data_P8F
#
_chem_comp.id P8F
_chem_comp.name Pentacycline
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C29 H30 F N3 O7"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms "(4S,4aS,5aR,14aS)-4-(dimethylamino)-10-[(3-fluoranylazetidin-1-yl)methyl]-3,12,14,14a-tetrakis(oxidanyl)-1,13-bis(oxidanylidene)-4a,5,5a,6-tetrahydro-4H-pentacene-2-carboxamide; Pentacycline TP-038"
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2023-02-09
_chem_comp.pdbx_modified_date 2023-07-25
_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 551.563
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code P8F
_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 8CGI
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site PDBE
#
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
P8F C1 C1 C 0 1 N N N 189.404 154.311 173.011 4.762 -3.793 -0.533 C1 P8F 1
P8F N1 N1 N 0 1 N N N 190.435 153.452 172.426 5.505 -2.537 -0.359 N1 P8F 2
P8F C2 C2 C 0 1 N N N 190.796 152.426 173.414 6.905 -2.692 -0.774 C2 P8F 3
P8F C3 C3 C 0 1 N N S 190.237 152.938 171.058 4.858 -1.438 -1.088 C3 P8F 4
P8F C4 C4 C 0 1 N N N 190.288 154.044 170.021 5.742 -0.229 -1.031 C4 P8F 5
P8F O1 O1 O 0 1 N N N 191.018 155.098 170.373 6.784 -0.148 -1.872 O1 P8F 6
P8F C5 C5 C 0 1 N N N 189.635 153.918 168.780 5.523 0.798 -0.147 C5 P8F 7
P8F C6 C6 C 0 1 N N N 190.073 154.752 167.613 6.442 1.946 -0.116 C6 P8F 8
P8F N2 N2 N 0 1 N N N 189.567 154.470 166.414 6.340 2.917 -1.045 N2 P8F 9
P8F O2 O2 O 0 1 N N N 190.833 155.706 167.815 7.295 2.020 0.748 O2 P8F 10
P8F C7 C7 C 0 1 N N N 188.504 153.048 168.689 4.379 0.757 0.763 C7 P8F 11
P8F O3 O3 O 0 1 N N N 188.027 152.603 167.643 4.053 1.743 1.391 O3 P8F 12
P8F C8 C8 C 0 1 N N S 187.882 152.663 170.051 3.606 -0.541 0.906 C8 P8F 13
P8F O4 O4 O 0 1 N N N 187.407 153.834 170.700 4.266 -1.418 1.821 O4 P8F 14
P8F C9 C9 C 0 1 N N N 186.741 151.698 169.832 2.228 -0.198 1.405 C9 P8F 15
P8F O5 O5 O 0 1 N N N 185.588 152.306 169.582 2.076 0.048 2.721 O5 P8F 16
P8F C10 C10 C 0 1 N N N 186.907 150.348 169.849 1.148 -0.122 0.624 C10 P8F 17
P8F C11 C11 C 0 1 N N N 185.795 149.470 169.561 -0.112 0.178 1.223 C11 P8F 18
P8F O6 O6 O 0 1 N N N 184.636 149.902 169.308 -0.231 0.207 2.435 O6 P8F 19
P8F C12 C12 C 0 1 Y N N 186.035 148.029 169.607 -1.269 0.452 0.349 C12 P8F 20
P8F C13 C13 C 0 1 Y N N 187.353 147.529 169.501 -1.063 0.681 -1.026 C13 P8F 21
P8F C14 C14 C 0 1 Y N N 187.571 146.174 169.567 -2.113 0.916 -1.853 C14 P8F 22
P8F C15 C15 C 0 1 Y N N 186.522 145.244 169.730 -3.426 0.952 -1.344 C15 P8F 23
P8F C16 C16 C 0 1 Y N N 186.766 143.847 169.774 -4.523 1.181 -2.190 C16 P8F 24
P8F C17 C17 C 0 1 Y N N 185.734 142.968 169.938 -5.781 1.218 -1.669 C17 P8F 25
P8F C18 C18 C 0 1 Y N N 184.383 143.429 170.077 -5.999 1.032 -0.306 C18 P8F 26
P8F C19 C19 C 0 1 N N N 183.263 142.429 170.240 -7.404 1.083 0.237 C19 P8F 27
P8F N3 N3 N 0 1 N N N 182.658 142.423 171.567 -7.990 -0.264 0.206 N3 P8F 28
P8F C20 C20 C 0 1 N N N 183.552 142.165 172.723 -8.762 -0.476 -1.033 C20 P8F 29
P8F C21 C21 C 0 1 N N N 182.999 140.744 172.779 -9.825 -1.185 -0.182 C21 P8F 30
P8F F1 F1 F 0 1 N N N 182.627 140.354 174.042 -9.596 -2.554 -0.003 F1 P8F 31
P8F C22 C22 C 0 1 N N N 181.847 141.224 171.901 -9.267 -0.302 0.942 C22 P8F 32
P8F C23 C23 C 0 1 Y N N 184.132 144.783 170.029 -4.958 0.804 0.544 C23 P8F 33
P8F C24 C24 C 0 1 Y N N 185.174 145.724 169.847 -3.648 0.755 0.041 C24 P8F 34
P8F C25 C25 C 0 1 Y N N 184.950 147.143 169.787 -2.550 0.508 0.890 C25 P8F 35
P8F O7 O7 O 0 1 N N N 183.699 147.620 169.891 -2.740 0.327 2.219 O7 P8F 36
P8F C26 C26 C 0 1 N N N 188.478 148.506 169.343 0.338 0.680 -1.585 C26 P8F 37
P8F C27 C27 C 0 1 N N R 188.218 149.690 170.268 1.188 -0.363 -0.862 C27 P8F 38
P8F C28 C28 C 0 1 N N N 189.382 150.675 170.238 2.630 -0.292 -1.372 C28 P8F 39
P8F C29 C29 C 0 1 N N S 189.000 152.019 170.879 3.494 -1.178 -0.478 C29 P8F 40
P8F H1 H1 H 0 1 N N N 189.704 154.605 174.027 5.291 -4.601 -0.026 H1 P8F 41
P8F H2 H2 H 0 1 N N N 189.281 155.211 172.390 3.765 -3.688 -0.105 H2 P8F 42
P8F H3 H3 H 0 1 N N N 188.451 153.763 173.055 4.680 -4.023 -1.595 H3 P8F 43
P8F H5 H5 H 0 1 N N N 190.923 152.895 174.401 6.949 -2.851 -1.852 H5 P8F 44
P8F H6 H6 H 0 1 N N N 189.997 151.671 173.467 7.462 -1.791 -0.516 H6 P8F 45
P8F H7 H7 H 0 1 N N N 191.737 151.943 173.113 7.343 -3.549 -0.263 H7 P8F 46
P8F H8 H8 H 0 1 N N N 191.105 152.296 170.847 4.728 -1.733 -2.130 H8 P8F 47
P8F H10 H10 H 0 1 N N N 191.185 155.638 169.609 7.295 0.673 -1.860 H10 P8F 48
P8F H12 H12 H 0 1 N N N 189.798 155.042 165.627 6.988 3.638 -1.067 H12 P8F 49
P8F H13 H13 H 0 1 N N N 188.956 153.687 166.301 5.617 2.895 -1.692 H13 P8F 50
P8F H14 H14 H 0 1 N N N 187.024 153.599 171.537 4.307 -1.083 2.727 H14 P8F 51
P8F H15 H15 H 0 1 N N N 184.917 151.656 169.413 2.369 -0.641 3.333 H15 P8F 52
P8F H16 H16 H 0 1 N N N 188.584 145.807 169.491 -1.941 1.077 -2.907 H16 P8F 53
P8F H17 H17 H 0 1 N N N 187.776 143.476 169.677 -4.371 1.327 -3.249 H17 P8F 54
P8F H18 H18 H 0 1 N N N 185.939 141.908 169.963 -6.622 1.395 -2.322 H18 P8F 55
P8F H19 H19 H 0 1 N N N 182.480 142.665 169.504 -7.384 1.447 1.264 H19 P8F 56
P8F H20 H20 H 0 1 N N N 183.665 141.425 170.039 -8.005 1.755 -0.375 H20 P8F 57
P8F H22 H22 H 0 1 N N N 184.625 142.227 172.491 -9.116 0.449 -1.487 H22 P8F 58
P8F H23 H23 H 0 1 N N N 183.333 142.774 173.613 -8.266 -1.135 -1.746 H23 P8F 59
P8F H24 H24 H 0 1 N N N 183.648 140.029 172.252 -10.851 -0.955 -0.467 H24 P8F 60
P8F H25 H25 H 0 1 N N N 180.917 141.441 172.448 -9.199 -0.813 1.903 H25 P8F 61
P8F H26 H26 H 0 1 N N N 181.625 140.571 171.044 -9.755 0.670 1.015 H26 P8F 62
P8F H27 H27 H 0 1 N N N 183.116 145.135 170.133 -5.140 0.662 1.599 H27 P8F 63
P8F H28 H28 H 0 1 N N N 183.700 148.553 169.712 -2.702 1.143 2.736 H28 P8F 64
P8F H29 H29 H 0 1 N N N 189.429 148.025 169.614 0.303 0.444 -2.648 H29 P8F 65
P8F H30 H30 H 0 1 N N N 188.526 148.852 168.300 0.782 1.666 -1.449 H30 P8F 66
P8F H31 H31 H 0 1 N N N 188.106 149.313 171.295 0.795 -1.357 -1.075 H31 P8F 67
P8F H32 H32 H 0 1 N N N 190.230 150.244 170.791 2.674 -0.651 -2.400 H32 P8F 68
P8F H33 H33 H 0 1 N N N 189.676 150.849 169.192 2.987 0.736 -1.324 H33 P8F 69
P8F H34 H34 H 0 1 N N N 188.596 151.809 171.880 2.993 -2.140 -0.369 H34 P8F 70
#
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
P8F N2 C6 SING N N 1
P8F C6 O2 DOUB N N 2
P8F C6 C5 SING N N 3
P8F O3 C7 DOUB N N 4
P8F C7 C5 SING N N 5
P8F C7 C8 SING N N 6
P8F C5 C4 DOUB N N 7
P8F O6 C11 DOUB N N 8
P8F C26 C13 SING N N 9
P8F C26 C27 SING N N 10
P8F C13 C14 DOUB Y N 11
P8F C13 C12 SING Y N 12
P8F C11 C12 SING N N 13
P8F C11 C10 SING N N 14
P8F C14 C15 SING Y N 15
P8F O5 C9 SING N N 16
P8F C12 C25 DOUB Y N 17
P8F C15 C16 SING Y N 18
P8F C15 C24 DOUB Y N 19
P8F C16 C17 DOUB Y N 20
P8F C25 C24 SING Y N 21
P8F C25 O7 SING N N 22
P8F C9 C10 DOUB N N 23
P8F C9 C8 SING N N 24
P8F C24 C23 SING Y N 25
P8F C10 C27 SING N N 26
P8F C17 C18 SING Y N 27
P8F C4 O1 SING N N 28
P8F C4 C3 SING N N 29
P8F C23 C18 DOUB Y N 30
P8F C8 O4 SING N N 31
P8F C8 C29 SING N N 32
P8F C18 C19 SING N N 33
P8F C28 C27 SING N N 34
P8F C28 C29 SING N N 35
P8F C19 N3 SING N N 36
P8F C29 C3 SING N N 37
P8F C3 N1 SING N N 38
P8F N3 C22 SING N N 39
P8F N3 C20 SING N N 40
P8F C22 C21 SING N N 41
P8F N1 C1 SING N N 42
P8F N1 C2 SING N N 43
P8F C20 C21 SING N N 44
P8F C21 F1 SING N N 45
P8F C1 H1 SING N N 46
P8F C1 H2 SING N N 47
P8F C1 H3 SING N N 48
P8F C2 H5 SING N N 49
P8F C2 H6 SING N N 50
P8F C2 H7 SING N N 51
P8F C3 H8 SING N N 52
P8F O1 H10 SING N N 53
P8F N2 H12 SING N N 54
P8F N2 H13 SING N N 55
P8F O4 H14 SING N N 56
P8F O5 H15 SING N N 57
P8F C14 H16 SING N N 58
P8F C16 H17 SING N N 59
P8F C17 H18 SING N N 60
P8F C19 H19 SING N N 61
P8F C19 H20 SING N N 62
P8F C20 H22 SING N N 63
P8F C20 H23 SING N N 64
P8F C21 H24 SING N N 65
P8F C22 H25 SING N N 66
P8F C22 H26 SING N N 67
P8F C23 H27 SING N N 68
P8F O7 H28 SING N N 69
P8F C26 H29 SING N N 70
P8F C26 H30 SING N N 71
P8F C27 H31 SING N N 72
P8F C28 H32 SING N N 73
P8F C28 H33 SING N N 74
P8F C29 H34 SING N N 75
#
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
P8F InChI InChI 1.06 "InChI=1S/C29H30FN3O7/c1-32(2)22-18-8-15-7-14-6-13-4-3-12(9-33-10-16(30)11-33)5-17(13)23(34)19(14)24(35)20(15)26(37)29(18,40)27(38)21(25(22)36)28(31)39/h3-6,15-16,18,22,34,36-37,40H,7-11H2,1-2H3,(H2,31,39)/t15-,18-,22-,29-/m0/s1"
P8F InChIKey InChI 1.06 DAUIQSOIFWOKJQ-MGVDVOGZSA-N
P8F SMILES_CANONICAL CACTVS 3.385 "CN(C)[C@H]1[C@@H]2C[C@@H]3Cc4cc5ccc(CN6CC(F)C6)cc5c(O)c4C(=O)C3=C(O)[C@]2(O)C(=O)C(=C1O)C(N)=O"
P8F SMILES CACTVS 3.385 "CN(C)[CH]1[CH]2C[CH]3Cc4cc5ccc(CN6CC(F)C6)cc5c(O)c4C(=O)C3=C(O)[C]2(O)C(=O)C(=C1O)C(N)=O"
P8F SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CN(C)[C@H]1[C@@H]2C[C@@H]3Cc4cc5ccc(cc5c(c4C(=O)C3=C([C@@]2(C(=O)C(=C1O)C(=O)N)O)O)O)CN6CC(C6)F"
P8F SMILES "OpenEye OEToolkits" 2.0.7 "CN(C)C1C2CC3Cc4cc5ccc(cc5c(c4C(=O)C3=C(C2(C(=O)C(=C1O)C(=O)N)O)O)O)CN6CC(C6)F"
#
_pdbx_chem_comp_identifier.comp_id P8F
_pdbx_chem_comp_identifier.type "SYSTEMATIC NAME"
_pdbx_chem_comp_identifier.program "OpenEye OEToolkits"
_pdbx_chem_comp_identifier.program_version 2.0.7
_pdbx_chem_comp_identifier.identifier "(4~{S},4~{a}~{S},5~{a}~{R},14~{a}~{S})-4-(dimethylamino)-10-[(3-fluoranylazetidin-1-yl)methyl]-3,12,14,14~{a}-tetrakis(oxidanyl)-1,13-bis(oxidanylidene)-4~{a},5,5~{a},6-tetrahydro-4~{H}-pentacene-2-carboxamide"
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
P8F "Create component" 2023-02-09 PDBE
P8F "Initial release" 2023-07-26 RCSB
P8F "Modify aromatic_flag" 2023-07-25 PDBE
P8F "Modify synonyms" 2023-07-25 PDBE
#
loop_
_pdbx_chem_comp_synonyms.ordinal
_pdbx_chem_comp_synonyms.comp_id
_pdbx_chem_comp_synonyms.name
_pdbx_chem_comp_synonyms.provenance
_pdbx_chem_comp_synonyms.type
1 P8F "(4S,4aS,5aR,14aS)-4-(dimethylamino)-10-[(3-fluoranylazetidin-1-yl)methyl]-3,12,14,14a-tetrakis(oxidanyl)-1,13-bis(oxidanylidene)-4a,5,5a,6-tetrahydro-4H-pentacene-2-carboxamide" PDB ?
2 P8F "Pentacycline TP-038" AUTHOR ?
#