data_6HB # _chem_comp.id 6HB _chem_comp.name ;2'-deoxy-N-[(2S)-2-hydroxybut-3-en-1-yl]adenosine 5'-(dihydrogen phosphate) ; _chem_comp.type "DNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C14 H20 N5 O7 P" _chem_comp.mon_nstd_parent_comp_id DA _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2014-04-18 _chem_comp.pdbx_modified_date 2014-10-03 _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 401.312 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 6HB _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag Y _chem_comp.pdbx_ideal_coordinates_details Corina _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 2MNX _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 6HB P P P 0 1 N N N 7.596 -6.448 18.878 -5.979 -1.628 0.223 P 6HB 1 6HB OP1 OP1 O 0 1 N N N 8.402 -7.632 19.271 -7.141 -1.040 -0.479 OP1 6HB 2 6HB OP2 OP2 O 0 1 N N N 7.968 -5.717 17.640 -5.362 -2.820 -0.666 OP2 6HB 3 6HB "O5'" "O5'" O 0 1 N N N 6.039 -6.886 18.754 -4.859 -0.493 0.451 "O5'" 6HB 4 6HB "C5'" "C5'" C 0 1 N N N 5.402 -7.669 19.764 -4.315 0.288 -0.614 "C5'" 6HB 5 6HB "C4'" "C4'" C 0 1 N N R 3.935 -8.017 19.466 -3.282 1.267 -0.052 "C4'" 6HB 6 6HB "O4'" "O4'" O 0 1 N N N 3.097 -6.863 19.572 -2.137 0.555 0.465 "O4'" 6HB 7 6HB "C1'" "C1'" C 0 1 N N R 2.416 -6.691 18.340 -1.042 1.486 0.495 "C1'" 6HB 8 6HB N9 N9 N 0 1 Y N N 2.400 -5.239 18.047 0.214 0.787 0.212 N9 6HB 9 6HB C8 C8 C 0 1 Y N N 3.475 -4.411 17.835 0.348 -0.389 -0.465 C8 6HB 10 6HB N7 N7 N 0 1 Y N N 3.152 -3.182 17.534 1.604 -0.722 -0.532 N7 6HB 11 6HB C5 C5 C 0 1 Y N N 1.747 -3.196 17.567 2.354 0.216 0.095 C5 6HB 12 6HB C6 C6 C 0 1 Y N N 0.721 -2.239 17.328 3.728 0.385 0.335 C6 6HB 13 6HB N6 N6 N 0 1 N N N 0.878 -0.957 16.961 4.646 -0.547 -0.119 N6 6HB 14 6HB CA CA C 0 1 N N N 2.128 -0.194 16.762 6.075 -0.353 0.140 CA 6HB 15 6HB CB CB C 0 1 N N S 2.470 -0.023 15.287 6.864 -1.517 -0.464 CB 6HB 16 6HB OB OB O 0 1 N N N 3.428 1.003 15.221 6.731 -1.496 -1.886 OB 6HB 17 6HB CC CC C 0 1 N N N 3.059 -1.295 14.723 8.319 -1.383 -0.093 CC 6HB 18 6HB CD CD C 0 1 N N N 4.182 -1.416 14.040 8.909 -2.329 0.594 CD 6HB 19 6HB C4 C4 C 0 1 Y N N 1.286 -4.449 17.893 1.471 1.198 0.575 C4 6HB 20 6HB N3 N3 N 0 1 Y N N -0.011 -4.856 18.016 1.963 2.241 1.236 N3 6HB 21 6HB C2 C2 C 0 1 Y N N -0.861 -3.864 17.786 3.259 2.356 1.440 C2 6HB 22 6HB N1 N1 N 0 1 Y N N -0.570 -2.610 17.452 4.127 1.460 1.007 N1 6HB 23 6HB "C3'" "C3'" C 0 1 N N S 3.767 -8.658 18.078 -2.683 2.139 -1.186 "C3'" 6HB 24 6HB "C2'" "C2'" C 0 1 N N N 3.158 -7.505 17.275 -1.312 2.545 -0.592 "C2'" 6HB 25 6HB "O3'" "O3'" O 0 1 N N N 2.958 -9.826 18.190 -3.495 3.289 -1.427 "O3'" 6HB 26 6HB H3 H3 H 0 1 N N N 8.722 -6.134 17.240 -4.595 -3.252 -0.267 H3 6HB 27 6HB "H5''" "H5''" H 0 0 N N N 5.963 -8.609 19.876 -3.836 -0.369 -1.340 "H5''" 6HB 28 6HB "H5'" "H5'" H 0 1 N N N 5.437 -7.107 20.709 -5.115 0.845 -1.102 "H5'" 6HB 29 6HB "H4'" "H4'" H 0 1 N N N 3.614 -8.758 20.212 -3.727 1.892 0.721 "H4'" 6HB 30 6HB "H1'" "H1'" H 0 1 N N N 1.383 -7.062 18.416 -0.988 1.964 1.472 "H1'" 6HB 31 6HB H8 H8 H 0 1 N N N 4.499 -4.747 17.911 -0.468 -0.960 -0.882 H8 6HB 32 6HB HN HN H 0 1 N N N 0.377 -0.437 17.653 4.343 -1.327 -0.609 HN 6HB 33 6HB HA1 HA1 H 0 1 N N N 2.952 -0.729 17.257 6.403 0.582 -0.314 HA1 6HB 34 6HB HA2 HA2 H 0 1 N N N 2.012 0.801 17.216 6.248 -0.316 1.215 HA2 6HB 35 6HB HB HB H 0 1 N N N 1.561 0.244 14.728 6.476 -2.459 -0.076 HB 6HB 36 6HB HOB HOB H 0 1 N N N 3.060 1.804 15.575 7.058 -0.685 -2.300 HOB 6HB 37 6HB HC HC H 0 1 N N N 2.501 -2.203 14.898 8.874 -0.507 -0.394 HC 6HB 38 6HB HD2 HD2 H 0 1 N N N 4.498 -2.387 13.688 9.952 -2.233 0.860 HD2 6HB 39 6HB HD1 HD1 H 0 1 N N N 4.785 -0.544 13.833 8.354 -3.205 0.895 HD1 6HB 40 6HB H2 H2 H 0 1 N N N -1.910 -4.102 17.881 3.625 3.216 1.981 H2 6HB 41 6HB "H3'" "H3'" H 0 1 N N N 4.758 -8.905 17.669 -2.555 1.556 -2.098 "H3'" 6HB 42 6HB "H2'" "H2'" H 0 1 N N N 3.942 -6.902 16.793 -1.367 3.540 -0.150 "H2'" 6HB 43 6HB "H2''" "H2''" H 0 0 N N N 2.462 -7.881 16.510 -0.539 2.510 -1.360 "H2''" 6HB 44 6HB H4 H4 H 0 1 N Y N 3.417 -10.482 18.702 -3.162 3.866 -2.128 H4 6HB 45 6HB OP3 OP3 O 0 1 N Y N ? ? ? -6.451 -2.210 1.648 OP3 6HB 46 6HB H1 H1 H 0 1 N Y N ? ? ? -7.126 -2.900 1.586 H1 6HB 47 # 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 6HB CD CC DOUB N N 1 6HB CC CB SING N N 2 6HB OB CB SING N N 3 6HB CB CA SING N N 4 6HB CA N6 SING N N 5 6HB N6 C6 SING N N 6 6HB "C2'" "C3'" SING N N 7 6HB "C2'" "C1'" SING N N 8 6HB C6 N1 DOUB Y N 9 6HB C6 C5 SING Y N 10 6HB N1 C2 SING Y N 11 6HB N7 C5 SING Y N 12 6HB N7 C8 DOUB Y N 13 6HB C5 C4 DOUB Y N 14 6HB OP2 P SING N N 15 6HB C2 N3 DOUB Y N 16 6HB C8 N9 SING Y N 17 6HB C4 N3 SING Y N 18 6HB C4 N9 SING Y N 19 6HB N9 "C1'" SING N N 20 6HB "C3'" "O3'" SING N N 21 6HB "C3'" "C4'" SING N N 22 6HB "C1'" "O4'" SING N N 23 6HB "O5'" P SING N N 24 6HB "O5'" "C5'" SING N N 25 6HB P OP1 DOUB N N 26 6HB "C4'" "O4'" SING N N 27 6HB "C4'" "C5'" SING N N 28 6HB OP2 H3 SING N N 29 6HB "C5'" "H5''" SING N N 30 6HB "C5'" "H5'" SING N N 31 6HB "C4'" "H4'" SING N N 32 6HB "C1'" "H1'" SING N N 33 6HB C8 H8 SING N N 34 6HB N6 HN SING N N 35 6HB CA HA1 SING N N 36 6HB CA HA2 SING N N 37 6HB CB HB SING N N 38 6HB OB HOB SING N N 39 6HB CC HC SING N N 40 6HB CD HD2 SING N N 41 6HB CD HD1 SING N N 42 6HB C2 H2 SING N N 43 6HB "C3'" "H3'" SING N N 44 6HB "C2'" "H2'" SING N N 45 6HB "C2'" "H2''" SING N N 46 6HB "O3'" H4 SING N N 47 6HB P OP3 SING N N 48 6HB OP3 H1 SING N N 49 # 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 6HB SMILES ACDLabs 12.01 "O=P(O)(O)OCC3OC(n2cnc1c(ncnc12)NCC(O)/C=C)CC3O" 6HB InChI InChI 1.03 "InChI=1S/C14H20N5O7P/c1-2-8(20)4-15-13-12-14(17-6-16-13)19(7-18-12)11-3-9(21)10(26-11)5-25-27(22,23)24/h2,6-11,20-21H,1,3-5H2,(H,15,16,17)(H2,22,23,24)/t8-,9-,10+,11+/m0/s1" 6HB InChIKey InChI 1.03 KQKWEOLKIBWBEK-UKKRHICBSA-N 6HB SMILES_CANONICAL CACTVS 3.385 "O[C@H](CNc1ncnc2n(cnc12)[C@H]3C[C@H](O)[C@@H](CO[P](O)(O)=O)O3)C=C" 6HB SMILES CACTVS 3.385 "O[CH](CNc1ncnc2n(cnc12)[CH]3C[CH](O)[CH](CO[P](O)(O)=O)O3)C=C" 6HB SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "C=C[C@@H](CNc1c2c(ncn1)n(cn2)[C@H]3C[C@@H]([C@H](O3)COP(=O)(O)O)O)O" 6HB SMILES "OpenEye OEToolkits" 1.7.6 "C=CC(CNc1c2c(ncn1)n(cn2)C3CC(C(O3)COP(=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 6HB "SYSTEMATIC NAME" ACDLabs 12.01 ;2'-deoxy-N-[(2S)-2-hydroxybut-3-en-1-yl]adenosine 5'-(dihydrogen phosphate) ; 6HB "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "[(2R,3S,5R)-3-oxidanyl-5-[6-[[(2S)-2-oxidanylbut-3-enyl]amino]purin-9-yl]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 6HB "Create component" 2014-04-18 RCSB 6HB "Initial release" 2014-10-08 RCSB #