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      ? 
# 
