data_MYD
#
_chem_comp.id MYD
_chem_comp.name
;{[5-(6-AMINO-PURIN-7-YL)-3,4-DIHYDROXY-TETRAHYDRO-FURAN-2-YLMETHOXY]-HYDROXY-PHOSPHORYLMETHYL}-PHOSPHONIC ACID
MONO-[2-(4-HYDROXY-6-METHOXY-7-METHYL-3-OXO-1,3-DIHYDRO-ISOBENZOFURAN-5-YL)-ETHYL] ESTER
;
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C23 H29 N5 O13 P2"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms "C2-MYCOPHENOLIC ADENINE DINUCLEOTIDE"
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2002-12-20
_chem_comp.pdbx_modified_date 2020-06-17
_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 645.450
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code MYD
_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 1NF7
_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
MYD C53 C53 C 0 1 N N N 98.539 91.170 51.536 1.743 2.826 -7.614 C53 MYD 1
MYD O51 O51 O 0 1 N N N 98.056 89.810 51.693 1.835 1.480 -7.145 O51 MYD 2
MYD C46 C46 C 0 1 Y N N 96.834 89.346 51.130 0.693 0.853 -7.525 C46 MYD 3
MYD C47 C47 C 0 1 Y N N 96.882 88.293 50.188 0.633 0.207 -8.757 C47 MYD 4
MYD C52 C52 C 0 1 N N N 98.239 87.678 49.813 1.836 0.206 -9.665 C52 MYD 5
MYD C48 C48 C 0 1 Y N N 95.686 87.800 49.598 -0.509 -0.423 -9.145 C48 MYD 6
MYD C49 C49 C 0 1 N N N 95.469 86.672 48.557 -0.895 -1.196 -10.381 C49 MYD 7
MYD O50 O50 O 0 1 N N N 94.026 86.711 48.404 -2.272 -1.620 -10.185 O50 MYD 8
MYD C42 C42 C 0 1 N N N 93.455 87.713 49.232 -2.700 -1.178 -8.990 C42 MYD 9
MYD O43 O43 O 0 1 N N N 92.230 87.944 49.281 -3.811 -1.371 -8.536 O43 MYD 10
MYD C41 C41 C 0 1 Y N N 94.450 88.387 49.961 -1.635 -0.429 -8.312 C41 MYD 11
MYD C40 C40 C 0 1 Y N N 94.410 89.440 50.911 -1.577 0.220 -7.069 C40 MYD 12
MYD O31 O31 O 0 1 N N N 93.201 89.985 51.239 -2.659 0.224 -6.250 O31 MYD 13
MYD C39 C39 C 0 1 Y N N 95.606 89.942 51.513 -0.408 0.854 -6.682 C39 MYD 14
MYD C38 C38 C 0 1 N N N 95.561 91.102 52.533 -0.337 1.554 -5.350 C38 MYD 15
MYD C37 C37 C 0 1 N N N 95.394 92.441 51.782 0.143 0.571 -4.281 C37 MYD 16
MYD O36 O36 O 0 1 N N N 96.466 92.755 50.857 0.211 1.235 -3.018 O36 MYD 17
MYD P35 P35 P 0 1 N N S 96.225 94.080 49.958 0.721 0.147 -1.947 P35 MYD 18
MYD O45 O45 O 0 1 N N N 95.972 95.098 51.224 2.171 -0.397 -2.384 O45 MYD 19
MYD O30 O30 O 0 1 N N N 94.881 93.905 49.342 -0.235 -0.981 -1.896 O30 MYD 20
MYD C34 C34 C 0 1 N N N 97.119 94.462 49.045 0.834 0.922 -0.300 C34 MYD 21
MYD P33 P33 P 0 1 N N R 98.067 95.305 49.489 1.411 -0.309 0.912 P33 MYD 22
MYD O44 O44 O 0 1 N N N 99.328 95.596 48.415 2.862 -0.854 0.474 O44 MYD 23
MYD O29 O29 O 0 1 N N N 98.780 94.928 50.757 0.455 -1.438 0.962 O29 MYD 24
MYD O32 O32 O 0 1 N N N 97.600 96.909 49.741 1.511 0.374 2.366 O32 MYD 25
MYD C28 C28 C 0 1 N N N 97.280 97.630 48.544 1.966 -0.636 3.268 C28 MYD 26
MYD C27 C27 C 0 1 N N R 97.103 99.115 48.540 2.084 -0.048 4.675 C27 MYD 27
MYD O24 O24 O 0 1 N N N 98.283 99.798 49.131 0.794 0.397 5.127 O24 MYD 28
MYD C26 C26 C 0 1 N N S 96.841 99.697 47.063 2.567 -1.133 5.657 C26 MYD 29
MYD O25 O25 O 0 1 N N N 95.430 99.583 46.910 3.804 -0.753 6.263 O25 MYD 30
MYD C22 C22 C 0 1 N N R 97.152 101.170 47.479 1.441 -1.205 6.722 C22 MYD 31
MYD O21 O21 O 0 1 N N N 96.030 101.833 48.185 1.989 -1.340 8.035 O21 MYD 32
MYD C23 C23 C 0 1 N N R 98.460 101.037 48.358 0.745 0.168 6.552 C23 MYD 33
MYD N20 N20 N 0 1 Y N N 99.646 100.840 47.520 -0.642 0.108 7.017 N20 MYD 34
MYD C16 C16 C 0 1 Y N N 100.255 99.751 47.127 -1.721 -0.294 6.287 C16 MYD 35
MYD N15 N15 N 0 1 Y N N 101.451 100.068 46.557 -2.800 -0.223 7.011 N15 MYD 36
MYD C14 C14 C 0 1 Y N N 101.567 101.432 46.550 -2.483 0.229 8.248 C14 MYD 37
MYD C19 C19 C 0 1 Y N N 100.424 101.927 47.159 -1.095 0.442 8.269 C19 MYD 38
MYD N18 N18 N 0 1 Y N N 100.284 103.286 47.319 -0.527 0.898 9.381 N18 MYD 39
MYD C17 C17 C 0 1 Y N N 101.194 104.147 46.825 -1.251 1.137 10.454 C17 MYD 40
MYD N12 N12 N 0 1 Y N N 102.274 103.675 46.179 -2.558 0.947 10.484 N12 MYD 41
MYD C13 C13 C 0 1 Y N N 102.478 102.348 46.016 -3.213 0.499 9.418 C13 MYD 42
MYD N11 N11 N 0 1 N N N 103.510 101.923 45.298 -4.582 0.302 9.460 N11 MYD 43
MYD H531 1H53 H 0 0 N N N 99.496 91.533 51.977 2.644 3.372 -7.330 H531 MYD 44
MYD H532 2H53 H 0 0 N N N 98.574 91.385 50.442 1.645 2.827 -8.699 H532 MYD 45
MYD H533 3H53 H 0 0 N N N 97.730 91.852 51.889 0.872 3.307 -7.169 H533 MYD 46
MYD H521 1H52 H 0 0 N N N 98.276 86.847 49.070 2.456 -0.662 -9.444 H521 MYD 47
MYD H522 2H52 H 0 0 N N N 98.917 88.493 49.470 1.508 0.164 -10.703 H522 MYD 48
MYD H523 3H52 H 0 0 N N N 98.749 87.344 50.746 2.414 1.115 -9.503 H523 MYD 49
MYD H491 1H49 H 0 0 N N N 96.054 86.771 47.613 -0.823 -0.556 -11.261 H491 MYD 50
MYD H492 2H49 H 0 0 N N N 95.895 85.678 48.830 -0.248 -2.065 -10.497 H492 MYD 51
MYD H31 H31 H 0 1 N N N 93.174 90.690 51.875 -2.584 -0.557 -5.685 H31 MYD 52
MYD H381 1H38 H 0 0 N N N 94.773 90.952 53.307 0.360 2.389 -5.415 H381 MYD 53
MYD H382 2H38 H 0 0 N N N 96.448 91.104 53.207 -1.326 1.927 -5.082 H382 MYD 54
MYD H371 1H37 H 0 0 N N N 94.410 92.470 51.258 -0.554 -0.264 -4.216 H371 MYD 55
MYD H372 2H37 H 0 0 N N N 95.251 93.276 52.507 1.132 0.198 -4.549 H372 MYD 56
MYD H45 H45 H 0 1 N N N 95.830 95.875 50.696 2.763 0.367 -2.405 H45 MYD 57
MYD H341 1H34 H 0 0 N N N 97.590 93.568 48.573 1.538 1.753 -0.338 H341 MYD 58
MYD H342 2H34 H 0 0 N N N 96.600 94.899 48.160 -0.147 1.291 -0.004 H342 MYD 59
MYD H44 H44 H 0 1 N N N 99.998 96.191 48.728 3.453 -0.089 0.454 H44 MYD 60
MYD H281 1H28 H 0 0 N N N 98.049 97.376 47.777 1.255 -1.462 3.277 H281 MYD 61
MYD H282 2H28 H 0 0 N N N 96.359 97.176 48.108 2.942 -0.999 2.943 H282 MYD 62
MYD H27 H27 H 0 1 N N N 96.201 99.321 49.162 2.784 0.786 4.671 H27 MYD 63
MYD H26 H26 H 0 1 N N N 97.362 99.281 46.169 2.671 -2.090 5.147 H26 MYD 64
MYD H25 H25 H 0 1 N N N 95.275 99.926 46.037 4.022 -1.439 6.908 H25 MYD 65
MYD H22 H22 H 0 1 N N N 97.300 101.837 46.598 0.750 -2.020 6.505 H22 MYD 66
MYD H21 H21 H 0 1 N N N 96.219 102.728 48.438 2.406 -2.212 8.075 H21 MYD 67
MYD H23 H23 H 0 1 N N N 98.601 101.953 48.976 1.293 0.945 7.085 H23 MYD 68
MYD H16 H16 H 0 1 N N N 99.832 98.739 47.254 -1.685 -0.625 5.259 H16 MYD 69
MYD H17 H17 H 0 1 N N N 101.055 105.234 46.949 -0.759 1.503 11.342 H17 MYD 70
MYD H111 1H11 H 0 0 N N N 104.174 102.591 44.908 -5.075 0.493 10.274 H111 MYD 71
MYD H112 2H11 H 0 0 N N N 103.155 101.342 44.537 -5.049 -0.025 8.676 H112 MYD 72
# #
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
MYD C53 O51 SING N N 1
MYD C53 H531 SING N N 2
MYD C53 H532 SING N N 3
MYD C53 H533 SING N N 4
MYD O51 C46 SING N N 5
MYD C46 C47 DOUB Y N 6
MYD C46 C39 SING Y N 7
MYD C47 C52 SING N N 8
MYD C47 C48 SING Y N 9
MYD C52 H521 SING N N 10
MYD C52 H522 SING N N 11
MYD C52 H523 SING N N 12
MYD C48 C49 SING N N 13
MYD C48 C41 DOUB Y N 14
MYD C49 O50 SING N N 15
MYD C49 H491 SING N N 16
MYD C49 H492 SING N N 17
MYD O50 C42 SING N N 18
MYD C42 O43 DOUB N N 19
MYD C42 C41 SING N N 20
MYD C41 C40 SING Y N 21
MYD C40 O31 SING N N 22
MYD C40 C39 DOUB Y N 23
MYD O31 H31 SING N N 24
MYD C39 C38 SING N N 25
MYD C38 C37 SING N N 26
MYD C38 H381 SING N N 27
MYD C38 H382 SING N N 28
MYD C37 O36 SING N N 29
MYD C37 H371 SING N N 30
MYD C37 H372 SING N N 31
MYD O36 P35 SING N N 32
MYD P35 O45 SING N N 33
MYD P35 O30 DOUB N N 34
MYD P35 C34 SING N N 35
MYD O45 H45 SING N N 36
MYD C34 P33 SING N N 37
MYD C34 H341 SING N N 38
MYD C34 H342 SING N N 39
MYD P33 O44 SING N N 40
MYD P33 O29 DOUB N N 41
MYD P33 O32 SING N N 42
MYD O44 H44 SING N N 43
MYD O32 C28 SING N N 44
MYD C28 C27 SING N N 45
MYD C28 H281 SING N N 46
MYD C28 H282 SING N N 47
MYD C27 O24 SING N N 48
MYD C27 C26 SING N N 49
MYD C27 H27 SING N N 50
MYD O24 C23 SING N N 51
MYD C26 O25 SING N N 52
MYD C26 C22 SING N N 53
MYD C26 H26 SING N N 54
MYD O25 H25 SING N N 55
MYD C22 O21 SING N N 56
MYD C22 C23 SING N N 57
MYD C22 H22 SING N N 58
MYD O21 H21 SING N N 59
MYD C23 N20 SING N N 60
MYD C23 H23 SING N N 61
MYD N20 C16 SING Y N 62
MYD N20 C19 SING Y N 63
MYD C16 N15 DOUB Y N 64
MYD C16 H16 SING N N 65
MYD N15 C14 SING Y N 66
MYD C14 C19 DOUB Y N 67
MYD C14 C13 SING Y N 68
MYD C19 N18 SING Y N 69
MYD N18 C17 DOUB Y N 70
MYD C17 N12 SING Y N 71
MYD C17 H17 SING N N 72
MYD N12 C13 DOUB Y N 73
MYD C13 N11 SING N N 74
MYD N11 H111 SING N N 75
MYD N11 H112 SING N N 76
# #
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
MYD SMILES ACDLabs 10.04 "O=C5OCc1c5c(O)c(c(OC)c1C)CCOP(=O)(O)CP(=O)(O)OCC4OC(n3cnc2c(ncnc23)N)C(O)C4O"
MYD SMILES_CANONICAL CACTVS 3.341 "COc1c(C)c2COC(=O)c2c(O)c1CCO[P@](O)(=O)C[P@](O)(=O)OC[C@H]3O[C@H]([C@H](O)[C@@H]3O)n4cnc5c(N)ncnc45"
MYD SMILES CACTVS 3.341 "COc1c(C)c2COC(=O)c2c(O)c1CCO[P](O)(=O)C[P](O)(=O)OC[CH]3O[CH]([CH](O)[CH]3O)n4cnc5c(N)ncnc45"
MYD SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "Cc1c2c(c(c(c1OC)CCO[P@](=O)(C[P@@](=O)(O)OC[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4ncnc5N)O)O)O)O)C(=O)OC2"
MYD SMILES "OpenEye OEToolkits" 1.5.0 "Cc1c2c(c(c(c1OC)CCOP(=O)(CP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)O)O)O)O)C(=O)OC2"
MYD InChI InChI 1.03 "InChI=1S/C23H29N5O13P2/c1-10-12-5-38-23(32)14(12)16(29)11(19(10)37-2)3-4-39-42(33,34)9-43(35,36)40-6-13-17(30)18(31)22(41-13)28-8-27-15-20(24)25-7-26-21(15)28/h7-8,13,17-18,22,29-31H,3-6,9H2,1-2H3,(H,33,34)(H,35,36)(H2,24,25,26)/t13-,17-,18-,22-/m1/s1"
MYD InChIKey InChI 1.03 AMYUZLUBFKOUEX-JKWAKEATSA-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
MYD "SYSTEMATIC NAME" ACDLabs 10.04 "5'-O-[(R)-hydroxy({(S)-hydroxy[2-(4-hydroxy-6-methoxy-7-methyl-3-oxo-1,3-dihydro-2-benzofuran-5-yl)ethoxy]phosphoryl}methyl)phosphoryl]adenosine"
MYD "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl]methyl-[2-(4-hydroxy-6-methoxy-7-methyl-3-oxo-1H-2-benzofuran-5-yl)ethoxy]phosphinic 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
MYD "Create component" 2002-12-20 RCSB
MYD "Modify descriptor" 2011-06-04 RCSB
MYD "Modify synonyms" 2020-06-05 PDBE
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id MYD
_pdbx_chem_comp_synonyms.name "C2-MYCOPHENOLIC ADENINE DINUCLEOTIDE"
_pdbx_chem_comp_synonyms.provenance ?
_pdbx_chem_comp_synonyms.type ?
##