data_DH3 # _chem_comp.id DH3 _chem_comp.name ;2,4-DIAMINO-5-[3',4'-DIMETHOXY-5'-(5-CARBOXYL-1-PENTYNYL)]BENZYL PYRIMIDINE ; _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C19 H22 N4 O4" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2006-02-15 _chem_comp.pdbx_modified_date 2024-09-27 _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 370.402 _chem_comp.one_letter_code ? _chem_comp.three_letter_code DH3 _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 Y _chem_comp.pdbx_model_coordinates_db_code 2FZI _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site RCSB _chem_comp.pdbx_pcm Y # 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.pdbx_backbone_atom_flag _chem_comp_atom.pdbx_n_terminal_atom_flag _chem_comp_atom.pdbx_c_terminal_atom_flag _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 DH3 N4 N4 N 0 1 N N N N N N 47.054 0.427 14.544 2.695 -2.573 -1.117 N4 DH3 1 DH3 C4 C4 C 0 1 Y N N N N N 47.533 -0.407 13.506 3.690 -1.908 -0.420 C4 DH3 2 DH3 N3 N3 N 0 1 Y N N N N N 46.839 -1.547 13.227 4.376 -2.529 0.534 N3 DH3 3 DH3 C2 C2 C 0 1 Y N N N N N 47.235 -2.410 12.238 5.328 -1.896 1.202 C2 DH3 4 DH3 N2 N2 N 0 1 N N N N N N 46.476 -3.574 11.990 6.020 -2.570 2.193 N2 DH3 5 DH3 N1 N1 N 0 1 Y N N N N N 48.349 -2.124 11.512 5.634 -0.632 0.946 N1 DH3 6 DH3 C6 C6 C 0 1 Y N N N N N 49.087 -1.005 11.743 4.994 0.046 0.006 C6 DH3 7 DH3 C5 C5 C 0 1 Y N N N N N 48.717 -0.074 12.756 3.994 -0.577 -0.715 C5 DH3 8 DH3 C51 C51 C 0 1 N N N N N N 49.343 1.301 13.243 3.244 0.164 -1.793 C51 DH3 9 DH3 "C1'" "C1'" C 0 1 Y N N N N N 50.658 1.599 12.465 1.973 0.733 -1.218 "C1'" DH3 10 DH3 "C6'" "C6'" C 0 1 Y N N N N N 50.680 2.033 11.095 0.813 -0.013 -1.244 "C6'" DH3 11 DH3 C52 C52 C 0 1 Y N N N N N 51.948 2.272 10.467 -0.366 0.511 -0.713 C52 DH3 12 DH3 C53 C53 C 0 1 N N N N N N 51.961 2.711 9.051 -1.572 -0.261 -0.737 C53 DH3 13 DH3 C54 C54 C 0 1 N N N N N N 51.948 3.357 8.048 -2.560 -0.895 -0.758 C54 DH3 14 DH3 C1 C1 C 0 1 N N N N N N 51.947 4.170 7.089 -3.800 -1.689 -0.783 C1 DH3 15 DH3 C3 C3 C 0 1 N N N N N N 51.191 4.812 6.262 -4.933 -0.885 -0.143 C3 DH3 16 DH3 C7 C7 C 0 1 N N N N N N 49.736 4.717 6.232 -6.221 -1.710 -0.169 C7 DH3 17 DH3 C8 C8 C 0 1 N N N N N N 48.369 5.323 6.247 -7.338 -0.919 0.462 C8 DH3 18 DH3 O10 O10 O 0 1 N N N N N N 48.109 6.278 5.533 -8.569 -1.447 0.549 O10 DH3 19 DH3 O9 O9 O 0 1 N N N N N N 47.503 4.867 6.978 -7.125 0.191 0.888 O9 DH3 20 DH3 "C4'" "C4'" C 0 1 Y N N N N N 53.182 2.098 11.175 -0.364 1.792 -0.152 "C4'" DH3 21 DH3 O5 O5 O 0 1 N N N N N N 54.401 2.347 10.504 -1.508 2.312 0.368 O5 DH3 22 DH3 "C5'" C5* C 0 1 N N N N N N 55.590 1.429 10.056 -1.544 1.935 1.746 "C5'" DH3 23 DH3 "C3'" "C3'" C 0 1 Y N N N N N 53.138 1.667 12.541 0.810 2.535 -0.137 "C3'" DH3 24 DH3 O4 O4 O 0 1 N N N N N N 54.309 1.483 13.271 0.818 3.783 0.404 O4 DH3 25 DH3 C4B C4* C 0 1 N N N N N N 55.132 2.893 13.798 2.152 4.280 0.277 C4B DH3 26 DH3 "C2'" "C2'" C 0 1 Y N N N N N 51.881 1.431 13.152 1.974 2.002 -0.667 "C2'" DH3 27 DH3 HN41 1HN4 H 0 0 N N N N N N 47.710 1.164 14.709 2.495 -3.499 -0.911 HN41 DH3 28 DH3 HN42 2HN4 H 0 0 N N N N N N 46.941 -0.111 15.379 2.199 -2.113 -1.812 HN42 DH3 29 DH3 HN21 1HN2 H 0 0 N N N N N N 46.683 -4.260 11.292 6.720 -2.118 2.690 HN21 DH3 30 DH3 HN22 2HN2 H 0 0 N N N N N N 45.700 -3.608 12.619 5.806 -3.495 2.390 HN22 DH3 31 DH3 H6 H6 H 0 1 N N N N N N 49.969 -0.819 11.148 5.251 1.076 -0.195 H6 DH3 32 DH3 H511 1H51 H 0 0 N N N N N N 49.569 1.232 14.317 3.001 -0.523 -2.604 H511 DH3 33 DH3 H512 2H51 H 0 0 N N N N N N 48.622 2.112 13.060 3.865 0.974 -2.176 H512 DH3 34 DH3 "H6'" "H6'" H 0 1 N N N N N N 49.760 2.177 10.548 0.818 -1.004 -1.675 "H6'" DH3 35 DH3 H11 1H1 H 0 1 N N N N N N 52.130 3.368 6.359 -4.059 -1.924 -1.815 H11 DH3 36 DH3 H12 2H1 H 0 1 N N N N N N 52.433 5.025 7.583 -3.650 -2.613 -0.225 H12 DH3 37 DH3 H31 1H3 H 0 1 N N N N N N 51.457 4.331 5.309 -4.674 -0.649 0.889 H31 DH3 38 DH3 H32 2H3 H 0 1 N N N N N N 51.399 5.874 6.459 -5.083 0.040 -0.700 H32 DH3 39 DH3 H71 1H7 H 0 1 N N N N N N 49.725 4.690 7.332 -6.481 -1.946 -1.201 H71 DH3 40 DH3 H72 2H7 H 0 1 N N N N N N 49.654 4.223 5.253 -6.072 -2.635 0.389 H72 DH3 41 DH3 HO9 HO9 H 0 1 N N N N N N 46.701 5.365 6.868 ? ? ? HO9 DH3 42 DH3 "H5'1" 1H5* H 0 0 N N N N N N 55.558 0.486 10.622 -0.669 2.338 2.256 "H5'1" DH3 43 DH3 "H5'2" 2H5* H 0 0 N N N N N N 56.543 1.942 10.251 -2.449 2.331 2.207 "H5'2" DH3 44 DH3 "H5'3" 3H5* H 0 0 N N N N N N 55.503 1.214 8.981 -1.542 0.847 1.825 "H5'3" DH3 45 DH3 "H4'1" 1H4* H 0 0 N N N N N N 54.520 3.779 13.576 2.207 5.284 0.699 "H4'1" DH3 46 DH3 "H4'2" 2H4* H 0 0 N N N N N N 56.096 2.972 13.274 2.836 3.622 0.812 "H4'2" DH3 47 DH3 "H4'3" 3H4* H 0 0 N N N N N N 55.308 2.832 14.882 2.428 4.313 -0.777 "H4'3" DH3 48 DH3 "H2'" "H2'" H 0 1 N N N N N N 51.857 1.110 14.183 2.886 2.581 -0.651 "H2'" DH3 49 # 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 DH3 N4 C4 SING N N 1 DH3 N4 HN41 SING N N 2 DH3 N4 HN42 SING N N 3 DH3 C4 N3 SING Y N 4 DH3 C4 C5 DOUB Y N 5 DH3 N3 C2 DOUB Y N 6 DH3 C2 N2 SING N N 7 DH3 C2 N1 SING Y N 8 DH3 N2 HN21 SING N N 9 DH3 N2 HN22 SING N N 10 DH3 N1 C6 DOUB Y N 11 DH3 C6 C5 SING Y N 12 DH3 C6 H6 SING N N 13 DH3 C5 C51 SING N N 14 DH3 C51 "C1'" SING N N 15 DH3 C51 H511 SING N N 16 DH3 C51 H512 SING N N 17 DH3 "C1'" "C6'" DOUB Y N 18 DH3 "C1'" "C2'" SING Y N 19 DH3 "C6'" C52 SING Y N 20 DH3 "C6'" "H6'" SING N N 21 DH3 C52 C53 SING N N 22 DH3 C52 "C4'" DOUB Y N 23 DH3 C53 C54 TRIP N N 24 DH3 C54 C1 SING N N 25 DH3 C1 C3 SING N N 26 DH3 C1 H11 SING N N 27 DH3 C1 H12 SING N N 28 DH3 C3 C7 SING N N 29 DH3 C3 H31 SING N N 30 DH3 C3 H32 SING N N 31 DH3 C7 C8 SING N N 32 DH3 C7 H71 SING N N 33 DH3 C7 H72 SING N N 34 DH3 C8 O10 DOUB N N 35 DH3 C8 O9 SING N N 36 DH3 O9 HO9 SING N N 37 DH3 "C4'" O5 SING N N 38 DH3 "C4'" "C3'" SING Y N 39 DH3 O5 "C5'" SING N N 40 DH3 "C5'" "H5'1" SING N N 41 DH3 "C5'" "H5'2" SING N N 42 DH3 "C5'" "H5'3" SING N N 43 DH3 "C3'" O4 SING N N 44 DH3 "C3'" "C2'" DOUB Y N 45 DH3 O4 C4B SING N N 46 DH3 C4B "H4'1" SING N N 47 DH3 C4B "H4'2" SING N N 48 DH3 C4B "H4'3" SING N N 49 DH3 "C2'" "H2'" SING N N 50 # 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 DH3 SMILES ACDLabs 10.04 "O=C(O)CCCC#Cc1cc(cc(OC)c1OC)Cc2cnc(nc2N)N" DH3 SMILES_CANONICAL CACTVS 3.341 "COc1cc(Cc2cnc(N)nc2N)cc(C#CCCCC(O)=O)c1OC" DH3 SMILES CACTVS 3.341 "COc1cc(Cc2cnc(N)nc2N)cc(C#CCCCC(O)=O)c1OC" DH3 SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "COc1cc(cc(c1OC)C#CCCCC(=O)O)Cc2cnc(nc2N)N" DH3 SMILES "OpenEye OEToolkits" 1.5.0 "COc1cc(cc(c1OC)C#CCCCC(=O)O)Cc2cnc(nc2N)N" DH3 InChI InChI 1.03 "InChI=1S/C19H22N4O4/c1-26-15-10-12(9-14-11-22-19(21)23-18(14)20)8-13(17(15)27-2)6-4-3-5-7-16(24)25/h8,10-11H,3,5,7,9H2,1-2H3,(H,24,25)(H4,20,21,22,23)" DH3 InChIKey InChI 1.03 JAGSWKLZBKKKJP-UHFFFAOYSA-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 DH3 "SYSTEMATIC NAME" ACDLabs 10.04 "6-{5-[(2,4-diaminopyrimidin-5-yl)methyl]-2,3-dimethoxyphenyl}hex-5-ynoic acid" DH3 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "6-[5-[(2,4-diaminopyrimidin-5-yl)methyl]-2,3-dimethoxy-phenyl]hex-5-ynoic acid" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site DH3 "Create component" 2006-02-15 RCSB DH3 "Modify descriptor" 2011-06-04 RCSB DH3 "Modify PCM" 2024-09-27 PDBE # _pdbx_chem_comp_pcm.pcm_id 1 _pdbx_chem_comp_pcm.comp_id DH3 _pdbx_chem_comp_pcm.modified_residue_id SER _pdbx_chem_comp_pcm.type None _pdbx_chem_comp_pcm.category "Covalent chemical modification" _pdbx_chem_comp_pcm.position "Amino-acid side chain" _pdbx_chem_comp_pcm.polypeptide_position "Any position" _pdbx_chem_comp_pcm.comp_id_linking_atom C4B _pdbx_chem_comp_pcm.modified_residue_id_linking_atom OG _pdbx_chem_comp_pcm.uniprot_specific_ptm_accession ? _pdbx_chem_comp_pcm.uniprot_generic_ptm_accession ? #