data_YNP # _chem_comp.id YNP _chem_comp.name "Cryptophycin 1" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C35 H43 Cl N2 O8" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "(3S,6R,10S,13E,16S)-10-[(3-chloro-4-methoxyphenyl)methyl]-6-methyl-3-(2-methylpropyl)-16-{(1S)-1-[(2R,3R)-3-phenyloxiran-2-yl]ethyl}-1,4-dioxa-8,11-diazacyclohexadec-13-ene-2,5,9,12-tetrone" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2021-03-15 _chem_comp.pdbx_modified_date 2021-09-03 _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 655.178 _chem_comp.one_letter_code ? _chem_comp.three_letter_code YNP _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 7M18 _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 YNP N1 N1 N 0 1 N N N 324.109 199.777 306.223 2.648 -1.303 -0.260 N1 YNP 1 YNP C2 C1 C 0 1 N N R 324.717 201.030 304.204 1.215 -3.092 0.590 C2 YNP 2 YNP C4 C2 C 0 1 N N N 323.977 200.463 307.500 3.282 -0.747 -1.341 C4 YNP 3 YNP C5 C3 C 0 1 N N S 324.812 201.700 307.851 3.562 0.736 -1.323 C5 YNP 4 YNP C6 C4 C 0 1 N N N 323.414 204.146 307.214 1.550 1.740 -0.455 C6 YNP 5 YNP O2 O1 O 0 1 N N N 322.395 204.423 308.125 1.976 1.482 0.654 O2 YNP 6 YNP N2 N2 N 0 1 N N N 324.138 202.895 307.366 2.290 1.454 -1.563 N2 YNP 7 YNP O4 O2 O 0 1 N N N 321.769 204.625 301.605 -2.737 0.050 2.074 O4 YNP 8 YNP C7 C5 C 0 1 N N N 323.745 205.192 306.152 0.230 2.367 -0.619 C7 YNP 9 YNP O6 O3 O 0 1 N N N 322.738 202.316 304.303 -0.464 -2.832 -1.043 O6 YNP 10 YNP C8 C6 C 0 1 N N N 322.798 205.778 305.446 -0.502 2.659 0.452 C8 YNP 11 YNP C10 C7 C 0 1 N N S 322.609 206.744 303.026 -2.943 2.260 0.650 C10 YNP 12 YNP C11 C8 C 0 1 N N N 322.918 204.702 301.894 -2.533 -0.088 0.891 C11 YNP 13 YNP C12 C9 C 0 1 N N S 323.845 203.494 301.808 -2.192 -1.456 0.358 C12 YNP 14 YNP C13 C10 C 0 1 N N N 323.844 202.245 303.874 -0.116 -2.593 0.089 C13 YNP 15 YNP C14 C11 C 0 1 N N N 323.229 202.245 301.176 -3.287 -2.446 0.758 C14 YNP 16 YNP C15 C12 C 0 1 N N N 323.947 201.879 299.875 -4.595 -2.072 0.058 C15 YNP 17 YNP C16 C13 C 0 1 N N N 325.325 202.534 299.763 -4.438 -2.262 -1.452 C16 YNP 18 YNP C17 C14 C 0 1 N N N 323.079 202.126 298.643 -5.723 -2.969 0.570 C17 YNP 19 YNP C18 C15 C 0 1 N N S 322.658 208.106 302.318 -4.294 2.728 0.106 C18 YNP 20 YNP C19 C16 C 0 1 N N N 322.275 209.275 303.217 -4.649 4.084 0.721 C19 YNP 21 YNP C20 C17 C 0 1 N N R 321.863 208.140 301.018 -5.372 1.706 0.470 C20 YNP 22 YNP C21 C18 C 0 1 N N R 322.754 207.571 299.836 -6.788 1.945 -0.057 C21 YNP 23 YNP C22 C19 C 0 1 Y N N 322.931 206.963 298.449 -7.620 0.739 -0.409 C22 YNP 24 YNP C23 C20 C 0 1 Y N N 323.827 207.517 297.551 -7.703 0.316 -1.723 C23 YNP 25 YNP C24 C21 C 0 1 Y N N 323.968 206.947 296.286 -8.466 -0.790 -2.046 C24 YNP 26 YNP C25 C22 C 0 1 Y N N 323.205 205.829 295.940 -9.147 -1.474 -1.056 C25 YNP 27 YNP C26 C23 C 0 1 Y N N 322.310 205.290 296.853 -9.063 -1.051 0.258 C26 YNP 28 YNP C27 C24 C 0 1 Y N N 322.183 205.862 298.098 -8.296 0.051 0.582 C27 YNP 29 YNP C28 C25 C 0 1 N N N 325.035 201.812 309.365 4.130 1.137 0.040 C28 YNP 30 YNP C29 C26 C 0 1 Y N N 325.848 203.042 309.787 5.542 0.625 0.166 C29 YNP 31 YNP C3 C27 C 0 1 N N N 323.910 199.865 304.783 2.307 -2.739 -0.422 C3 YNP 32 YNP C30 C28 C 0 1 Y N N 325.412 203.879 310.822 6.600 1.412 -0.248 C30 YNP 33 YNP C31 C29 C 0 1 Y N N 326.163 204.992 311.198 7.896 0.945 -0.134 C31 YNP 34 YNP C32 C30 C 0 1 Y N N 327.351 205.279 310.551 8.134 -0.315 0.398 C32 YNP 35 YNP C33 C31 C 0 1 Y N N 327.790 204.468 309.531 7.069 -1.102 0.813 C33 YNP 36 YNP C34 C32 C 0 1 Y N N 327.048 203.362 309.155 5.776 -0.628 0.701 C34 YNP 37 YNP C35 C33 C 0 1 N N N 328.048 206.702 312.287 9.576 -2.083 1.068 C35 YNP 38 YNP C49 C34 C 0 1 N N N 325.648 200.617 303.062 1.533 -2.432 1.934 C49 YNP 39 YNP C9 C35 C 0 1 N N N 323.207 206.842 304.425 -1.865 3.283 0.286 C9 YNP 40 YNP O1 O4 O 0 1 N N N 323.057 199.968 308.436 3.610 -1.429 -2.288 O1 YNP 41 YNP O3 O5 O 0 1 N N N 323.486 205.904 302.330 -2.608 0.973 0.068 O3 YNP 42 YNP O5 O6 O 0 1 N N N 324.383 203.277 303.091 -0.916 -1.884 0.901 O5 YNP 43 YNP O7 O7 O 0 1 N N N 322.486 208.900 300.105 -6.439 2.135 1.317 O7 YNP 44 YNP O8 O8 O 0 1 N N N 328.110 206.400 310.921 9.407 -0.777 0.512 O8 YNP 45 YNP CL1 CL1 CL 0 0 N N N 325.592 206.048 312.520 9.226 1.933 -0.654 CL1 YNP 46 YNP H1 H1 H 0 1 N N N 324.495 198.874 306.412 2.444 -0.801 0.544 H1 YNP 47 YNP H2 H2 H 0 1 N N N 325.380 201.359 305.018 1.173 -4.173 0.717 H2 YNP 48 YNP H3 H3 H 0 1 N N N 325.793 201.608 307.361 4.278 0.984 -2.106 H3 YNP 49 YNP H4 H4 H 0 1 N N N 324.287 202.727 306.392 2.001 1.705 -2.454 H4 YNP 50 YNP H5 H5 H 0 1 N N N 324.777 205.458 305.975 -0.147 2.587 -1.608 H5 YNP 51 YNP H6 H6 H 0 1 N N N 321.760 205.514 305.585 -0.125 2.444 1.439 H6 YNP 52 YNP H7 H7 H 0 1 N N N 321.580 206.357 303.062 -3.001 2.164 1.734 H7 YNP 53 YNP H8 H8 H 0 1 N N N 324.673 203.792 301.148 -2.120 -1.414 -0.729 H8 YNP 54 YNP H9 H9 H 0 1 N N N 322.168 202.437 300.960 -2.992 -3.453 0.462 H9 YNP 55 YNP H10 H10 H 0 1 N N N 323.313 201.406 301.882 -3.431 -2.413 1.838 H10 YNP 56 YNP H11 H11 H 0 1 N N N 324.124 200.794 299.915 -4.835 -1.030 0.270 H11 YNP 57 YNP H12 H12 H 0 1 N N N 325.906 202.325 300.673 -4.225 -3.309 -1.666 H12 YNP 58 YNP H13 H13 H 0 1 N N N 325.854 202.127 298.889 -5.360 -1.968 -1.953 H13 YNP 59 YNP H14 H14 H 0 1 N N N 325.206 203.621 299.646 -3.615 -1.643 -1.813 H14 YNP 60 YNP H15 H15 H 0 1 N N N 322.104 201.635 298.776 -5.835 -2.833 1.646 H15 YNP 61 YNP H16 H16 H 0 1 N N N 322.930 203.208 298.511 -6.655 -2.702 0.071 H16 YNP 62 YNP H17 H17 H 0 1 N N N 323.578 201.713 297.754 -5.483 -4.011 0.358 H17 YNP 63 YNP H18 H18 H 0 1 N N N 323.710 208.266 302.038 -4.236 2.825 -0.978 H18 YNP 64 YNP H19 H19 H 0 1 N N N 322.860 209.230 304.147 -3.881 4.813 0.462 H19 YNP 65 YNP H20 H20 H 0 1 N N N 322.485 210.221 302.697 -5.612 4.418 0.334 H20 YNP 66 YNP H21 H21 H 0 1 N N N 321.203 209.218 303.455 -4.707 3.987 1.805 H21 YNP 67 YNP H22 H22 H 0 1 N N N 320.785 207.922 301.023 -5.033 0.674 0.564 H22 YNP 68 YNP H23 H23 H 0 1 N N N 323.718 207.372 300.328 -6.961 2.833 -0.665 H23 YNP 69 YNP H24 H24 H 0 1 N N N 324.411 208.382 297.827 -7.172 0.851 -2.497 H24 YNP 70 YNP H25 H25 H 0 1 N N N 324.665 207.368 295.576 -8.531 -1.120 -3.072 H25 YNP 71 YNP H26 H26 H 0 1 N N N 323.312 205.384 294.962 -9.744 -2.338 -1.309 H26 YNP 72 YNP H27 H27 H 0 1 N N N 321.717 204.427 296.588 -9.595 -1.585 1.031 H27 YNP 73 YNP H28 H28 H 0 1 N N N 321.487 205.442 298.809 -8.231 0.381 1.608 H28 YNP 74 YNP H29 H29 H 0 1 N N N 324.052 201.862 309.857 4.128 2.223 0.130 H29 YNP 75 YNP H30 H30 H 0 1 N N N 325.569 200.912 309.703 3.515 0.706 0.831 H30 YNP 76 YNP H31 H31 H 0 1 N N N 322.842 200.024 304.574 1.942 -2.918 -1.433 H31 YNP 77 YNP H32 H32 H 0 1 N N N 324.240 198.927 304.313 3.191 -3.349 -0.236 H32 YNP 78 YNP H33 H33 H 0 1 N N N 324.486 203.660 311.333 6.414 2.392 -0.662 H33 YNP 79 YNP H34 H34 H 0 1 N N N 328.715 204.695 309.022 7.251 -2.083 1.227 H34 YNP 80 YNP H35 H35 H 0 1 N N N 327.407 202.733 308.354 4.948 -1.241 1.024 H35 YNP 81 YNP H36 H36 H 0 1 N N N 328.666 207.588 312.496 9.054 -2.812 0.449 H36 YNP 82 YNP H37 H37 H 0 1 N N N 327.005 206.907 312.570 10.637 -2.329 1.102 H37 YNP 83 YNP H38 H38 H 0 1 N N N 328.424 205.848 312.869 9.166 -2.104 2.078 H38 YNP 84 YNP H39 H39 H 0 1 N N N 326.241 199.743 303.369 1.443 -1.350 1.838 H39 YNP 85 YNP H40 H40 H 0 1 N N N 325.049 200.361 302.176 0.832 -2.789 2.688 H40 YNP 86 YNP H41 H41 H 0 1 N N N 326.323 201.451 302.820 2.549 -2.688 2.232 H41 YNP 87 YNP H42 H42 H 0 1 N N N 324.301 206.794 304.320 -1.950 4.149 0.943 H42 YNP 88 YNP H43 H43 H 0 1 N N N 322.921 207.821 304.837 -1.997 3.598 -0.749 H43 YNP 89 # # 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 YNP C25 C24 DOUB Y N 1 YNP C25 C26 SING Y N 2 YNP C24 C23 SING Y N 3 YNP C26 C27 DOUB Y N 4 YNP C23 C22 DOUB Y N 5 YNP C27 C22 SING Y N 6 YNP C22 C21 SING N N 7 YNP C17 C15 SING N N 8 YNP C16 C15 SING N N 9 YNP C21 O7 SING N N 10 YNP C21 C20 SING N N 11 YNP C15 C14 SING N N 12 YNP O7 C20 SING N N 13 YNP C20 C18 SING N N 14 YNP C14 C12 SING N N 15 YNP O4 C11 DOUB N N 16 YNP C12 C11 SING N N 17 YNP C12 O5 SING N N 18 YNP C11 O3 SING N N 19 YNP C18 C10 SING N N 20 YNP C18 C19 SING N N 21 YNP O3 C10 SING N N 22 YNP C10 C9 SING N N 23 YNP C49 C2 SING N N 24 YNP O5 C13 SING N N 25 YNP C13 C2 SING N N 26 YNP C13 O6 DOUB N N 27 YNP C2 C3 SING N N 28 YNP C9 C8 SING N N 29 YNP C3 N1 SING N N 30 YNP C8 C7 DOUB N E 31 YNP C7 C6 SING N N 32 YNP N1 C4 SING N N 33 YNP C6 N2 SING N N 34 YNP C6 O2 DOUB N N 35 YNP N2 C5 SING N N 36 YNP C4 C5 SING N N 37 YNP C4 O1 DOUB N N 38 YNP C5 C28 SING N N 39 YNP C34 C33 DOUB Y N 40 YNP C34 C29 SING Y N 41 YNP C28 C29 SING N N 42 YNP C33 C32 SING Y N 43 YNP C29 C30 DOUB Y N 44 YNP C32 O8 SING N N 45 YNP C32 C31 DOUB Y N 46 YNP C30 C31 SING Y N 47 YNP O8 C35 SING N N 48 YNP C31 CL1 SING N N 49 YNP N1 H1 SING N N 50 YNP C2 H2 SING N N 51 YNP C5 H3 SING N N 52 YNP N2 H4 SING N N 53 YNP C7 H5 SING N N 54 YNP C8 H6 SING N N 55 YNP C10 H7 SING N N 56 YNP C12 H8 SING N N 57 YNP C14 H9 SING N N 58 YNP C14 H10 SING N N 59 YNP C15 H11 SING N N 60 YNP C16 H12 SING N N 61 YNP C16 H13 SING N N 62 YNP C16 H14 SING N N 63 YNP C17 H15 SING N N 64 YNP C17 H16 SING N N 65 YNP C17 H17 SING N N 66 YNP C18 H18 SING N N 67 YNP C19 H19 SING N N 68 YNP C19 H20 SING N N 69 YNP C19 H21 SING N N 70 YNP C20 H22 SING N N 71 YNP C21 H23 SING N N 72 YNP C23 H24 SING N N 73 YNP C24 H25 SING N N 74 YNP C25 H26 SING N N 75 YNP C26 H27 SING N N 76 YNP C27 H28 SING N N 77 YNP C28 H29 SING N N 78 YNP C28 H30 SING N N 79 YNP C3 H31 SING N N 80 YNP C3 H32 SING N N 81 YNP C30 H33 SING N N 82 YNP C33 H34 SING N N 83 YNP C34 H35 SING N N 84 YNP C35 H36 SING N N 85 YNP C35 H37 SING N N 86 YNP C35 H38 SING N N 87 YNP C49 H39 SING N N 88 YNP C49 H40 SING N N 89 YNP C49 H41 SING N N 90 YNP C9 H42 SING N N 91 YNP C9 H43 SING N N 92 # # 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 YNP SMILES ACDLabs 12.01 "COc1ccc(cc1Cl)CC1NC(=O)C=CCC(OC(=O)C(OC(=O)C(C)CNC1=O)CC(C)C)C(C)C1OC1c1ccccc1" YNP InChI InChI 1.03 "InChI=1S/C35H43ClN2O8/c1-20(2)16-29-35(42)44-27(22(4)31-32(46-31)24-10-7-6-8-11-24)12-9-13-30(39)38-26(33(40)37-19-21(3)34(41)45-29)18-23-14-15-28(43-5)25(36)17-23/h6-11,13-15,17,20-22,26-27,29,31-32H,12,16,18-19H2,1-5H3,(H,37,40)(H,38,39)/b13-9+/t21-,22+,26+,27+,29+,31-,32-/m1/s1" YNP InChIKey InChI 1.03 PSNOPSMXOBPNNV-XUMGCJJFSA-N YNP SMILES_CANONICAL CACTVS 3.385 "COc1ccc(C[C@@H]2NC(=O)/C=C/C[C@H](OC(=O)[C@H](CC(C)C)OC(=O)[C@H](C)CNC2=O)[C@H](C)[C@H]3O[C@@H]3c4ccccc4)cc1Cl" YNP SMILES CACTVS 3.385 "COc1ccc(C[CH]2NC(=O)C=CC[CH](OC(=O)[CH](CC(C)C)OC(=O)[CH](C)CNC2=O)[CH](C)[CH]3O[CH]3c4ccccc4)cc1Cl" YNP SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C[C@@H]1CNC(=O)[C@@H](NC(=O)/C=C/C[C@H](OC(=O)[C@@H](OC1=O)CC(C)C)[C@H](C)[C@@H]2[C@H](O2)c3ccccc3)Cc4ccc(c(c4)Cl)OC" YNP SMILES "OpenEye OEToolkits" 2.0.7 "CC1CNC(=O)C(NC(=O)C=CCC(OC(=O)C(OC1=O)CC(C)C)C(C)C2C(O2)c3ccccc3)Cc4ccc(c(c4)Cl)OC" # # 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 YNP "SYSTEMATIC NAME" ACDLabs 12.01 "(3S,6R,10S,13E,16S)-10-[(3-chloro-4-methoxyphenyl)methyl]-6-methyl-3-(2-methylpropyl)-16-{(1S)-1-[(2R,3R)-3-phenyloxiran-2-yl]ethyl}-1,4-dioxa-8,11-diazacyclohexadec-13-ene-2,5,9,12-tetrone" YNP "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "(3~{S},6~{R},10~{S},13~{E},16~{S})-10-[(3-chloranyl-4-methoxy-phenyl)methyl]-6-methyl-3-(2-methylpropyl)-16-[(1~{S})-1-[(2~{R},3~{R})-3-phenyloxiran-2-yl]ethyl]-1,4-dioxa-8,11-diazacyclohexadec-13-ene-2,5,9,12-tetrone" # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site YNP "Create component" 2021-03-15 RCSB YNP "Initial release" 2021-09-08 RCSB ##