGV InChIKey InChI 1.03 FGNMGARNYLAFLT-XDJZACDYSA-N KGV SMILES_CANONICAL CACTVS 3.385 "N[C@H](Cc1ccccc1)C(=O)N[C@H]2[C@@H](O)[C@@H](O[C@@H]2CO[P](O)(O)=O)n3cnc4c(N)ncnc34" KGV SMILES CACTVS 3.385 "N[CH](Cc1ccccc1)C(=O)N[CH]2[CH](O)[CH](O[CH]2CO[P](O)(O)=O)n3cnc4c(N)ncnc34" KGV SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "c1ccc(cc1)C[C@H](C(=O)N[C@@H]2[C@H](O[C@H]([C@@H]2O)n3cnc4c3ncnc4N)COP(=O)(O)O)N" KGV SMILES "OpenEye OEToolkits" 2.0.6 "c1ccc(cc1)CC(C(=O)NC2C(OC(C2O)n3cnc4c3ncnc4N)COP(=O)(O)O)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 KGV "SYSTEMATIC NAME" ACDLabs 12.01 ;3'-deoxy-3'-(D-phenylalanylamino)adenosine 5'-(dihydrogen phosphate) ; KGV "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "[(2~{S},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3-[[(2~{R})-2-azanyl-3-phenyl-propanoyl]amino]-4-oxidanyl-oxolan-2-yl]methyl dihydrogen 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 KGV "Create component" 2018-12-04 RCSB KGV "Initial release" 2018-12-12 RCSB #