data_PMT
#
_chem_comp.id PMT
_chem_comp.name "PHOSPHORIC ACID MONO-[3-(3-{[5-(4-AMINO-2-OXO-2H-PYRIMIDIN-1-YL)-3,4- DIHYDROXY-TETRAHYDRO-FURAN-2- YLMETHOXY]-HYDROXY-PHOSPHORYLOXY}-3-OXO-PROPYLCARBAMOYL)-3-HYDROXY-2,2- DIMETHYL-PROPYL] ESTER"
_chem_comp.type "RNA LINKING"
_chem_comp.pdbx_type ATOMN
_chem_comp.formula "C18 H30 N4 O15 P2"
_chem_comp.mon_nstd_parent_comp_id C
_chem_comp.pdbx_synonyms "4'-PHOSPHOPANTOTHENOYL- CYTIDINE-5'-MONOPHOSPHATE"
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2004-08-06
_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 604.396
_chem_comp.one_letter_code C
_chem_comp.three_letter_code PMT
_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 N
_chem_comp.pdbx_model_coordinates_db_code 1U7Z
_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
PMT O11 "1OP'" O 0 1 N N N 42.372 51.833 139.039 -9.567 1.219 -0.830 O11 PMT 1
PMT "P'" "P'" P 0 1 N N N 41.277 52.535 138.091 -8.747 1.623 0.334 "P'" PMT 2
PMT O12 "3OP'" O 0 1 N N N 39.975 51.591 138.144 -9.620 2.563 1.306 O12 PMT 3
PMT O13 "2OP'" O 0 1 N N N 41.768 52.719 136.707 -7.453 2.434 -0.176 O13 PMT 4
PMT "O7'" "O7'" O 0 1 N N N 40.874 53.912 138.828 -8.275 0.310 1.139 "O7'" PMT 5
PMT "C7'" "C7'" C 0 1 N N N 40.374 53.864 140.167 -7.610 -0.534 0.197 "C7'" PMT 6
PMT "C6'" "C6'" C 0 1 N N N 39.198 54.826 140.350 -7.133 -1.806 0.902 "C6'" PMT 7
PMT "C9'" "C9'" C 0 1 N N N 38.136 54.530 139.288 -6.165 -1.435 2.026 "C9'" PMT 8
PMT "C8'" "C8'" C 0 1 N N N 39.700 56.259 140.160 -8.337 -2.546 1.489 "C8'" PMT 9
PMT "C5'" "C5'" C 0 1 N N R 38.624 54.622 141.758 -6.421 -2.711 -0.106 "C5'" PMT 10
PMT "O5'" "O5'" O 0 1 N N N 39.573 55.022 142.749 -7.358 -3.161 -1.087 "O5'" PMT 11
PMT "C4'" "C4'" C 0 1 N N N 37.341 55.426 141.972 -5.318 -1.939 -0.783 "C4'" PMT 12
PMT "O4'" "O4'" O 0 1 N N N 37.381 56.610 142.304 -5.453 -1.568 -1.930 "O4'" PMT 13
PMT "N3'" "N3'" N 0 1 N N N 36.226 54.728 141.778 -4.182 -1.659 -0.113 "N3'" PMT 14
PMT "C3'" "C3'" C 0 1 N N N 34.890 55.323 141.905 -3.099 -0.932 -0.779 "C3'" PMT 15
PMT "C2'" "C2'" C 0 1 N N N 34.300 55.555 140.511 -1.934 -0.747 0.195 "C2'" PMT 16
PMT "C1'" "C1'" C 0 1 N N N 33.007 56.366 140.615 -0.820 0.001 -0.490 "C1'" PMT 17
PMT "O1'" "O1'" O 0 1 N N N 31.996 56.035 139.997 -0.945 0.351 -1.640 "O1'" PMT 18
PMT OP2 O2P O 0 1 N N N 33.101 57.420 141.470 0.311 0.279 0.177 OP2 PMT 19
PMT P P P 0 1 N N S 31.787 58.343 141.594 1.501 1.079 -0.556 P PMT 20
PMT OP1 O1P O 0 1 N N N 32.393 59.814 141.829 1.879 0.372 -1.800 OP1 PMT 21
PMT OP3 O3P O 0 1 N Y N 30.842 58.274 140.458 1.006 2.568 -0.914 OP3 PMT 22
PMT O5B O5* O 0 1 N N N 31.146 58.063 143.038 2.776 1.159 0.424 O5B PMT 23
PMT C5B C5* C 0 1 N N N 30.016 57.215 143.194 3.831 1.771 -0.320 C5B PMT 24
PMT C4B C4* C 0 1 N N R 30.257 56.263 144.369 5.080 1.878 0.558 C4B PMT 25
PMT O4B O4* O 0 1 N N N 29.135 55.377 144.441 5.586 0.564 0.850 O4B PMT 26
PMT C3B C3* C 0 1 N N S 31.427 55.314 144.102 6.186 2.642 -0.194 C3B PMT 27
PMT "O3'" O3* O 0 1 N N N 31.671 54.505 145.255 6.562 3.822 0.518 "O3'" PMT 28
PMT C2B C2* C 0 1 N N R 30.813 54.452 142.999 7.368 1.638 -0.245 C2B PMT 29
PMT "O2'" O2* O 0 1 N N N 31.452 53.173 142.980 8.610 2.303 -0.004 "O2'" PMT 30
PMT C1B C1* C 0 1 N N R 29.388 54.294 143.532 7.024 0.672 0.917 C1B PMT 31
PMT N1 N1 N 0 1 N N N 28.342 54.299 142.487 7.649 -0.636 0.706 N1 PMT 32
PMT C6 C6 C 0 1 N N N 28.284 55.310 141.517 8.542 -1.115 1.618 C6 PMT 33
PMT C5 C5 C 0 1 N N N 27.231 55.354 140.610 9.114 -2.325 1.412 C5 PMT 34
PMT C4 C4 C 0 1 N N N 26.236 54.385 140.671 8.767 -3.057 0.258 C4 PMT 35
PMT N4 N4 N 0 1 N N N 25.219 54.412 139.816 9.333 -4.289 0.024 N4 PMT 36
PMT N3 N3 N 0 1 N N N 26.290 53.369 141.632 7.892 -2.551 -0.601 N3 PMT 37
PMT C2 C2 C 0 1 N N N 27.344 53.320 142.548 7.335 -1.361 -0.383 C2 PMT 38
PMT O2 O2 O 0 1 N N N 27.362 52.457 143.425 6.533 -0.917 -1.188 O2 PMT 39
PMT "HP'" "HP'" H 0 1 N N N 39.329 52.005 137.585 -9.882 3.335 0.787 "HP'" PMT 40
PMT H4 H4 H 0 1 N N N 41.122 53.133 136.148 -6.947 2.677 0.611 H4 PMT 41
PMT "H7'1" "1H7'" H 0 0 N N N 41.180 54.054 140.914 -6.752 -0.008 -0.221 "H7'1" PMT 42
PMT "H7'2" "2H7'" H 0 0 N N N 40.105 52.825 140.468 -8.300 -0.799 -0.604 "H7'2" PMT 43
PMT "H9'1" "1H9'" H 0 0 N N N 37.815 53.462 139.297 -5.726 -2.342 2.442 "H9'1" PMT 44
PMT "H9'2" "2H9'" H 0 0 N N N 37.279 55.231 139.421 -5.375 -0.798 1.629 "H9'2" PMT 45
PMT "H9'3" "3H9'" H 0 0 N N N 38.551 54.561 138.254 -6.704 -0.900 2.808 "H9'3" PMT 46
PMT "H8'1" "1H8'" H 0 0 N N N 40.220 56.403 139.184 -8.881 -1.880 2.159 "H8'1" PMT 47
PMT "H8'2" "2H8'" H 0 0 N N N 38.843 56.960 140.293 -8.997 -2.865 0.681 "H8'2" PMT 48
PMT "H8'3" "3H8'" H 0 0 N N N 40.558 56.502 140.830 -7.993 -3.418 2.043 "H8'3" PMT 49
PMT H1 H1 H 0 1 N N N 38.394 53.536 141.856 -5.997 -3.570 0.413 H1 PMT 50
PMT "H5'" "H5'" H 0 1 N N N 39.218 54.896 143.621 -7.709 -2.372 -1.522 "H5'" PMT 51
PMT "H3'" "H3'" H 0 1 N N N 36.393 53.751 141.536 -4.082 -1.940 0.810 "H3'" PMT 52
PMT "H3'1" "1H3'" H 0 0 N N N 34.900 56.254 142.519 -2.761 -1.498 -1.647 "H3'1" PMT 53
PMT "H3'2" "2H3'" H 0 0 N N N 34.217 54.713 142.551 -3.462 0.045 -1.101 "H3'2" PMT 54
PMT "H2'1" "1H2'" H 0 0 N N N 34.149 54.599 139.958 -2.273 -0.181 1.063 "H2'1" PMT 55
PMT "H2'2" "2H2'" H 0 0 N N N 35.036 56.030 139.821 -1.572 -1.723 0.517 "H2'2" PMT 56
PMT H3P H3P H 0 1 N N N 30.067 58.818 140.531 0.770 2.994 -0.078 H3P PMT 57
PMT "H5'1" 1H5* H 0 0 N N N 29.763 56.671 142.254 4.056 1.165 -1.198 "H5'1" PMT 58
PMT "H5''" 2H5* H 0 0 N N N 29.067 57.791 143.304 3.523 2.768 -0.635 "H5''" PMT 59
PMT "H4'" H4* H 0 1 N N N 30.436 56.890 145.274 4.837 2.396 1.486 "H4'" PMT 60
PMT H3B H3* H 0 1 N N N 32.394 55.809 143.850 5.857 2.894 -1.202 H3B PMT 61
PMT H3 H3 H 0 1 N N N 32.398 53.916 145.089 7.295 4.221 0.031 H3 PMT 62
PMT "H2'" H2* H 0 1 N N N 30.894 54.874 141.970 7.391 1.109 -1.198 "H2'" PMT 63
PMT H2 H2 H 0 1 N N N 31.070 52.637 142.295 8.766 2.886 -0.759 H2 PMT 64
PMT "H1'" H1* H 0 1 N N N 29.332 53.294 144.023 7.333 1.095 1.872 "H1'" PMT 65
PMT H6 H6 H 0 1 N N N 29.074 56.078 141.467 8.792 -0.535 2.494 H6 PMT 66
PMT H5 H5 H 0 1 N N N 27.185 56.151 139.849 9.824 -2.723 2.121 H5 PMT 67
PMT HN41 1HN4 H 0 0 N N N 25.597 54.424 138.869 9.972 -4.656 0.654 HN41 PMT 68
PMT HN42 2HN4 H 0 0 N N N 24.489 53.701 139.861 9.092 -4.790 -0.770 HN42 PMT 69
# #
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
PMT O11 "P'" DOUB N N 1
PMT "P'" O12 SING N N 2
PMT "P'" O13 SING N N 3
PMT "P'" "O7'" SING N N 4
PMT O12 "HP'" SING N N 5
PMT O13 H4 SING N N 6
PMT "O7'" "C7'" SING N N 7
PMT "C7'" "C6'" SING N N 8
PMT "C7'" "H7'1" SING N N 9
PMT "C7'" "H7'2" SING N N 10
PMT "C6'" "C9'" SING N N 11
PMT "C6'" "C8'" SING N N 12
PMT "C6'" "C5'" SING N N 13
PMT "C9'" "H9'1" SING N N 14
PMT "C9'" "H9'2" SING N N 15
PMT "C9'" "H9'3" SING N N 16
PMT "C8'" "H8'1" SING N N 17
PMT "C8'" "H8'2" SING N N 18
PMT "C8'" "H8'3" SING N N 19
PMT "C5'" "O5'" SING N N 20
PMT "C5'" "C4'" SING N N 21
PMT "C5'" H1 SING N N 22
PMT "O5'" "H5'" SING N N 23
PMT "C4'" "O4'" DOUB N N 24
PMT "C4'" "N3'" SING N N 25
PMT "N3'" "C3'" SING N N 26
PMT "N3'" "H3'" SING N N 27
PMT "C3'" "C2'" SING N N 28
PMT "C3'" "H3'1" SING N N 29
PMT "C3'" "H3'2" SING N N 30
PMT "C2'" "C1'" SING N N 31
PMT "C2'" "H2'1" SING N N 32
PMT "C2'" "H2'2" SING N N 33
PMT "C1'" "O1'" DOUB N N 34
PMT "C1'" OP2 SING N N 35
PMT OP2 P SING N N 36
PMT P OP1 DOUB N N 37
PMT P OP3 SING N N 38
PMT P O5B SING N N 39
PMT OP3 H3P SING N N 40
PMT O5B C5B SING N N 41
PMT C5B C4B SING N N 42
PMT C5B "H5'1" SING N N 43
PMT C5B "H5''" SING N N 44
PMT C4B O4B SING N N 45
PMT C4B C3B SING N N 46
PMT C4B "H4'" SING N N 47
PMT O4B C1B SING N N 48
PMT C3B "O3'" SING N N 49
PMT C3B C2B SING N N 50
PMT C3B H3B SING N N 51
PMT "O3'" H3 SING N N 52
PMT C2B "O2'" SING N N 53
PMT C2B C1B SING N N 54
PMT C2B "H2'" SING N N 55
PMT "O2'" H2 SING N N 56
PMT C1B N1 SING N N 57
PMT C1B "H1'" SING N N 58
PMT N1 C6 SING N N 59
PMT N1 C2 SING N N 60
PMT C6 C5 DOUB N N 61
PMT C6 H6 SING N N 62
PMT C5 C4 SING N N 63
PMT C5 H5 SING N N 64
PMT C4 N4 SING N N 65
PMT C4 N3 DOUB N N 66
PMT N4 HN41 SING N N 67
PMT N4 HN42 SING N N 68
PMT N3 C2 SING N N 69
PMT C2 O2 DOUB N N 70
# #
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
PMT SMILES ACDLabs 10.04 "O=P(O)(O)OCC(C)(C)C(O)C(=O)NCCC(=O)OP(=O)(O)OCC2OC(N1C(=O)N=C(N)C=C1)C(O)C2O"
PMT SMILES_CANONICAL CACTVS 3.341 "CC(C)(CO[P](O)(O)=O)[C@@H](O)C(=O)NCCC(=O)O[P@](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)N2C=CC(=NC2=O)N"
PMT SMILES CACTVS 3.341 "CC(C)(CO[P](O)(O)=O)[CH](O)C(=O)NCCC(=O)O[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O)N2C=CC(=NC2=O)N"
PMT SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "CC(C)(COP(=O)(O)O)[C@H](C(=O)NCCC(=O)O[P@@](=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)N2C=CC(=NC2=O)N)O)O)O"
PMT SMILES "OpenEye OEToolkits" 1.5.0 "CC(C)(COP(=O)(O)O)C(C(=O)NCCC(=O)OP(=O)(O)OCC1C(C(C(O1)N2C=CC(=NC2=O)N)O)O)O"
PMT InChI InChI 1.03 "InChI=1S/C18H30N4O15P2/c1-18(2,8-35-38(29,30)31)14(26)15(27)20-5-3-11(23)37-39(32,33)34-7-9-12(24)13(25)16(36-9)22-6-4-10(19)21-17(22)28/h4,6,9,12-14,16,24-26H,3,5,7-8H2,1-2H3,(H,20,27)(H,32,33)(H2,19,21,28)(H2,29,30,31)/t9-,12-,13-,14+,16-/m1/s1"
PMT InChIKey InChI 1.03 JURRMAHLXBVXRF-FIEZRUJPSA-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
PMT "SYSTEMATIC NAME" ACDLabs 10.04 "5'-O-{(S)-hydroxy[(3-{[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]amino}propanoyl)oxy]phosphoryl}cytidine"
PMT "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[[(2R,3S,4R,5R)-5-(4-amino-2-oxo-pyrimidin-1-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl] 3-[[(2R)-2-hydroxy-3,3-dimethyl-4-phosphonooxy-butanoyl]amino]propanoate"
# #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
PMT "Create component" 2004-08-06 RCSB
PMT "Modify descriptor" 2011-06-04 RCSB
PMT "Modify synonyms" 2021-03-01 PDBE
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id PMT
_pdbx_chem_comp_synonyms.name "4'-PHOSPHOPANTOTHENOYL- CYTIDINE-5'-MONOPHOSPHATE"
_pdbx_chem_comp_synonyms.provenance ?
_pdbx_chem_comp_synonyms.type ?
##