data_2MD # _chem_comp.id 2MD _chem_comp.name ;GUANYLATE-O'-PHOSPHORIC ACID MONO-(2-AMINO-5,6-DIMERCAPTO-4-OXO-3,5,6,7,8A,9,10,10A-OCTAHYDRO-4H-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-7-YLMETHYL) ESTER ; _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C20 H28 N10 O13 P2 S2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "MOLYBDENUM COFACTOR,BIS (MOLYBDOPTERIN GUANINE DINUCLEOTIDE)" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 1999-10-08 _chem_comp.pdbx_modified_date 2020-06-17 _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 742.573 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 2MD _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag N _chem_comp.pdbx_ideal_coordinates_details ? _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 1TMO _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 2MD PB PB P 0 1 N N S 42.894 34.969 21.395 -0.641 0.962 1.181 PB 2MD 1 2MD O3B O3B O 0 1 N N N 42.337 35.695 22.739 0.012 0.207 -0.081 O3B 2MD 2 2MD O1B O1B O 0 1 N N N 44.218 34.337 21.522 0.284 2.013 1.661 O1B 2MD 3 2MD O2B O2B O 0 1 N N N 42.002 33.919 20.852 -2.036 1.635 0.742 O2B 2MD 4 2MD O3A O3A O 0 1 N N N 43.007 36.151 20.254 -0.906 -0.098 2.363 O3A 2MD 5 2MD C10 C10 C 0 1 N N N 43.817 37.354 20.405 -1.483 0.628 3.449 C10 2MD 6 2MD C11 C11 C 0 1 N N R 43.783 38.434 19.275 -1.761 -0.327 4.611 C11 2MD 7 2MD O11 O11 O 0 1 N N N 43.130 39.438 19.980 -0.540 -0.927 5.034 O11 2MD 8 2MD C12 C12 C 0 1 N N S 45.096 38.961 18.606 -2.380 0.452 5.775 C12 2MD 9 2MD S12 S12 S 0 1 N N N 46.369 37.793 18.570 -1.210 1.709 6.360 S12 2MD 10 2MD C13 C13 C 0 1 N N R 45.532 40.281 18.762 -2.693 -0.526 6.912 C13 2MD 11 2MD S13 S13 S 0 1 N N N 47.287 40.411 18.954 -3.246 0.395 8.373 S13 2MD 12 2MD C14 C14 C 0 1 N N R 44.652 41.239 19.620 -1.429 -1.315 7.254 C14 2MD 13 2MD N15 N15 N 0 1 N N N 45.102 41.820 20.908 -0.411 -0.408 7.805 N15 2MD 14 2MD C16 C16 C 0 1 N N N 44.203 42.316 21.829 0.920 -0.876 7.885 C16 2MD 15 2MD C15 C15 C 0 1 N N N 44.612 42.998 23.037 1.863 -0.220 8.682 C15 2MD 16 2MD O14 O14 O 0 1 N N N 45.946 42.927 23.413 1.555 0.772 9.325 O14 2MD 17 2MD N17 N17 N 0 1 N N N 43.699 43.633 23.833 3.121 -0.710 8.729 N17 2MD 18 2MD C17 C17 C 0 1 N N N 42.361 43.623 23.527 3.452 -1.813 8.004 C17 2MD 19 2MD N16 N16 N 0 1 N N N 41.425 44.052 24.398 4.736 -2.292 8.064 N16 2MD 20 2MD N18 N18 N 0 1 N N N 41.944 43.069 22.358 2.569 -2.435 7.252 N18 2MD 21 2MD C20 C20 C 0 1 N N N 42.770 42.339 21.551 1.306 -2.000 7.168 C20 2MD 22 2MD N8 N8 N 0 1 N N N 42.251 41.654 20.495 0.386 -2.664 6.371 N8 2MD 23 2MD C7 C7 C 0 1 N N R 43.142 40.807 19.681 -0.851 -1.963 5.988 C7 2MD 24 2MD PA PA P 0 1 N N R 42.600 35.127 24.230 0.249 1.322 -1.218 PA 2MD 25 2MD O1A O1A O 0 1 N N N 41.889 36.101 25.094 1.160 2.368 -0.701 O1A 2MD 26 2MD O2A O2A O 0 1 N N N 44.034 35.010 24.546 -1.160 1.989 -1.617 O2A 2MD 27 2MD "O5'" O5* O 0 1 N N N 41.920 33.682 24.380 0.904 0.633 -2.517 "O5'" 2MD 28 2MD "C5'" C5* C 0 1 N N N 40.516 33.387 24.187 1.089 1.668 -3.485 "C5'" 2MD 29 2MD "C4'" C4* C 0 1 N N R 40.057 32.159 24.988 1.711 1.077 -4.751 "C4'" 2MD 30 2MD "O4'" O4* O 0 1 N N N 40.771 30.935 24.692 0.827 0.096 -5.318 "O4'" 2MD 31 2MD "C1'" C1* C 0 1 N N R 40.591 30.095 25.875 0.978 0.171 -6.752 "C1'" 2MD 32 2MD N9 N9 N 0 1 Y N N 41.492 28.897 25.914 -0.193 -0.394 -7.425 N9 2MD 33 2MD C4 C4 C 0 1 Y N N 41.184 27.578 25.622 -0.212 -0.982 -8.660 C4 2MD 34 2MD N3 N3 N 0 1 N N N 39.936 27.085 25.287 0.719 -1.235 -9.587 N3 2MD 35 2MD C2 C2 C 0 1 N N N 39.870 25.718 25.287 0.410 -1.837 -10.714 C2 2MD 36 2MD N2 N2 N 0 1 N N N 38.706 25.111 25.075 1.398 -2.072 -11.637 N2 2MD 37 2MD N1 N1 N 0 1 N N N 40.996 24.904 25.445 -0.863 -2.236 -10.992 N1 2MD 38 2MD C6 C6 C 0 1 N N N 42.324 25.385 25.551 -1.856 -2.018 -10.102 C6 2MD 39 2MD O6 O6 O 0 1 N N N 43.257 24.585 25.396 -2.998 -2.371 -10.342 O6 2MD 40 2MD C5 C5 C 0 1 Y N N 42.364 26.839 25.750 -1.537 -1.372 -8.885 C5 2MD 41 2MD N7 N7 N 0 1 Y N N 43.419 27.683 26.095 -2.255 -1.002 -7.796 N7 2MD 42 2MD C8 C8 C 0 1 Y N N 42.846 28.867 26.188 -1.467 -0.427 -6.936 C8 2MD 43 2MD "C2'" C2* C 0 1 N N R 40.843 31.100 27.010 1.086 1.693 -7.025 "C2'" 2MD 44 2MD "O2'" O2* O 0 1 N N N 40.265 30.698 28.249 1.786 1.944 -8.245 "O2'" 2MD 45 2MD "C3'" C3* C 0 1 N N S 40.150 32.390 26.514 1.908 2.184 -5.804 "C3'" 2MD 46 2MD "O3'" O3* O 0 1 N N N 38.821 32.470 27.046 3.288 2.315 -6.151 "O3'" 2MD 47 2MD HO2B BHO2 H 0 0 N N N 42.327 33.494 20.066 -2.608 0.918 0.437 HO2B 2MD 48 2MD H101 1H10 H 0 0 N N N 43.561 37.840 21.375 -2.417 1.086 3.124 H101 2MD 49 2MD H102 2H10 H 0 0 N N N 44.875 37.054 20.584 -0.791 1.405 3.775 H102 2MD 50 2MD H11 H11 H 0 1 N N N 43.331 38.008 18.348 -2.454 -1.103 4.285 H11 2MD 51 2MD H12 H12 H 0 1 N N N 44.681 39.097 17.580 -3.300 0.934 5.444 H12 2MD 52 2MD HS2 HS2 H 0 1 N N N 47.166 38.112 18.163 -1.076 2.442 5.240 HS2 2MD 53 2MD H13 H13 H 0 1 N N N 45.323 40.744 17.769 -3.478 -1.213 6.596 H13 2MD 54 2MD HS3 HS3 H 0 1 N N N 47.583 41.307 19.059 -4.336 1.001 7.868 HS3 2MD 55 2MD H14 H14 H 0 1 N N N 44.818 42.135 18.977 -1.667 -2.088 7.986 H14 2MD 56 2MD HNF HNF H 0 1 N N N 45.777 42.556 20.701 -0.645 0.483 8.105 HNF 2MD 57 2MD HNH HNH H 0 1 N N N 44.021 44.121 24.668 3.791 -0.271 9.276 HNH 2MD 58 2MD HNG1 1HNG H 0 0 N N N 40.430 44.044 24.170 4.984 -3.080 7.555 HNG1 2MD 59 2MD HNG2 2HNG H 0 0 N N N 41.672 45.001 24.677 5.397 -1.841 8.611 HNG2 2MD 60 2MD HN8 HN8 H 0 1 N N N 41.773 42.312 19.880 0.557 -3.570 6.066 HN8 2MD 61 2MD H7 H7 H 0 1 N N N 42.666 40.981 18.687 -1.560 -2.669 5.556 H7 2MD 62 2MD HO2A AHO2 H 0 0 N N N 44.188 34.676 25.421 -1.723 1.276 -1.948 HO2A 2MD 63 2MD "H5'1" 1H5* H 0 0 N N N 39.883 34.275 24.418 0.124 2.114 -3.728 "H5'1" 2MD 64 2MD "H5'2" 2H5* H 0 0 N N N 40.275 33.272 23.104 1.750 2.433 -3.077 "H5'2" 2MD 65 2MD "H4'" H4* H 0 1 N N N 38.998 32.030 24.663 2.671 0.618 -4.513 "H4'" 2MD 66 2MD "H1'" H1* H 0 1 N N N 39.588 29.609 25.925 1.886 -0.340 -7.070 "H1'" 2MD 67 2MD HN21 1HN2 H 0 0 N N N 38.656 24.092 25.075 2.309 -1.794 -11.453 HN21 2MD 68 2MD HN22 2HN2 H 0 0 N N N 38.318 25.453 24.195 1.186 -2.515 -12.473 HN22 2MD 69 2MD HN1 HN1 H 0 1 N N N 40.838 23.897 25.485 -1.057 -2.678 -11.833 HN1 2MD 70 2MD H8 H8 H 0 1 N N N 43.443 29.750 26.468 -1.774 -0.034 -5.978 H8 2MD 71 2MD "H2'" H2* H 0 1 N N N 41.933 31.209 27.213 0.099 2.156 -7.043 "H2'" 2MD 72 2MD "HO2'" *HO2 H 0 0 N N N 40.420 31.319 28.950 1.819 2.904 -8.356 "HO2'" 2MD 73 2MD "H3'" H3* H 0 1 N N N 40.689 33.319 26.809 1.516 3.133 -5.438 "H3'" 2MD 74 2MD "HO3'" *HO3 H 0 0 N N N 38.878 32.611 27.983 3.338 2.977 -6.854 "HO3'" 2MD 75 # # 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 2MD PB O3B SING N N 1 2MD PB O1B DOUB N N 2 2MD PB O2B SING N N 3 2MD PB O3A SING N N 4 2MD O3B PA SING N N 5 2MD O2B HO2B SING N N 6 2MD O3A C10 SING N N 7 2MD C10 C11 SING N N 8 2MD C10 H101 SING N N 9 2MD C10 H102 SING N N 10 2MD C11 O11 SING N N 11 2MD C11 C12 SING N N 12 2MD C11 H11 SING N N 13 2MD O11 C7 SING N N 14 2MD C12 S12 SING N N 15 2MD C12 C13 SING N N 16 2MD C12 H12 SING N N 17 2MD S12 HS2 SING N N 18 2MD C13 S13 SING N N 19 2MD C13 C14 SING N N 20 2MD C13 H13 SING N N 21 2MD S13 HS3 SING N N 22 2MD C14 N15 SING N N 23 2MD C14 C7 SING N N 24 2MD C14 H14 SING N N 25 2MD N15 C16 SING N N 26 2MD N15 HNF SING N N 27 2MD C16 C15 SING N N 28 2MD C16 C20 DOUB N N 29 2MD C15 O14 DOUB N N 30 2MD C15 N17 SING N N 31 2MD N17 C17 SING N N 32 2MD N17 HNH SING N N 33 2MD C17 N16 SING N N 34 2MD C17 N18 DOUB N N 35 2MD N16 HNG1 SING N N 36 2MD N16 HNG2 SING N N 37 2MD N18 C20 SING N N 38 2MD C20 N8 SING N N 39 2MD N8 C7 SING N N 40 2MD N8 HN8 SING N N 41 2MD C7 H7 SING N N 42 2MD PA O1A DOUB N N 43 2MD PA O2A SING N N 44 2MD PA "O5'" SING N N 45 2MD O2A HO2A SING N N 46 2MD "O5'" "C5'" SING N N 47 2MD "C5'" "C4'" SING N N 48 2MD "C5'" "H5'1" SING N N 49 2MD "C5'" "H5'2" SING N N 50 2MD "C4'" "O4'" SING N N 51 2MD "C4'" "C3'" SING N N 52 2MD "C4'" "H4'" SING N N 53 2MD "O4'" "C1'" SING N N 54 2MD "C1'" N9 SING N N 55 2MD "C1'" "C2'" SING N N 56 2MD "C1'" "H1'" SING N N 57 2MD N9 C4 SING Y N 58 2MD N9 C8 SING Y N 59 2MD C4 N3 SING N N 60 2MD C4 C5 DOUB Y N 61 2MD N3 C2 DOUB N N 62 2MD C2 N2 SING N N 63 2MD C2 N1 SING N N 64 2MD N2 HN21 SING N N 65 2MD N2 HN22 SING N N 66 2MD N1 C6 SING N N 67 2MD N1 HN1 SING N N 68 2MD C6 O6 DOUB N N 69 2MD C6 C5 SING N N 70 2MD C5 N7 SING Y N 71 2MD N7 C8 DOUB Y N 72 2MD C8 H8 SING N N 73 2MD "C2'" "O2'" SING N N 74 2MD "C2'" "C3'" SING N N 75 2MD "C2'" "H2'" SING N N 76 2MD "O2'" "HO2'" SING N N 77 2MD "C3'" "O3'" SING N N 78 2MD "C3'" "H3'" SING N N 79 2MD "O3'" "HO3'" SING N N 80 # # 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 2MD SMILES ACDLabs 10.04 "O=C1C=2NC3C(S)C(S)C(OC3NC=2N=C(N)N1)COP(=O)(O)OP(=O)(O)OCC6OC(n5cnc4c5N=C(N)NC4=O)C(O)C6O" 2MD SMILES_CANONICAL CACTVS 3.341 "NC1=NC2=C(N[C@H]3[C@@H](S)[C@@H](S)[C@@H](CO[P@@](O)(=O)O[P@@](O)(=O)OC[C@H]4O[C@H]([C@H](O)[C@@H]4O)n5cnc6C(=O)NC(=Nc56)N)O[C@H]3N2)C(=O)N1" 2MD SMILES CACTVS 3.341 "NC1=NC2=C(N[CH]3[CH](S)[CH](S)[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]4O[CH]([CH](O)[CH]4O)n5cnc6C(=O)NC(=Nc56)N)O[CH]3N2)C(=O)N1" 2MD SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(O)O[P@@](=O)(O)OC[C@@H]4[C@@H]([C@@H]([C@H]5[C@@H](O4)NC6=C(N5)C(=O)NC(=N6)N)S)S)O)O)N=C(NC2=O)N" 2MD SMILES "OpenEye OEToolkits" 1.5.0 "c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(C(C5C(O4)NC6=C(N5)C(=O)NC(=N6)N)S)S)O)O)N=C(NC2=O)N" 2MD InChI InChI 1.03 "InChI=1S/C20H28N10O13P2S2/c21-19-26-13-7(15(33)28-19)24-6-12(47)11(46)5(41-17(6)25-13)2-40-45(37,38)43-44(35,36)39-1-4-9(31)10(32)18(42-4)30-3-23-8-14(30)27-20(22)29-16(8)34/h3-6,9-12,17-18,24,31-32,46-47H,1-2H2,(H,35,36)(H,37,38)(H3,22,27,29,34)(H4,21,25,26,28,33)/t4-,5-,6+,9-,10-,11+,12-,17-,18-/m1/s1" 2MD InChIKey InChI 1.03 YDYCAANTTOPADF-JKOCJXFLSA-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 2MD "SYSTEMATIC NAME" ACDLabs 10.04 "5'-O-[(R)-{[(S)-{[(5aR,6R,7S,8R,9aR)-2-amino-4-oxo-6,7-disulfanyl-3,5,5a,6,7,8,9a,10-octahydro-4H-pyrano[3,2-g]pteridin-8-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]guanosine" 2MD "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(5aR,6R,7S,8R,9aR)-2-amino-4-oxo-6,7-bis-sulfanyl-3,5,5a,6,7,8,9a,10-octahydropyrano[5,6-g]pteridin-8-yl]methyl [[(2R,3S,4R,5R)-5-(2-amino-6-oxo-1H-purin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl] 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 2MD "Create component" 1999-10-08 RCSB 2MD "Modify descriptor" 2011-06-04 RCSB 2MD "Modify synonyms" 2020-06-05 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id 2MD _pdbx_chem_comp_synonyms.name "MOLYBDENUM COFACTOR,BIS (MOLYBDOPTERIN GUANINE DINUCLEOTIDE)" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##