data_PUM
#
_chem_comp.id PUM
_chem_comp.name "(1S)-1,4-anhydro-5-[(N-carbamimidoylglycyl-N~2~-hydroxy-L-glutaminyl)amino]-5-deoxy-1-(2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)-D-ribitol"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C17 H26 N8 O9"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms pseudouridimycin
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2017-02-13
_chem_comp.pdbx_modified_date 2021-03-01
_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 486.437
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code PUM
_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 5X21
_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
PUM OAH O1 O 0 1 N N N -3.216 0.268 78.351 3.506 -0.151 2.014 OAH PUM 1
PUM CBB C1 C 0 1 N N N -2.639 -0.600 78.988 4.327 0.590 1.504 CBB PUM 2
PUM NAT N1 N 0 1 N N N -1.958 -1.634 78.302 4.894 1.577 2.227 NAT PUM 3
PUM CBA C2 C 0 1 N N N -1.284 -2.650 79.038 5.801 2.395 1.662 CBA PUM 4
PUM OAG O2 O 0 1 N N N -0.694 -3.542 78.448 6.304 3.282 2.326 OAG PUM 5
PUM NAS N2 N 0 1 N N N -1.292 -2.623 80.475 6.160 2.247 0.374 NAS PUM 6
PUM CAL C3 C 0 1 N N N -1.989 -1.557 81.175 5.608 1.257 -0.394 CAL PUM 7
PUM CAZ C4 C 0 1 N N N -2.651 -0.570 80.469 4.699 0.419 0.149 CAZ PUM 8
PUM CBG C5 C 0 1 N N S -3.369 0.527 81.225 4.085 -0.681 -0.678 CBG PUM 9
PUM OAU O3 O 0 1 N N N -2.915 0.567 82.566 2.644 -0.606 -0.626 OAU PUM 10
PUM CBD C6 C 0 1 N N R -4.838 0.356 81.175 4.431 -2.062 -0.078 CBD PUM 11
PUM OAJ O4 O 0 1 N N N -5.467 1.582 81.015 5.533 -2.649 -0.773 OAJ PUM 12
PUM CBC C7 C 0 1 N N S -5.128 -0.242 82.467 3.148 -2.897 -0.295 CBC PUM 13
PUM OAI O5 O 0 1 N N N -6.389 0.042 82.931 3.419 -4.024 -1.130 OAI PUM 14
PUM CBE C8 C 0 1 N N R -4.095 0.397 83.321 2.180 -1.921 -1.000 CBE PUM 15
PUM CAP C9 C 0 1 N N N -3.778 -0.403 84.584 0.749 -2.141 -0.507 CAP PUM 16
PUM NAR N3 N 0 1 N N N -2.915 -1.535 84.230 -0.158 -1.237 -1.219 NAR PUM 17
PUM C C10 C 0 1 N N N -3.466 -2.729 83.978 -1.478 -1.255 -0.947 C PUM 18
PUM O O6 O 0 1 N N N -4.690 -2.868 84.042 -1.915 -2.018 -0.112 O PUM 19
PUM CA C11 C 0 1 N N S -2.579 -3.905 83.606 -2.410 -0.325 -1.679 CA PUM 20
PUM CB C12 C 0 1 N N N -3.410 -5.155 83.413 -1.997 1.125 -1.415 CB PUM 21
PUM CG C13 C 0 1 N N N -3.393 -6.032 84.630 -2.864 2.063 -2.256 CG PUM 22
PUM CD C14 C 0 1 N N N -2.521 -7.203 84.333 -2.457 3.491 -1.996 CD PUM 23
PUM OE1 O7 O 0 1 N N N -2.875 -8.024 83.488 -1.562 3.733 -1.215 OE1 PUM 24
PUM NE2 N4 N 0 1 N N N -1.367 -7.348 84.974 -3.088 4.498 -2.632 NE2 PUM 25
PUM N N5 N 0 1 N N N -1.539 -4.079 84.608 -3.781 -0.536 -1.207 N PUM 26
PUM OAK O8 O 0 1 N N N -1.875 -3.676 85.805 -4.788 -0.942 -2.115 OAK PUM 27
PUM CAX C15 C 0 1 N N N -0.288 -4.554 84.406 -4.083 -0.343 0.092 CAX PUM 28
PUM OAE O9 O 0 1 N N N 0.483 -4.660 85.345 -3.220 0.006 0.870 OAE PUM 29
PUM CAN C16 C 0 1 N N N 0.154 -4.875 82.996 -5.493 -0.559 0.578 CAN PUM 30
PUM NAQ N6 N 0 1 N N N 1.611 -4.900 83.039 -5.561 -0.287 2.016 NAQ PUM 31
PUM CAV C17 C 0 1 N N N 2.438 -4.669 82.005 -6.755 -0.419 2.685 CAV PUM 32
PUM NAB N7 N 0 1 N N N 3.778 -4.708 82.119 -7.885 -0.807 2.004 NAB PUM 33
PUM NAA N8 N 0 1 N N N 1.905 -4.388 80.805 -6.816 -0.176 3.964 NAA PUM 34
PUM H1 H1 H 0 1 N N N -1.950 -1.651 77.302 4.647 1.698 3.157 H1 PUM 35
PUM H2 H2 H 0 1 N N N -1.990 -1.536 82.255 5.901 1.145 -1.427 H2 PUM 36
PUM H4 H4 H 0 1 N N N -3.122 1.482 80.738 4.431 -0.617 -1.710 H4 PUM 37
PUM H5 H5 H 0 1 N N N -5.106 -0.338 80.365 4.652 -1.972 0.985 H5 PUM 38
PUM H6 H6 H 0 1 N N N -6.408 1.454 80.985 5.792 -3.518 -0.437 H6 PUM 39
PUM H7 H7 H 0 1 N N N -4.953 -1.327 82.427 2.737 -3.221 0.662 H7 PUM 40
PUM H8 H8 H 0 1 N N N -6.518 -0.375 83.775 4.068 -4.640 -0.761 H8 PUM 41
PUM H9 H9 H 0 1 N N N -4.469 1.383 83.635 2.234 -2.049 -2.081 H9 PUM 42
PUM H10 H10 H 0 1 N N N -3.260 0.242 85.309 0.454 -3.174 -0.695 H10 PUM 43
PUM H11 H11 H 0 1 N N N -4.713 -0.777 85.028 0.698 -1.938 0.563 H11 PUM 44
PUM H12 H12 H 0 1 N N N -1.924 -1.416 84.177 0.192 -0.627 -1.886 H12 PUM 45
PUM H13 H13 H 0 1 N N N -2.100 -3.670 82.644 -2.359 -0.528 -2.749 H13 PUM 46
PUM H14 H14 H 0 1 N N N -4.449 -4.862 83.200 -2.133 1.354 -0.358 H14 PUM 47
PUM H15 H15 H 0 1 N N N -3.007 -5.722 82.561 -0.950 1.258 -1.685 H15 PUM 48
PUM H16 H16 H 0 1 N N N -2.991 -5.474 85.488 -2.729 1.834 -3.313 H16 PUM 49
PUM H17 H17 H 0 1 N N N -4.413 -6.373 84.860 -3.912 1.929 -1.987 H17 PUM 50
PUM H18 H18 H 0 1 N N N -0.777 -8.130 84.771 -3.804 4.304 -3.257 H18 PUM 51
PUM H19 H19 H 0 1 N N N -1.088 -6.675 85.659 -2.826 5.417 -2.464 H19 PUM 52
PUM H20 H20 H 0 1 N N N -1.147 -3.809 86.400 -5.660 -1.056 -1.711 H20 PUM 53
PUM H21 H21 H 0 1 N N N -0.196 -4.101 82.298 -6.168 0.113 0.048 H21 PUM 54
PUM H22 H22 H 0 1 N N N -0.238 -5.854 82.684 -5.787 -1.592 0.390 H22 PUM 55
PUM H23 H23 H 0 1 N N N 2.035 -5.109 83.920 -4.764 -0.013 2.496 H23 PUM 56
PUM H24 H24 H 0 1 N N N 4.199 -4.916 83.002 -7.840 -0.988 1.052 H24 PUM 57
PUM H25 H25 H 0 1 N N N 4.353 -4.529 81.321 -8.727 -0.900 2.476 H25 PUM 58
PUM H26 H26 H 0 1 N N N 0.905 -4.385 80.830 -6.019 0.098 4.444 H26 PUM 59
PUM H3 H3 H 0 1 N N N -0.819 -3.336 80.992 6.815 2.846 -0.015 H3 PUM 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
PUM NAT CBB SING N N 1
PUM NAT CBA SING N N 2
PUM OAH CBB DOUB N N 3
PUM OAG CBA DOUB N N 4
PUM CBB CAZ SING N N 5
PUM CBA NAS SING N N 6
PUM CAZ CAL DOUB N N 7
PUM CAZ CBG SING N N 8
PUM NAS CAL SING N N 9
PUM NAA CAV DOUB N N 10
PUM OAJ CBD SING N N 11
PUM CBD CBG SING N N 12
PUM CBD CBC SING N N 13
PUM CBG OAU SING N N 14
PUM CAV NAB SING N N 15
PUM CAV NAQ SING N N 16
PUM CBC OAI SING N N 17
PUM CBC CBE SING N N 18
PUM OAU CBE SING N N 19
PUM CAN NAQ SING N N 20
PUM CAN CAX SING N N 21
PUM CBE CAP SING N N 22
PUM CB CA SING N N 23
PUM CB CG SING N N 24
PUM OE1 CD DOUB N N 25
PUM CA C SING N N 26
PUM CA N SING N N 27
PUM C O DOUB N N 28
PUM C NAR SING N N 29
PUM NAR CAP SING N N 30
PUM CD CG SING N N 31
PUM CD NE2 SING N N 32
PUM CAX N SING N N 33
PUM CAX OAE DOUB N N 34
PUM N OAK SING N N 35
PUM NAT H1 SING N N 36
PUM CAL H2 SING N N 37
PUM CBG H4 SING N N 38
PUM CBD H5 SING N N 39
PUM OAJ H6 SING N N 40
PUM CBC H7 SING N N 41
PUM OAI H8 SING N N 42
PUM CBE H9 SING N N 43
PUM CAP H10 SING N N 44
PUM CAP H11 SING N N 45
PUM NAR H12 SING N N 46
PUM CA H13 SING N N 47
PUM CB H14 SING N N 48
PUM CB H15 SING N N 49
PUM CG H16 SING N N 50
PUM CG H17 SING N N 51
PUM NE2 H18 SING N N 52
PUM NE2 H19 SING N N 53
PUM OAK H20 SING N N 54
PUM CAN H21 SING N N 55
PUM CAN H22 SING N N 56
PUM NAQ H23 SING N N 57
PUM NAB H24 SING N N 58
PUM NAB H25 SING N N 59
PUM NAA H26 SING N N 60
PUM NAS H3 SING N N 61
# #
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
PUM SMILES ACDLabs 12.01 "O=C1C(=CNC(N1)=O)C2OC(C(C2O)O)CNC(=O)C(N(O)C(=O)CN/C(N)=N)CCC(N)=O"
PUM InChI InChI 1.03 "InChI=1S/C17H26N8O9/c18-9(26)2-1-7(25(33)10(27)5-22-16(19)20)15(31)21-4-8-11(28)12(29)13(34-8)6-3-23-17(32)24-14(6)30/h3,7-8,11-13,28-29,33H,1-2,4-5H2,(H2,18,26)(H,21,31)(H4,19,20,22)(H2,23,24,30,32)/t7-,8+,11+,12+,13-/m0/s1"
PUM InChIKey InChI 1.03 XDEYHXABZOKKDZ-YFKLLHAASA-N
PUM SMILES_CANONICAL CACTVS 3.385 "NC(=N)NCC(=O)N(O)[C@@H](CCC(N)=O)C(=O)NC[C@H]1O[C@H]([C@H](O)[C@@H]1O)C2=CNC(=O)NC2=O"
PUM SMILES CACTVS 3.385 "NC(=N)NCC(=O)N(O)[CH](CCC(N)=O)C(=O)NC[CH]1O[CH]([CH](O)[CH]1O)C2=CNC(=O)NC2=O"
PUM SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "[H]/N=C(/N)\NCC(=O)N([C@@H](CCC(=O)N)C(=O)NC[C@@H]1[C@H]([C@H]([C@@H](O1)C2=CNC(=O)NC2=O)O)O)O"
PUM SMILES "OpenEye OEToolkits" 2.0.6 "C1=C(C(=O)NC(=O)N1)C2C(C(C(O2)CNC(=O)C(CCC(=O)N)N(C(=O)CNC(=N)N)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
PUM "SYSTEMATIC NAME" ACDLabs 12.01 "(1S)-1,4-anhydro-5-[(N-carbamimidoylglycyl-N~2~-hydroxy-L-glutaminyl)amino]-5-deoxy-1-(2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)-D-ribitol"
PUM "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "(2~{S})-~{N}-[[(2~{R},3~{S},4~{R},5~{S})-5-[2,4-bis(oxidanylidene)-1~{H}-pyrimidin-5-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl]-2-[2-carbamimidamidoethanoyl(oxidanyl)amino]pentanediamide"
# #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
PUM "Create component" 2017-02-13 RCSB
PUM "Other modification" 2017-02-24 RCSB
PUM "Initial release" 2017-07-05 RCSB
PUM "Modify synonyms" 2021-03-01 PDBE
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id PUM
_pdbx_chem_comp_synonyms.name pseudouridimycin
_pdbx_chem_comp_synonyms.provenance ?
_pdbx_chem_comp_synonyms.type ?
##