data_VDO # _chem_comp.id VDO _chem_comp.name "[(1R,2R,3S,4S,5S)-2,3,4-TRIHYDROXY-5-{[(1S,4R,5S,6S)-4,5,6-TRIHYDROXY-3-(HYDROXYMETHYL)CYCLOHEX-2-EN-1-YL]AMINO}CYCLOHEXYL]METHYL DIHYDROGEN PHOSPHATE" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C14 H26 N O11 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2009-09-25 _chem_comp.pdbx_modified_date 2011-06-04 _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 415.330 _chem_comp.one_letter_code ? _chem_comp.three_letter_code VDO _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 2WTX _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site EBI # 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 VDO OAY OAY O 0 1 N N N 21.373 21.145 56.516 6.132 -0.375 0.994 OAY VDO 1 VDO PBA PBA P 0 1 N N N 20.382 21.356 55.248 5.176 -1.271 0.057 PBA VDO 2 VDO OAZ OAZ O 0 1 N N N 21.315 21.254 53.949 5.875 -1.481 -1.378 OAZ VDO 3 VDO OAX OAX O 0 1 N N N 19.609 22.625 55.270 4.954 -2.588 0.695 OAX VDO 4 VDO OAW OAW O 0 1 N N N 19.352 20.135 55.190 3.763 -0.524 -0.138 OAW VDO 5 VDO CAG CAG C 0 1 N N N 18.287 20.159 54.187 2.854 -0.287 0.938 CAG VDO 6 VDO CAF CAF C 0 1 N N R 16.913 19.986 54.841 1.616 0.440 0.408 CAF VDO 7 VDO CAV CAV C 0 1 N N N 16.817 18.592 55.481 0.589 0.584 1.533 CAV VDO 8 VDO CAE CAE C 0 1 N N R 16.659 21.081 55.905 2.017 1.828 -0.097 CAE VDO 9 VDO OAU OAU O 0 1 N N N 16.844 22.374 55.341 2.976 1.694 -1.147 OAU VDO 10 VDO CAC CAC C 0 1 N N S 15.255 20.964 56.509 0.779 2.555 -0.626 CAC VDO 11 VDO OAP OAP O 0 1 N N N 15.076 21.942 57.568 1.153 3.851 -1.098 OAP VDO 12 VDO CAB CAB C 0 1 N N S 15.037 19.543 57.069 -0.248 2.699 0.498 CAB VDO 13 VDO OAO OAO O 0 1 N N N 13.696 19.424 57.488 -1.404 3.378 0.004 OAO VDO 14 VDO CAA CAA C 0 1 N N S 15.407 18.382 56.090 -0.649 1.311 1.003 CAA VDO 15 VDO NAN NAN N 0 1 N N N 14.399 18.154 54.994 -1.236 0.539 -0.100 NAN VDO 16 VDO CAM CAM C 0 1 N N S 13.086 17.535 55.369 -2.158 -0.486 0.407 CAM VDO 17 VDO CAL CAL C 0 1 N N N 12.021 18.126 54.434 -3.523 0.113 0.579 CAL VDO 18 VDO CAJ CAJ C 0 1 N N S 13.070 15.980 55.330 -2.215 -1.651 -0.583 CAJ VDO 19 VDO OAT OAT O 0 1 N N N 14.360 15.476 55.648 -2.448 -1.151 -1.901 OAT VDO 20 VDO CAI CAI C 0 1 N N S 12.637 15.346 53.997 -3.364 -2.581 -0.174 CAI VDO 21 VDO OAS OAS O 0 1 N N N 12.437 13.949 54.176 -3.230 -2.932 1.205 OAS VDO 22 VDO CAH CAH C 0 1 N N R 11.319 15.852 53.460 -4.686 -1.840 -0.389 CAH VDO 23 VDO OAR OAR O 0 1 N N N 11.227 15.475 52.072 -4.931 -1.707 -1.791 OAR VDO 24 VDO CAK CAK C 0 1 N N N 11.231 17.371 53.563 -4.622 -0.477 0.237 CAK VDO 25 VDO CAD CAD C 0 1 N N N 10.198 18.080 52.698 -5.920 0.248 0.482 CAD VDO 26 VDO OAQ OAQ O 0 1 N N N 9.930 19.364 53.232 -5.650 1.518 1.079 OAQ VDO 27 VDO HAY HAY H 0 1 N N N 22.272 21.104 56.212 6.321 0.503 0.637 HAY VDO 28 VDO HAZ HAZ H 0 1 N N N 20.772 21.234 53.170 6.733 -1.926 -1.337 HAZ VDO 29 VDO HAG1 HAG1 H 0 0 N N N 18.313 21.125 53.661 2.556 -1.238 1.379 HAG1 VDO 30 VDO HAG2 HAG2 H 0 0 N N N 18.448 19.329 53.484 3.340 0.328 1.696 HAG2 VDO 31 VDO HAF HAF H 0 1 N N N 16.142 20.086 54.063 1.181 -0.133 -0.410 HAF VDO 32 VDO HAV1 HAV1 H 0 0 N N N 16.998 17.826 54.712 0.303 -0.404 1.893 HAV1 VDO 33 VDO HAV2 HAV2 H 0 0 N N N 17.570 18.509 56.278 1.024 1.157 2.352 HAV2 VDO 34 VDO HAE HAE H 0 1 N N N 17.389 20.934 56.715 2.452 2.401 0.722 HAE VDO 35 VDO HAA HAA H 0 1 N N N 15.402 17.472 56.708 -1.381 1.414 1.805 HAA VDO 36 VDO HAU HAU H 0 1 N N N 16.885 23.020 56.036 3.276 2.536 -1.516 HAU VDO 37 VDO HAC HAC H 0 1 N N N 14.516 21.158 55.717 0.344 1.982 -1.445 HAC VDO 38 VDO HAP HAP H 0 1 N N N 15.037 21.498 58.407 0.416 4.369 -1.449 HAP VDO 39 VDO HAB HAB H 0 1 N N N 15.735 19.429 57.912 0.187 3.272 1.317 HAB VDO 40 VDO HAO HAO H 0 1 N N N 13.661 19.397 58.437 -1.225 4.266 -0.334 HAO VDO 41 VDO HAN HAN H 0 1 N N N 14.194 19.050 54.600 -1.698 1.146 -0.761 HAN VDO 42 VDO HAM HAM H 0 1 N N N 12.881 17.776 56.423 -1.799 -0.850 1.370 HAM VDO 43 VDO HAL HAL H 0 1 N N N 11.873 19.196 54.451 -3.592 1.099 1.015 HAL VDO 44 VDO HAJ HAJ H 0 1 N N N 12.306 15.701 56.071 -1.272 -2.198 -0.561 HAJ VDO 45 VDO HAT HAT H 0 1 N N N 14.862 15.364 54.849 -2.496 -1.838 -2.580 HAT VDO 46 VDO HAI HAI H 0 1 N N N 13.443 15.605 53.295 -3.342 -3.483 -0.785 HAI VDO 47 VDO HAS HAS H 0 1 N N N 12.392 13.524 53.328 -3.926 -3.519 1.531 HAS VDO 48 VDO HAH HAH H 0 1 N N N 10.499 15.416 54.050 -5.497 -2.407 0.067 HAH VDO 49 VDO HAR HAR H 0 1 N N N 11.207 16.256 51.532 -5.754 -1.245 -2.004 HAR VDO 50 VDO HAD1 HAD1 H 0 0 N N N 10.587 18.184 51.675 -6.439 0.395 -0.465 HAD1 VDO 51 VDO HAD2 HAD2 H 0 0 N N N 9.269 17.491 52.682 -6.546 -0.342 1.152 HAD2 VDO 52 VDO HAQ HAQ H 0 1 N N N 9.870 19.308 54.178 -6.442 2.042 1.266 HAQ VDO 53 # 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 VDO OAY PBA SING N N 1 VDO PBA OAZ SING N N 2 VDO PBA OAX DOUB N N 3 VDO PBA OAW SING N N 4 VDO OAW CAG SING N N 5 VDO CAG CAF SING N N 6 VDO CAF CAV SING N N 7 VDO CAF CAE SING N N 8 VDO CAV CAA SING N N 9 VDO CAE OAU SING N N 10 VDO CAE CAC SING N N 11 VDO CAC OAP SING N N 12 VDO CAC CAB SING N N 13 VDO CAB OAO SING N N 14 VDO CAB CAA SING N N 15 VDO CAA NAN SING N N 16 VDO NAN CAM SING N N 17 VDO CAM CAL SING N N 18 VDO CAM CAJ SING N N 19 VDO CAL CAK DOUB N N 20 VDO CAJ OAT SING N N 21 VDO CAJ CAI SING N N 22 VDO CAI OAS SING N N 23 VDO CAI CAH SING N N 24 VDO CAH OAR SING N N 25 VDO CAH CAK SING N N 26 VDO CAK CAD SING N N 27 VDO CAD OAQ SING N N 28 VDO OAY HAY SING N N 29 VDO OAZ HAZ SING N N 30 VDO CAG HAG1 SING N N 31 VDO CAG HAG2 SING N N 32 VDO CAF HAF SING N N 33 VDO CAV HAV1 SING N N 34 VDO CAV HAV2 SING N N 35 VDO CAE HAE SING N N 36 VDO CAA HAA SING N N 37 VDO OAU HAU SING N N 38 VDO CAC HAC SING N N 39 VDO OAP HAP SING N N 40 VDO CAB HAB SING N N 41 VDO OAO HAO SING N N 42 VDO NAN HAN SING N N 43 VDO CAM HAM SING N N 44 VDO CAL HAL SING N N 45 VDO CAJ HAJ SING N N 46 VDO OAT HAT SING N N 47 VDO CAI HAI SING N N 48 VDO OAS HAS SING N N 49 VDO CAH HAH SING N N 50 VDO OAR HAR SING N N 51 VDO CAD HAD1 SING N N 52 VDO CAD HAD2 SING N N 53 VDO OAQ HAQ SING N N 54 # 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 VDO SMILES ACDLabs 10.04 "O=P(O)(O)OCC2C(O)C(O)C(O)C(NC1C=C(CO)C(O)C(O)C1O)C2" VDO SMILES_CANONICAL CACTVS 3.352 "OCC1=C[C@H](N[C@H]2C[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H](O)[C@H]2O)[C@H](O)[C@@H](O)[C@@H]1O" VDO SMILES CACTVS 3.352 "OCC1=C[CH](N[CH]2C[CH](CO[P](O)(O)=O)[CH](O)[CH](O)[CH]2O)[CH](O)[CH](O)[CH]1O" VDO SMILES_CANONICAL "OpenEye OEToolkits" 1.6.1 "C1[C@@H]([C@H]([C@@H]([C@H]([C@H]1N[C@H]2C=C([C@H]([C@@H]([C@H]2O)O)O)CO)O)O)O)COP(=O)(O)O" VDO SMILES "OpenEye OEToolkits" 1.6.1 "C1C(C(C(C(C1NC2C=C(C(C(C2O)O)O)CO)O)O)O)COP(=O)(O)O" VDO InChI InChI 1.03 "InChI=1S/C14H26NO11P/c16-3-5-1-7(11(19)13(21)9(5)17)15-8-2-6(4-26-27(23,24)25)10(18)14(22)12(8)20/h1,6-22H,2-4H2,(H2,23,24,25)/t6-,7+,8+,9-,10-,11+,12+,13+,14+/m1/s1" VDO InChIKey InChI 1.03 ZKSTYMJGEHZSFH-MBABXGOBSA-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 VDO "SYSTEMATIC NAME" ACDLabs 10.04 "[(1R,2R,3S,4S,5S)-2,3,4-trihydroxy-5-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}cyclohexyl]methyl dihydrogen phosphate" VDO "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.6.1 "[(1R,2R,3S,4S,5S)-2,3,4-trihydroxy-5-[[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)-1-cyclohex-2-enyl]amino]cyclohexyl]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 VDO "Create component" 2009-09-25 EBI VDO "Modify descriptor" 2011-06-04 RCSB #