data_PJ3
#
_chem_comp.id PJ3
_chem_comp.name "(2~{S})-2-azanyl-3-[1-[[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-7-methyl-6-oxidanylidene-1,8-dihydropurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]imidazol-4-yl]propanoic acid"
_chem_comp.type "L-peptide linking"
_chem_comp.pdbx_type ATOMP
_chem_comp.formula "C17 H25 N8 O9 P"
_chem_comp.mon_nstd_parent_comp_id HIS
_chem_comp.pdbx_synonyms "7GMP capped histidine"
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2022-10-04
_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 516.402
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code PJ3
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag Y
_chem_comp.pdbx_ideal_coordinates_details Corina
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code 8APX
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site PDBE
_chem_comp.pdbx_pcm N
#
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
PJ3 N N1 N 0 1 N N N N N N 124.873 203.969 139.387 -5.873 2.418 0.044 N PJ3 1
PJ3 CA C1 C 0 1 N N S N N N 123.765 203.344 139.622 -6.646 1.472 -0.772 CA PJ3 2
PJ3 C C2 C 0 1 N N N N N N 123.409 202.995 137.826 -8.089 1.907 -0.813 C PJ3 3
PJ3 O O1 O 0 1 N N N N N N 123.020 203.769 137.104 -8.518 2.656 0.032 O PJ3 4
PJ3 CB C3 C 0 1 N N N N N N 122.538 204.013 140.262 -6.552 0.074 -0.159 CB PJ3 5
PJ3 CG C4 C 0 1 Y N N N N N 122.284 205.298 139.489 -5.127 -0.411 -0.230 CG PJ3 6
PJ3 N2 N2 N 0 1 N N N N N N 112.911 207.745 144.680 2.746 1.470 3.284 N2 PJ3 7
PJ3 C2 C5 C 0 1 N N N N N N 113.004 208.297 143.408 3.364 1.717 2.084 C2 PJ3 8
PJ3 N1 N3 N 0 1 N N N N N N 112.308 209.477 143.168 4.023 2.894 1.906 N1 PJ3 9
PJ3 ND1 N4 N 0 1 Y N N N N N 123.117 206.444 139.368 -4.376 -0.492 -1.338 ND1 PJ3 10
PJ3 CD2 C6 C 0 1 Y N N N N N 121.150 205.601 138.741 -4.382 -0.834 0.809 CD2 PJ3 11
PJ3 CE1 C7 C 0 1 Y N N N N N 122.467 207.378 138.561 -3.196 -0.953 -1.026 CE1 PJ3 12
PJ3 NE2 N5 N 0 1 Y N N N N N 121.254 206.882 138.162 -3.158 -1.180 0.305 NE2 PJ3 13
PJ3 "C1'" C8 C 0 1 N N R N N N 115.268 206.379 139.920 3.356 -1.131 -1.314 "C1'" PJ3 14
PJ3 "C2'" C9 C 0 1 N N R N N N 114.544 205.489 138.867 4.024 -2.135 -0.341 "C2'" PJ3 15
PJ3 "C3'" C10 C 0 1 N N S N N N 115.654 205.044 137.846 2.915 -3.199 -0.160 "C3'" PJ3 16
PJ3 C4 C11 C 0 1 N N N N N N 113.806 208.274 141.218 3.898 1.008 -0.055 C4 PJ3 17
PJ3 "C4'" C12 C 0 1 N N R N N N 116.992 205.432 138.523 1.620 -2.468 -0.563 "C4'" PJ3 18
PJ3 C5 C13 C 0 1 N N N N N N 113.142 209.481 140.845 4.577 2.193 -0.288 C5 PJ3 19
PJ3 "C5'" C14 C 0 1 N N N N N N 118.069 205.936 137.467 0.630 -2.482 0.603 "C5'" PJ3 20
PJ3 C6 C15 C 0 1 N N N N N N 112.319 210.169 141.866 4.636 3.154 0.732 C6 PJ3 21
PJ3 C8 C16 C 0 1 N N N N N N 114.129 208.484 138.946 4.734 0.905 -2.201 C8 PJ3 22
PJ3 CM7 C17 C 0 1 N N N N N N 114.192 210.918 138.827 5.898 3.255 -2.221 CM7 PJ3 23
PJ3 N3 N6 N 0 1 N N N N N N 113.765 207.668 142.463 3.309 0.810 1.135 N3 PJ3 24
PJ3 N7 N7 N 0 1 N N N N N N 113.463 209.762 139.444 5.114 2.188 -1.594 N7 PJ3 25
PJ3 N9 N8 N 0 1 N N N N N N 114.565 207.731 140.147 3.956 0.198 -1.178 N9 PJ3 26
PJ3 O1A O2 O 0 1 N N N N N N 120.291 207.230 135.716 -2.225 -3.081 1.724 O1A PJ3 27
PJ3 "O2'" O3 O 0 1 N N N N N N 114.032 204.381 139.528 5.194 -2.711 -0.926 "O2'" PJ3 28
PJ3 "O3'" O4 O 0 1 N N N N N N 115.611 203.661 137.654 3.148 -4.315 -1.021 "O3'" PJ3 29
PJ3 O3A O5 O 0 1 N N N N N N 120.237 209.214 137.358 -1.528 -0.737 2.351 O3A PJ3 30
PJ3 "O4'" O6 O 0 1 N N N N N N 116.616 206.465 139.454 1.977 -1.113 -0.885 "O4'" PJ3 31
PJ3 "O5'" O7 O 0 1 N N N N N N 118.439 207.285 137.585 -0.608 -1.906 0.183 "O5'" PJ3 32
PJ3 O6 O8 O 0 1 N N N N N N 111.646 211.175 141.879 5.231 4.207 0.561 O6 PJ3 33
PJ3 PA P1 P 0 1 N N N N N N 120.014 207.781 137.065 -1.882 -1.758 1.157 PA PJ3 34
PJ3 H H1 H 0 1 N N N N N N 125.529 203.340 138.969 -5.866 3.336 -0.375 H PJ3 35
PJ3 H2 H2 H 0 1 N Y N N N N 124.700 204.732 138.764 -6.227 2.454 0.988 H2 PJ3 36
PJ3 HA H4 H 0 1 N N N N N N 123.921 202.360 140.089 -6.244 1.453 -1.785 HA PJ3 37
PJ3 HB2 H6 H 0 1 N N N N N N 121.664 203.349 140.190 -6.872 0.111 0.883 HB2 PJ3 38
PJ3 HB3 H7 H 0 1 N N N N N N 122.739 204.241 141.319 -7.197 -0.610 -0.712 HB3 PJ3 39
PJ3 H8 H8 H 0 1 N N N N N N 113.397 206.898 144.894 2.783 2.131 3.994 H8 PJ3 40
PJ3 H9 H9 H 0 1 N N N N N N 112.358 208.195 145.381 2.273 0.635 3.423 H9 PJ3 41
PJ3 H10 H10 H 0 1 N N N N N N 111.775 209.875 143.914 4.053 3.547 2.623 H10 PJ3 42
PJ3 HD2 H11 H 0 1 N N N N N N 120.303 204.942 138.620 -4.692 -0.889 1.843 HD2 PJ3 43
PJ3 HE1 H12 H 0 1 N N N N N N 122.861 208.347 138.291 -2.384 -1.124 -1.717 HE1 PJ3 44
PJ3 H13 H13 H 0 1 N N N N N N 115.254 205.834 140.875 3.436 -1.483 -2.343 H13 PJ3 45
PJ3 H14 H14 H 0 1 N N N N N N 113.768 206.071 138.348 4.262 -1.655 0.609 H14 PJ3 46
PJ3 H15 H15 H 0 1 N N N N N N 115.535 205.599 136.904 2.863 -3.523 0.880 H15 PJ3 47
PJ3 H16 H16 H 0 1 N N N N N N 117.398 204.558 139.053 1.176 -2.953 -1.433 H16 PJ3 48
PJ3 H17 H17 H 0 1 N N N N N N 118.975 205.323 137.587 0.462 -3.510 0.924 H17 PJ3 49
PJ3 H18 H18 H 0 1 N N N N N N 117.654 205.784 136.460 1.037 -1.904 1.432 H18 PJ3 50
PJ3 H19 H19 H 0 1 N N N N N N 113.413 207.886 138.364 4.120 1.075 -3.086 H19 PJ3 51
PJ3 H20 H20 H 0 1 N N N N N N 114.998 208.730 138.317 5.625 0.335 -2.464 H20 PJ3 52
PJ3 H21 H21 H 0 1 N N N N N N 114.240 210.782 137.736 6.015 4.081 -1.519 H21 PJ3 53
PJ3 H22 H22 H 0 1 N N N N N N 113.659 211.852 139.057 6.880 2.870 -2.496 H22 PJ3 54
PJ3 H23 H23 H 0 1 N N N N N N 115.212 210.968 139.235 5.382 3.607 -3.114 H23 PJ3 55
PJ3 H24 H24 H 0 1 N N N N N N 113.584 203.820 138.906 5.648 -3.345 -0.355 H24 PJ3 56
PJ3 H25 H25 H 0 1 N N N N N N 116.286 203.406 137.036 3.980 -4.778 -0.849 H25 PJ3 57
PJ3 H26 H26 H 0 1 N N N N N N 120.560 209.651 136.578 -1.293 0.152 2.052 H26 PJ3 58
PJ3 OXT OXT O 0 1 N Y N N N N ? ? ? -8.896 1.461 -1.788 OXT PJ3 59
PJ3 HXT H3 H 0 1 N Y N N N N ? ? ? -9.814 1.768 -1.773 HXT PJ3 60
#
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
PJ3 N CA SING N N 1
PJ3 CA CB SING N N 2
PJ3 C O DOUB N N 3
PJ3 CB CG SING N N 4
PJ3 CG ND1 SING Y N 5
PJ3 CG CD2 DOUB Y N 6
PJ3 N2 C2 SING N N 7
PJ3 C2 N1 SING N N 8
PJ3 C2 N3 DOUB N N 9
PJ3 N1 C6 SING N N 10
PJ3 ND1 CE1 DOUB Y N 11
PJ3 CD2 NE2 SING Y N 12
PJ3 CE1 NE2 SING Y N 13
PJ3 NE2 PA SING N N 14
PJ3 "C1'" "C2'" SING N N 15
PJ3 "C1'" N9 SING N N 16
PJ3 "C1'" "O4'" SING N N 17
PJ3 "C2'" "C3'" SING N N 18
PJ3 "C2'" "O2'" SING N N 19
PJ3 "C3'" "C4'" SING N N 20
PJ3 "C3'" "O3'" SING N N 21
PJ3 C4 C5 DOUB N N 22
PJ3 C4 N3 SING N N 23
PJ3 C4 N9 SING N N 24
PJ3 "C4'" "C5'" SING N N 25
PJ3 "C4'" "O4'" SING N N 26
PJ3 C5 C6 SING N N 27
PJ3 C5 N7 SING N N 28
PJ3 "C5'" "O5'" SING N N 29
PJ3 C6 O6 DOUB N N 30
PJ3 C8 N7 SING N N 31
PJ3 C8 N9 SING N N 32
PJ3 CM7 N7 SING N N 33
PJ3 O1A PA DOUB N N 34
PJ3 O3A PA SING N N 35
PJ3 "O5'" PA SING N N 36
PJ3 CA C SING N N 37
PJ3 N H SING N N 38
PJ3 N H2 SING N N 39
PJ3 CA HA SING N N 40
PJ3 CB HB2 SING N N 41
PJ3 CB HB3 SING N N 42
PJ3 N2 H8 SING N N 43
PJ3 N2 H9 SING N N 44
PJ3 N1 H10 SING N N 45
PJ3 CD2 HD2 SING N N 46
PJ3 CE1 HE1 SING N N 47
PJ3 "C1'" H13 SING N N 48
PJ3 "C2'" H14 SING N N 49
PJ3 "C3'" H15 SING N N 50
PJ3 "C4'" H16 SING N N 51
PJ3 "C5'" H17 SING N N 52
PJ3 "C5'" H18 SING N N 53
PJ3 C8 H19 SING N N 54
PJ3 C8 H20 SING N N 55
PJ3 CM7 H21 SING N N 56
PJ3 CM7 H22 SING N N 57
PJ3 CM7 H23 SING N N 58
PJ3 "O2'" H24 SING N N 59
PJ3 "O3'" H25 SING N N 60
PJ3 O3A H26 SING N N 61
PJ3 C OXT SING N N 62
PJ3 OXT HXT SING N N 63
#
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
PJ3 InChI InChI 1.06 "InChI=1S/C17H25N8O9P/c1-23-6-25(13-10(23)14(28)22-17(19)21-13)15-12(27)11(26)9(34-15)4-33-35(31,32)24-3-7(20-5-24)2-8(18)16(29)30/h3,5,8-9,11-12,15,26-27H,2,4,6,18H2,1H3,(H,29,30)(H,31,32)(H3,19,21,22,28)/t8-,9+,11+,12+,15+/m0/s1"
PJ3 InChIKey InChI 1.06 GHFKLICNYXEREV-OPYVMVOTSA-N
PJ3 SMILES_CANONICAL CACTVS 3.385 "CN1CN([C@@H]2O[C@H](CO[P](O)(=O)n3cnc(C[C@H](N)C(O)=O)c3)[C@@H](O)[C@H]2O)C4=C1C(=O)NC(=N4)N"
PJ3 SMILES CACTVS 3.385 "CN1CN([CH]2O[CH](CO[P](O)(=O)n3cnc(C[CH](N)C(O)=O)c3)[CH](O)[CH]2O)C4=C1C(=O)NC(=N4)N"
PJ3 SMILES_CANONICAL "OpenEye OEToolkits" 3.1.0.0 "CN1CN(C2=C1C(=O)NC(=N2)N)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(n4cc(nc4)C[C@@H](C(=O)O)N)O)O)O"
PJ3 SMILES "OpenEye OEToolkits" 3.1.0.0 "CN1CN(C2=C1C(=O)NC(=N2)N)C3C(C(C(O3)COP(=O)(n4cc(nc4)CC(C(=O)O)N)O)O)O"
#
_pdbx_chem_comp_identifier.comp_id PJ3
_pdbx_chem_comp_identifier.type "SYSTEMATIC NAME"
_pdbx_chem_comp_identifier.program "OpenEye OEToolkits"
_pdbx_chem_comp_identifier.program_version 3.1.0.0
_pdbx_chem_comp_identifier.identifier "(2~{S})-2-azanyl-3-[1-[[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-7-methyl-6-oxidanylidene-1,8-dihydropurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]imidazol-4-yl]propanoic 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
PJ3 "Create component" 2022-10-04 PDBE
PJ3 "Modify linking type" 2022-10-11 PDBE
PJ3 "Initial release" 2023-05-03 RCSB
PJ3 "Modify PCM" 2024-09-27 PDBE
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id PJ3
_pdbx_chem_comp_synonyms.name "7GMP capped histidine"
_pdbx_chem_comp_synonyms.provenance AUTHOR
_pdbx_chem_comp_synonyms.type ?
#