data_MJ3
#
_chem_comp.id MJ3
_chem_comp.name "(2~{S},3~{S},4~{R},5~{S},6~{R})-4,5-diacetamido-6-[[[(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3-oxidanyl-oxane-2-carboxylic acid"
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C19 H28 N4 O18 P2"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms "UDP-2,3-diacetamido-2,3-dideoxy-alpha-D-mannuronic acid"
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2023-05-25
_chem_comp.pdbx_modified_date 2023-09-08
_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 662.389
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code MJ3
_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 8SY0
_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
MJ3 N1 N1 N 0 1 N N N -17.155 74.290 0.791 -6.331 -1.242 -0.140 N1 MJ3 1
MJ3 C2 C1 C 0 1 N N N -18.547 73.979 0.839 -6.631 -2.387 -0.781 C2 MJ3 2
MJ3 O2 O1 O 0 1 N N N -19.077 73.272 1.747 -6.468 -2.460 -1.984 O2 MJ3 3
MJ3 N3 N2 N 0 1 N N N -19.288 74.423 -0.173 -7.107 -3.451 -0.109 N3 MJ3 4
MJ3 C4 C2 C 0 1 N N N -18.749 75.161 -1.166 -7.293 -3.386 1.224 C4 MJ3 5
MJ3 O4 O2 O 0 1 N N N -19.508 75.550 -2.051 -7.724 -4.349 1.833 O4 MJ3 6
MJ3 C5 C3 C 0 1 N N N -17.473 75.482 -1.205 -6.982 -2.188 1.911 C5 MJ3 7
MJ3 C6 C4 C 0 1 N N N -16.686 75.066 -0.234 -6.500 -1.137 1.214 C6 MJ3 8
MJ3 PA P1 P 0 1 N N N -13.459 78.355 1.637 -0.868 2.587 0.739 PA MJ3 9
MJ3 PB P2 P 0 1 N N N -10.752 78.555 2.350 2.045 2.213 0.343 PB MJ3 10
MJ3 "O'P" O3 O 0 1 N N N -10.920 79.014 8.406 4.115 -2.538 3.477 "O'P" MJ3 11
MJ3 "O'Q" O4 O 0 1 N N N -10.300 81.215 8.217 5.315 -0.689 3.621 "O'Q" MJ3 12
MJ3 "C1'" C5 C 0 1 N N R -9.814 80.200 4.087 4.330 0.864 0.029 "C1'" MJ3 13
MJ3 O1A O5 O 0 1 N N N -13.004 77.726 0.356 -0.780 4.048 0.520 O1A MJ3 14
MJ3 O1B O6 O 0 1 N N N -10.003 79.267 1.262 2.351 2.565 1.748 O1B MJ3 15
MJ3 C1C C6 C 0 1 N N R -16.251 73.883 1.884 -5.814 -0.100 -0.898 C1C MJ3 16
MJ3 "C2'" C7 C 0 1 N N S -8.275 80.332 4.034 4.892 -0.054 -1.060 "C2'" MJ3 17
MJ3 "N2'" N3 N 0 1 N N N -8.022 81.737 4.192 6.355 -0.072 -0.977 "N2'" MJ3 18
MJ3 O2A O7 O 0 1 N N N -14.574 79.301 1.623 -1.040 2.289 2.312 O2A MJ3 19
MJ3 O2B O8 O 0 1 N N N -10.748 77.046 2.250 2.421 3.452 -0.614 O2B MJ3 20
MJ3 C2C C8 C 0 1 N N R -15.043 73.060 1.534 -6.779 1.101 -0.786 C2C MJ3 21
MJ3 O2C O9 O 0 1 N N N -15.329 71.675 1.436 -7.618 1.178 -1.940 O2C MJ3 22
MJ3 "C3'" C9 C 0 1 N N R -7.710 79.423 5.128 4.350 -1.471 -0.852 "C3'" MJ3 23
MJ3 "N3'" N4 N 0 1 N N N -6.271 79.444 5.241 4.942 -2.372 -1.844 "N3'" MJ3 24
MJ3 O3A O10 O 0 1 N N N -12.258 79.081 2.360 0.476 1.882 0.202 O3A MJ3 25
MJ3 O3B O11 O 0 1 N N N -10.117 78.880 3.792 2.907 0.923 -0.086 O3B MJ3 26
MJ3 C3C C10 C 0 1 N N S -14.114 73.406 2.656 -5.844 2.329 -0.714 C3C MJ3 27
MJ3 O3C O12 O 0 1 N N N -14.380 72.510 3.746 -6.077 3.201 -1.822 O3C MJ3 28
MJ3 "C4'" C11 C 0 1 N N S -8.346 79.603 6.497 4.720 -1.946 0.556 "C4'" MJ3 29
MJ3 "O4'" O13 O 0 1 N N N -7.982 78.480 7.338 4.157 -3.239 0.787 "O4'" MJ3 30
MJ3 C4C C12 C 0 1 N N R -14.469 74.872 3.049 -4.424 1.724 -0.791 C4C MJ3 31
MJ3 O4C O14 O 0 1 N N N -15.709 75.113 2.396 -4.575 0.367 -0.321 O4C MJ3 32
MJ3 "C5'" C13 C 0 1 N N S -9.875 79.633 6.408 4.164 -0.956 1.582 "C5'" MJ3 33
MJ3 "O5'" O15 O 0 1 N N N -10.313 80.508 5.403 4.683 0.348 1.314 "O5'" MJ3 34
MJ3 C5C C14 C 0 1 N N N -13.465 75.842 2.506 -3.465 2.500 0.114 C5C MJ3 35
MJ3 O5C O16 O 0 1 N N N -13.896 77.196 2.638 -2.137 2.000 -0.060 O5C MJ3 36
MJ3 "C6'" C15 C 0 1 N N N -10.421 80.005 7.758 4.574 -1.384 2.968 "C6'" MJ3 37
MJ3 "C7'" C16 C 0 1 N N N -8.268 82.688 3.227 7.077 0.885 -1.593 "C7'" MJ3 38
MJ3 "O7'" O17 O 0 1 N N N -8.546 82.443 2.072 6.515 1.762 -2.216 "O7'" MJ3 39
MJ3 "C8'" C17 C 0 1 N N N -8.140 84.128 3.638 8.581 0.867 -1.508 "C8'" MJ3 40
MJ3 O43 O18 O 0 1 N N N -5.921 77.558 4.063 3.220 -3.765 -1.706 O43 MJ3 41
MJ3 C41 C18 C 0 1 N N N -5.486 78.500 4.697 4.294 -3.498 -2.204 C41 MJ3 42
MJ3 C42 C19 C 0 1 N N N -4.021 78.670 4.830 4.903 -4.425 -3.224 C42 MJ3 43
MJ3 H1 H1 H 0 1 N N N -20.264 74.205 -0.198 -7.319 -4.269 -0.587 H1 MJ3 44
MJ3 H2 H2 H 0 1 N N N -17.079 76.075 -2.017 -7.124 -2.116 2.979 H2 MJ3 45
MJ3 H3 H3 H 0 1 N N N -15.643 75.345 -0.247 -6.257 -0.215 1.720 H3 MJ3 46
MJ3 H4 H4 H 0 1 N N N -11.186 79.303 9.271 4.405 -2.771 4.369 H4 MJ3 47
MJ3 H5 H5 H 0 1 N N N -10.254 80.882 3.344 4.746 1.865 -0.089 H5 MJ3 48
MJ3 H6 H6 H 0 1 N N N -16.827 73.368 2.667 -5.666 -0.374 -1.943 H6 MJ3 49
MJ3 H7 H7 H 0 1 N N N -7.919 79.983 3.053 4.588 0.314 -2.040 H7 MJ3 50
MJ3 H8 H8 H 0 1 N N N -7.641 82.046 5.063 6.804 -0.773 -0.479 H8 MJ3 51
MJ3 H9 H9 H 0 1 N N N -14.892 79.403 0.734 -1.104 1.349 2.529 H9 MJ3 52
MJ3 H10 H10 H 0 1 N N N -10.252 76.780 1.484 2.246 3.292 -1.551 H10 MJ3 53
MJ3 H11 H11 H 0 1 N N N -14.619 73.429 0.588 -7.380 1.025 0.120 H11 MJ3 54
MJ3 H12 H12 H 0 1 N N N -14.535 71.202 1.214 -8.244 1.915 -1.923 H12 MJ3 55
MJ3 H13 H13 H 0 1 N N N -7.976 78.402 4.818 3.266 -1.467 -0.965 H13 MJ3 56
MJ3 H14 H14 H 0 1 N N N -5.841 80.193 5.745 5.801 -2.159 -2.242 H14 MJ3 57
MJ3 H15 H15 H 0 1 N N N -13.066 73.349 2.328 -5.982 2.860 0.228 H15 MJ3 58
MJ3 H16 H16 H 0 1 N N N -13.800 72.712 4.471 -6.973 3.562 -1.856 H16 MJ3 59
MJ3 H17 H17 H 0 1 N N N -7.991 80.544 6.942 5.805 -1.999 0.650 H17 MJ3 60
MJ3 H18 H18 H 0 1 N N N -8.376 78.585 8.196 4.352 -3.602 1.662 H18 MJ3 61
MJ3 H19 H19 H 0 1 N N N -14.552 74.961 4.142 -4.064 1.731 -1.820 H19 MJ3 62
MJ3 H20 H20 H 0 1 N N N -10.214 78.613 6.175 3.076 -0.935 1.515 H20 MJ3 63
MJ3 H21 H21 H 0 1 N N N -13.303 75.624 1.440 -3.493 3.557 -0.150 H21 MJ3 64
MJ3 H22 H22 H 0 1 N N N -12.519 75.716 3.054 -3.767 2.376 1.154 H22 MJ3 65
MJ3 H23 H23 H 0 1 N N N -8.331 84.776 2.770 8.901 0.012 -0.912 H23 MJ3 66
MJ3 H24 H24 H 0 1 N N N -8.871 84.350 4.429 9.001 0.788 -2.511 H24 MJ3 67
MJ3 H25 H25 H 0 1 N N N -7.124 84.312 4.016 8.930 1.787 -1.040 H25 MJ3 68
MJ3 H26 H26 H 0 1 N N N -3.507 77.858 4.295 4.573 -4.134 -4.222 H26 MJ3 69
MJ3 H27 H27 H 0 1 N N N -3.724 79.638 4.400 5.990 -4.363 -3.168 H27 MJ3 70
MJ3 H28 H28 H 0 1 N N N -3.744 78.641 5.894 4.586 -5.448 -3.021 H28 MJ3 71
#
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
MJ3 O4 C4 DOUB N N 1
MJ3 C5 C4 SING N N 2
MJ3 C5 C6 DOUB N N 3
MJ3 C4 N3 SING N N 4
MJ3 C6 N1 SING N N 5
MJ3 N3 C2 SING N N 6
MJ3 O1A PA DOUB N N 7
MJ3 N1 C2 SING N N 8
MJ3 N1 C1C SING N N 9
MJ3 C2 O2 DOUB N N 10
MJ3 O1B PB DOUB N N 11
MJ3 O2C C2C SING N N 12
MJ3 C2C C1C SING N N 13
MJ3 C2C C3C SING N N 14
MJ3 O2A PA SING N N 15
MJ3 PA O3A SING N N 16
MJ3 PA O5C SING N N 17
MJ3 C1C O4C SING N N 18
MJ3 "O7'" "C7'" DOUB N N 19
MJ3 O2B PB SING N N 20
MJ3 PB O3A SING N N 21
MJ3 PB O3B SING N N 22
MJ3 O4C C4C SING N N 23
MJ3 C5C O5C SING N N 24
MJ3 C5C C4C SING N N 25
MJ3 C3C C4C SING N N 26
MJ3 C3C O3C SING N N 27
MJ3 "C7'" "C8'" SING N N 28
MJ3 "C7'" "N2'" SING N N 29
MJ3 O3B "C1'" SING N N 30
MJ3 "C2'" "C1'" SING N N 31
MJ3 "C2'" "N2'" SING N N 32
MJ3 "C2'" "C3'" SING N N 33
MJ3 O43 C41 DOUB N N 34
MJ3 "C1'" "O5'" SING N N 35
MJ3 C41 C42 SING N N 36
MJ3 C41 "N3'" SING N N 37
MJ3 "C3'" "N3'" SING N N 38
MJ3 "C3'" "C4'" SING N N 39
MJ3 "O5'" "C5'" SING N N 40
MJ3 "C5'" "C4'" SING N N 41
MJ3 "C5'" "C6'" SING N N 42
MJ3 "C4'" "O4'" SING N N 43
MJ3 "C6'" "O'Q" DOUB N N 44
MJ3 "C6'" "O'P" SING N N 45
MJ3 N3 H1 SING N N 46
MJ3 C5 H2 SING N N 47
MJ3 C6 H3 SING N N 48
MJ3 "O'P" H4 SING N N 49
MJ3 "C1'" H5 SING N N 50
MJ3 C1C H6 SING N N 51
MJ3 "C2'" H7 SING N N 52
MJ3 "N2'" H8 SING N N 53
MJ3 O2A H9 SING N N 54
MJ3 O2B H10 SING N N 55
MJ3 C2C H11 SING N N 56
MJ3 O2C H12 SING N N 57
MJ3 "C3'" H13 SING N N 58
MJ3 "N3'" H14 SING N N 59
MJ3 C3C H15 SING N N 60
MJ3 O3C H16 SING N N 61
MJ3 "C4'" H17 SING N N 62
MJ3 "O4'" H18 SING N N 63
MJ3 C4C H19 SING N N 64
MJ3 "C5'" H20 SING N N 65
MJ3 C5C H21 SING N N 66
MJ3 C5C H22 SING N N 67
MJ3 "C8'" H23 SING N N 68
MJ3 "C8'" H24 SING N N 69
MJ3 "C8'" H25 SING N N 70
MJ3 C42 H26 SING N N 71
MJ3 C42 H27 SING N N 72
MJ3 C42 H28 SING N N 73
#
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
MJ3 SMILES ACDLabs 12.01 "O=C1C=CN(C(=O)N1)C1OC(COP(=O)(O)OP(=O)(O)OC2OC(C(O)C(NC(C)=O)C2NC(C)=O)C(=O)O)C(O)C1O"
MJ3 InChI InChI 1.06 "InChI=1S/C19H28N4O18P2/c1-6(24)20-10-11(21-7(2)25)18(39-15(13(10)28)17(30)31)40-43(35,36)41-42(33,34)37-5-8-12(27)14(29)16(38-8)23-4-3-9(26)22-19(23)32/h3-4,8,10-16,18,27-29H,5H2,1-2H3,(H,20,24)(H,21,25)(H,30,31)(H,33,34)(H,35,36)(H,22,26,32)/t8-,10-,11+,12-,13+,14-,15+,16-,18-/m1/s1"
MJ3 InChIKey InChI 1.06 GZLIMKLKXDFTJR-ZVWGYSLJSA-N
MJ3 SMILES_CANONICAL CACTVS 3.385 "CC(=O)N[C@H]1[C@H](O)[C@H](O[C@H](O[P](O)(=O)O[P](O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)N3C=CC(=O)NC3=O)[C@H]1NC(C)=O)C(O)=O"
MJ3 SMILES CACTVS 3.385 "CC(=O)N[CH]1[CH](O)[CH](O[CH](O[P](O)(=O)O[P](O)(=O)OC[CH]2O[CH]([CH](O)[CH]2O)N3C=CC(=O)NC3=O)[CH]1NC(C)=O)C(O)=O"
MJ3 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CC(=O)N[C@@H]1[C@@H]([C@H](O[C@@H]([C@H]1O)C(=O)O)OP(=O)(O)OP(=O)(O)OC[C@@H]2[C@H]([C@H]([C@@H](O2)N3C=CC(=O)NC3=O)O)O)NC(=O)C"
MJ3 SMILES "OpenEye OEToolkits" 2.0.7 "CC(=O)NC1C(C(OC(C1O)C(=O)O)OP(=O)(O)OP(=O)(O)OCC2C(C(C(O2)N3C=CC(=O)NC3=O)O)O)NC(=O)C"
#
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
MJ3 "SYSTEMATIC NAME" ACDLabs 12.01 "(2S,3S,4R,5S,6R)-4,5-diacetamido-6-{[(R)-{[(R)-{[(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}-3-hydroxyoxane-2-carboxylic acid (non-preferred name)"
MJ3 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "(2~{S},3~{S},4~{R},5~{S},6~{R})-4,5-diacetamido-6-[[[(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3-oxidanyl-oxane-2-carboxylic 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
MJ3 "Create component" 2023-05-25 RCSB
MJ3 "Initial release" 2023-09-13 RCSB
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id MJ3
_pdbx_chem_comp_synonyms.name "UDP-2,3-diacetamido-2,3-dideoxy-alpha-D-mannuronic acid"
_pdbx_chem_comp_synonyms.provenance PUBCHEM
_pdbx_chem_comp_synonyms.type ?
#