data_C4J
# 
_chem_comp.id                                    C4J 
_chem_comp.name                                  "(5S)-5-{3-[(3S)-3-amino-3-carboxypropyl]-1-methyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl}-2,5-anhydro-1-O-phosphono-L-arabinitol" 
_chem_comp.type                                  "RNA linking" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C14 H22 N3 O11 P" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2017-09-13 
_chem_comp.pdbx_modified_date                    2017-12-01 
_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                        439.312 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     C4J 
_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        6AZ1 
_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 
C4J C6    C1  C 0 1 N N N 131.174 205.672 192.159 -1.326 -2.937 1.266  C6    C4J 1  
C4J C5    C2  C 0 1 N N N 130.486 204.742 192.861 -0.624 -2.169 0.405  C5    C4J 2  
C4J N1    N1  N 0 1 N N N 131.623 206.761 192.722 -2.673 -2.742 1.404  N1    C4J 3  
C4J C2    C3  C 0 1 N N N 131.431 206.955 194.032 -3.305 -1.793 0.689  C2    C4J 4  
C4J N3    N2  N 0 1 N N N 130.761 206.039 194.749 -2.630 -1.014 -0.176 N3    C4J 5  
C4J C4    C4  C 0 1 N N N 130.313 204.948 194.186 -1.301 -1.174 -0.341 C4    C4J 6  
C4J C1    C5  C 0 1 N N N 132.334 207.734 191.923 -3.434 -3.575 2.338  C1    C4J 7  
C4J "C1'" C6  C 0 1 N N S 129.999 203.478 192.180 0.861  -2.368 0.239  "C1'" C4J 8  
C4J "C2'" C7  C 0 1 N N R 128.532 203.116 192.344 1.167  -2.857 -1.193 "C2'" C4J 9  
C4J C3    C8  C 0 1 N N N 130.544 206.237 196.159 -3.342 0.011  -0.943 C3    C4J 10 
C4J "C3'" C9  C 0 1 N N S 127.891 203.765 191.113 2.471  -2.085 -1.533 "C3'" C4J 11 
C4J C31   C10 C 0 1 N N N 131.747 205.737 196.930 -3.345 1.325  -0.158 C31   C4J 12 
C4J C32   C11 C 0 1 N N S 131.678 206.257 198.347 -4.088 2.396  -0.958 C32   C4J 13 
C4J C34   C12 C 0 1 N N N 131.962 207.754 198.311 -4.197 3.653  -0.135 C34   C4J 14 
C4J "C4'" C13 C 0 1 N N S 129.058 204.083 190.171 2.228  -0.752 -0.780 "C4'" C4J 15 
C4J "C5'" C14 C 0 1 N N N 128.963 203.573 188.766 3.561  -0.079 -0.449 "C5'" C4J 16 
C4J N33   N3  N 0 1 N N N 130.349 206.020 198.866 -3.349 2.684  -2.195 N33   C4J 17 
C4J O2    O1  O 0 1 N N N 131.827 207.936 194.545 -4.503 -1.638 0.827  O2    C4J 18 
C4J "O2'" O2  O 0 1 N N N 128.423 201.709 192.270 1.388  -4.269 -1.211 "O2'" C4J 19 
C4J "O3'" O3  O 0 1 N N N 126.885 202.974 190.514 3.620  -2.763 -1.022 "O3'" C4J 20 
C4J O35   O4  O 0 1 N N N 131.058 208.491 198.785 -5.142 3.754  0.814  O35   C4J 21 
C4J O36   O5  O 0 1 N N N 133.051 208.155 197.825 -3.435 4.570  -0.328 O36   C4J 22 
C4J O4    O6  O 0 1 N N N 129.736 204.172 194.867 -0.690 -0.469 -1.123 O4    C4J 23 
C4J "O4'" O7  O 0 1 N N N 130.227 203.542 190.812 1.542  -1.122 0.426  "O4'" C4J 24 
C4J "O5'" O8  O 0 1 N N N 130.213 203.694 188.123 3.315  1.171  0.199  "O5'" C4J 25 
C4J OP1   O9  O 0 1 N N N 132.110 205.210 188.122 5.412  1.409  1.584  OP1   C4J 26 
C4J OP2   O10 O 0 1 N N N 129.797 206.221 187.849 5.310  2.693  -0.587 OP2   C4J 27 
C4J P     P1  P 0 1 N N N 130.733 205.080 187.550 4.494  2.151  0.691  P     C4J 28 
C4J H1    H1  H 0 1 N N N 131.356 205.509 191.107 -0.826 -3.704 1.839  H1    C4J 29 
C4J H2    H2  H 0 1 N N N 132.636 208.580 192.558 -3.448 -3.101 3.319  H2    C4J 30 
C4J H3    H3  H 0 1 N N N 133.228 207.266 191.486 -4.456 -3.688 1.975  H3    C4J 31 
C4J H4    H4  H 0 1 N N N 131.679 208.096 191.117 -2.966 -4.556 2.415  H4    C4J 32 
C4J H5    H5  H 0 1 N N N 130.584 202.644 192.595 1.219  -3.099 0.964  H5    C4J 33 
C4J H6    H6  H 0 1 N N N 128.118 203.532 193.274 0.364  -2.583 -1.877 H6    C4J 34 
C4J H7    H7  H 0 1 N N N 130.399 207.309 196.361 -2.843 0.161  -1.900 H7    C4J 35 
C4J H8    H8  H 0 1 N N N 129.649 205.680 196.474 -4.369 -0.311 -1.115 H8    C4J 36 
C4J H9    H9  H 0 1 N N N 127.453 204.722 191.433 2.561  -1.919 -2.606 H9    C4J 37 
C4J H10   H10 H 0 1 N N N 131.746 204.637 196.941 -3.843 1.175  0.799  H10   C4J 38 
C4J H11   H11 H 0 1 N N N 132.668 206.098 196.450 -2.318 1.647  0.014  H11   C4J 39 
C4J H12   H12 H 0 1 N N N 132.434 205.752 198.967 -5.087 2.036  -1.207 H12   C4J 40 
C4J H13   H13 H 0 1 N N N 129.157 205.178 190.127 1.606  -0.087 -1.380 H13   C4J 41 
C4J H14   H14 H 0 1 N N N 128.212 204.159 188.216 4.139  -0.723 0.213  H14   C4J 42 
C4J H15   H15 H 0 1 N N N 128.663 202.515 188.782 4.120  0.093  -1.368 H15   C4J 43 
C4J H16   H16 H 0 1 N N N 130.292 206.361 199.804 -2.420 3.019  -1.992 H16   C4J 44 
C4J H17   H17 H 0 1 N N N 129.679 206.497 198.297 -3.318 1.872  -2.795 H17   C4J 45 
C4J H19   H19 H 0 1 N N N 128.824 201.319 193.038 1.585  -4.624 -2.089 H19   C4J 46 
C4J H20   H20 H 0 1 N N N 126.193 202.811 191.144 3.749  -3.649 -1.388 H20   C4J 47 
C4J H21   H21 H 0 1 N N N 131.324 209.401 198.720 -5.173 4.579  1.316  H21   C4J 48 
C4J H23   H23 H 0 1 N N N 130.247 206.871 188.376 4.769  3.190  -1.216 H23   C4J 49 
C4J OP3   OP3 O 0 1 N Y N 130.944 204.750 185.991 3.859  3.396  1.490  OP3   C4J 50 
C4J H24   H24 H 0 1 N N N 131.873 204.715 185.797 4.513  4.029  1.816  H24   C4J 51 
# 
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 
C4J P     OP2   SING N N 1  
C4J P     OP1   DOUB N N 2  
C4J P     "O5'" SING N N 3  
C4J "O5'" "C5'" SING N N 4  
C4J "C5'" "C4'" SING N N 5  
C4J "C4'" "O4'" SING N N 6  
C4J "C4'" "C3'" SING N N 7  
C4J "O3'" "C3'" SING N N 8  
C4J "O4'" "C1'" SING N N 9  
C4J "C3'" "C2'" SING N N 10 
C4J C1    N1    SING N N 11 
C4J C6    N1    SING N N 12 
C4J C6    C5    DOUB N N 13 
C4J "C1'" "C2'" SING N N 14 
C4J "C1'" C5    SING N N 15 
C4J "O2'" "C2'" SING N N 16 
C4J N1    C2    SING N N 17 
C4J C5    C4    SING N N 18 
C4J C2    O2    DOUB N N 19 
C4J C2    N3    SING N N 20 
C4J C4    N3    SING N N 21 
C4J C4    O4    DOUB N N 22 
C4J N3    C3    SING N N 23 
C4J C3    C31   SING N N 24 
C4J C31   C32   SING N N 25 
C4J O36   C34   DOUB N N 26 
C4J C34   C32   SING N N 27 
C4J C34   O35   SING N N 28 
C4J C32   N33   SING N N 29 
C4J C6    H1    SING N N 30 
C4J C1    H2    SING N N 31 
C4J C1    H3    SING N N 32 
C4J C1    H4    SING N N 33 
C4J "C1'" H5    SING N N 34 
C4J "C2'" H6    SING N N 35 
C4J C3    H7    SING N N 36 
C4J C3    H8    SING N N 37 
C4J "C3'" H9    SING N N 38 
C4J C31   H10   SING N N 39 
C4J C31   H11   SING N N 40 
C4J C32   H12   SING N N 41 
C4J "C4'" H13   SING N N 42 
C4J "C5'" H14   SING N N 43 
C4J "C5'" H15   SING N N 44 
C4J N33   H16   SING N N 45 
C4J N33   H17   SING N N 46 
C4J "O2'" H19   SING N N 47 
C4J "O3'" H20   SING N N 48 
C4J O35   H21   SING N N 49 
C4J OP2   H23   SING N N 50 
C4J P     OP3   SING N N 51 
C4J OP3   H24   SING N N 52 
# 
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 
C4J SMILES           ACDLabs              12.01 "C=1N(C(=O)N(CCC(N)C(O)=O)C(C=1C2C(C(C(O2)COP(=O)(O)O)O)O)=O)C"                                                                                                                           
C4J InChI            InChI                1.03  "InChI=1S/C14H22N3O11P/c1-16-4-6(12(20)17(14(16)23)3-2-7(15)13(21)22)11-10(19)9(18)8(28-11)5-27-29(24,25)26/h4,7-11,18-19H,2-3,5,15H2,1H3,(H,21,22)(H2,24,25,26)/t7-,8-,9+,10+,11-/m0/s1" 
C4J InChIKey         InChI                1.03  BVRIEBGMUPJSJF-DAWVFNFOSA-N                                                                                                                                                               
C4J SMILES_CANONICAL CACTVS               3.385 "CN1C=C([C@@H]2O[C@@H](CO[P](O)(O)=O)[C@@H](O)[C@H]2O)C(=O)N(CC[C@H](N)C(O)=O)C1=O"                                                                                                       
C4J SMILES           CACTVS               3.385 "CN1C=C([CH]2O[CH](CO[P](O)(O)=O)[CH](O)[CH]2O)C(=O)N(CC[CH](N)C(O)=O)C1=O"                                                                                                               
C4J SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "CN1C=C(C(=O)N(C1=O)CC[C@@H](C(=O)O)N)[C@H]2[C@@H]([C@@H]([C@@H](O2)COP(=O)(O)O)O)O"                                                                                                      
C4J SMILES           "OpenEye OEToolkits" 2.0.6 "CN1C=C(C(=O)N(C1=O)CCC(C(=O)O)N)C2C(C(C(O2)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 
C4J "SYSTEMATIC NAME" ACDLabs              12.01 "(5S)-5-{3-[(3S)-3-amino-3-carboxypropyl]-1-methyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl}-2,5-anhydro-1-O-phosphono-L-arabinitol"                              
C4J "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "(2~{S})-2-azanyl-4-[5-[(2~{S},3~{R},4~{S},5~{S})-3,4-bis(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]-3-methyl-2,6-bis(oxidanylidene)pyrimidin-1-yl]butanoic 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 
C4J "Create component" 2017-09-13 RCSB 
C4J "Initial release"  2017-12-06 RCSB 
# 
