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.pdbx_backbone_atom_flag
_chem_comp_atom.pdbx_n_terminal_atom_flag
_chem_comp_atom.pdbx_c_terminal_atom_flag
_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 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 N N N 324.717 201.030 304.204 1.215 -3.092 0.590 C2 YNP 2
YNP C4 C2 C 0 1 N N N 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 N N N 324.812 201.700 307.851 3.562 0.736 -1.323 C5 YNP 4
YNP C6 C4 C 0 1 N N N 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 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 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 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 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 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 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 N N N 322.609 206.744 303.026 -2.943 2.260 0.650 C10 YNP 12
YNP C11 C8 C 0 1 N N N 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 N N N 323.845 203.494 301.808 -2.192 -1.456 0.358 C12 YNP 14
YNP C13 C10 C 0 1 N N N 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 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 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 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 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 N N N 322.658 208.106 302.318 -4.294 2.728 0.106 C18 YNP 20
YNP C19 C16 C 0 1 N N N 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 N N N 321.863 208.140 301.018 -5.372 1.706 0.470 C20 YNP 22
YNP C21 C18 C 0 1 N N R N N N 322.754 207.571 299.836 -6.788 1.945 -0.057 C21 YNP 23
YNP C22 C19 C 0 1 Y N N N 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 N 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 N 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 N 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 N 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 N 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 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 N 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 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 N 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 N 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 N 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 N 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 N 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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
#
loop_
_software.name
_software.version
_software.description
rdkit 2025.03.3 'Core functionality.'
pdbeccdutils 1.0.0 'Wrapper to provide 2D templates and molecular fragments.'
#
loop_
_pdbe_chem_comp_atom_depiction.comp_id
_pdbe_chem_comp_atom_depiction.atom_id
_pdbe_chem_comp_atom_depiction.element
_pdbe_chem_comp_atom_depiction.model_Cartn_x
_pdbe_chem_comp_atom_depiction.model_Cartn_y
_pdbe_chem_comp_atom_depiction.pdbx_ordinal
YNP N1 N 6.897 0.750 1
YNP C2 C 8.196 3.000 2
YNP C4 C 6.897 -0.750 3
YNP C5 C 8.196 -1.500 4
YNP C6 C 10.794 -1.500 5
YNP O2 O 10.794 -3.000 6
YNP N2 N 9.495 -0.750 7
YNP O4 O 14.691 3.750 8
YNP C7 C 12.093 -0.750 9
YNP O6 O 9.495 5.250 10
YNP C8 C 13.392 -1.500 11
YNP C10 C 14.691 0.750 12
YNP C11 C 13.392 3.000 13
YNP C12 C 12.093 3.750 14
YNP C13 C 9.495 3.750 15
YNP C14 C 12.093 5.250 16
YNP C15 C 13.392 6.000 17
YNP C16 C 14.691 5.250 18
YNP C17 C 13.392 7.500 19
YNP C18 C 15.990 1.500 20
YNP C19 C 15.990 3.000 21
YNP C20 C 17.290 0.750 22
YNP C21 C 18.790 0.750 23
YNP C22 C 20.088 1.500 24
YNP C23 C 20.088 3.000 25
YNP C24 C 21.387 3.750 26
YNP C25 C 22.687 3.000 27
YNP C26 C 22.687 1.500 28
YNP C27 C 21.387 0.750 29
YNP C28 C 8.196 -3.000 30
YNP C29 C 6.897 -3.750 31
YNP C3 C 8.196 1.500 32
YNP C30 C 5.598 -3.000 33
YNP C31 C 4.299 -3.750 34
YNP C32 C 4.299 -5.250 35
YNP C33 C 5.598 -6.000 36
YNP C34 C 6.897 -5.250 37
YNP C35 C 3.000 -7.500 38
YNP C49 C 6.897 3.750 39
YNP C9 C 14.691 -0.750 40
YNP O1 O 5.598 -1.500 41
YNP O3 O 13.392 1.500 42
YNP O5 O 10.794 3.000 43
YNP O7 O 18.040 -0.549 44
YNP O8 O 3.000 -6.000 45
YNP CL1 Cl 3.000 -3.000 46
#
loop_
_pdbe_chem_comp_bond_depiction.comp_id
_pdbe_chem_comp_bond_depiction.atom_id_1
_pdbe_chem_comp_bond_depiction.atom_id_2
_pdbe_chem_comp_bond_depiction.value_order
_pdbe_chem_comp_bond_depiction.bond_dir
_pdbe_chem_comp_bond_depiction.pdbx_ordinal
YNP C25 C24 SINGLE NONE 1
YNP C25 C26 DOUBLE NONE 2
YNP C24 C23 DOUBLE NONE 3
YNP C26 C27 SINGLE NONE 4
YNP C23 C22 SINGLE NONE 5
YNP C27 C22 DOUBLE NONE 6
YNP C21 C22 SINGLE BEGINWEDGE 7
YNP C17 C15 SINGLE NONE 8
YNP C16 C15 SINGLE NONE 9
YNP C21 O7 SINGLE NONE 10
YNP C21 C20 SINGLE NONE 11
YNP C15 C14 SINGLE NONE 12
YNP C20 O7 SINGLE BEGINDASH 13
YNP C20 C18 SINGLE NONE 14
YNP C12 C14 SINGLE BEGINWEDGE 15
YNP O4 C11 DOUBLE NONE 16
YNP C12 C11 SINGLE NONE 17
YNP C12 O5 SINGLE NONE 18
YNP C11 O3 SINGLE NONE 19
YNP C18 C10 SINGLE NONE 20
YNP C18 C19 SINGLE BEGINDASH 21
YNP O3 C10 SINGLE NONE 22
YNP C10 C9 SINGLE BEGINDASH 23
YNP C2 C49 SINGLE BEGINWEDGE 24
YNP O5 C13 SINGLE NONE 25
YNP C13 C2 SINGLE NONE 26
YNP C13 O6 DOUBLE NONE 27
YNP C2 C3 SINGLE NONE 28
YNP C9 C8 SINGLE ENDUPRIGHT 29
YNP C3 N1 SINGLE NONE 30
YNP C8 C7 DOUBLE NONE 31
YNP C7 C6 SINGLE ENDUPRIGHT 32
YNP N1 C4 SINGLE NONE 33
YNP C6 N2 SINGLE NONE 34
YNP C6 O2 DOUBLE NONE 35
YNP N2 C5 SINGLE NONE 36
YNP C4 C5 SINGLE NONE 37
YNP C4 O1 DOUBLE NONE 38
YNP C5 C28 SINGLE BEGINWEDGE 39
YNP C34 C33 DOUBLE NONE 40
YNP C34 C29 SINGLE NONE 41
YNP C28 C29 SINGLE NONE 42
YNP C33 C32 SINGLE NONE 43
YNP C29 C30 DOUBLE NONE 44
YNP C32 O8 SINGLE NONE 45
YNP C32 C31 DOUBLE NONE 46
YNP C30 C31 SINGLE NONE 47
YNP O8 C35 SINGLE NONE 48
YNP C31 CL1 SINGLE NONE 49
#
loop_
_pdbe_chem_comp_substructure.comp_id
_pdbe_chem_comp_substructure.substructure_name
_pdbe_chem_comp_substructure.id
_pdbe_chem_comp_substructure.substructure_type
_pdbe_chem_comp_substructure.substructure_smiles
_pdbe_chem_comp_substructure.substructure_inchis
_pdbe_chem_comp_substructure.substructure_inchikeys
YNP MurckoScaffold S1 scaffold 'O=C1/C=C/C[C@@H](C[C@H]2O[C@@H]2c2ccccc2)OC(=O)COC(=O)CCNC(=O)[C@H](Cc2ccccc2)N1' InChI=1S/C28H30N2O7/c31-24-13-7-12-21(17-23-27(37-23)20-10-5-2-6-11-20)36-26(33)18-35-25(32)14-15-29-28(34)22(30-24)16-19-8-3-1-4-9-19/h1-11,13,21-23,27H,12,14-18H2,(H,29,34)(H,30,31)/b13-7+/t21-,22-,23+,27+/m0/s1 HVNRHEWFHKQQJQ-SFXMHJNVSA-N
YNP amide F1 fragment CC(N)=O InChI=1S/C2H5NO/c1-2(3)4/h1H3,(H2,3,4) DLFVBJFMPXGRIB-UHFFFAOYSA-N
YNP peptide F2 fragment NCC=O InChI=1S/C2H5NO/c3-1-2-4/h2H,1,3H2 LYIIBVSRGJSHAV-UHFFFAOYSA-N
YNP phenyl F3 fragment c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-UHFFFAOYSA-N
#
loop_
_pdbe_chem_comp_substructure_mapping.comp_id
_pdbe_chem_comp_substructure_mapping.atom_id
_pdbe_chem_comp_substructure_mapping.substructure_id
_pdbe_chem_comp_substructure_mapping.substructure_ordinal
YNP N1 S1 1
YNP C2 S1 1
YNP C4 S1 1
YNP C5 S1 1
YNP C6 S1 1
YNP O2 S1 1
YNP N2 S1 1
YNP O4 S1 1
YNP C7 S1 1
YNP O6 S1 1
YNP C8 S1 1
YNP C10 S1 1
YNP C11 S1 1
YNP C12 S1 1
YNP C13 S1 1
YNP C18 S1 1
YNP C20 S1 1
YNP C21 S1 1
YNP C22 S1 1
YNP C23 S1 1
YNP C24 S1 1
YNP C25 S1 1
YNP C26 S1 1
YNP C27 S1 1
YNP C28 S1 1
YNP C29 S1 1
YNP C3 S1 1
YNP C30 S1 1
YNP C31 S1 1
YNP C32 S1 1
YNP C33 S1 1
YNP C34 S1 1
YNP C9 S1 1
YNP O1 S1 1
YNP O3 S1 1
YNP O5 S1 1
YNP O7 S1 1
YNP N1 F1 1
YNP C4 F1 1
YNP O1 F1 1
YNP C5 F1 1
YNP N2 F1 2
YNP C6 F1 2
YNP O2 F1 2
YNP C7 F1 2
YNP O1 F2 1
YNP C4 F2 1
YNP C5 F2 1
YNP N2 F2 1
YNP C22 F3 1
YNP C23 F3 1
YNP C24 F3 1
YNP C25 F3 1
YNP C26 F3 1
YNP C27 F3 1
YNP C29 F3 2
YNP C34 F3 2
YNP C33 F3 2
YNP C32 F3 2
YNP C31 F3 2
YNP C30 F3 2
#
_pdbe_chem_comp_rdkit_properties.comp_id YNP
_pdbe_chem_comp_rdkit_properties.exactmw 654.271
_pdbe_chem_comp_rdkit_properties.amw 655.188
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 10
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 2
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 13
_pdbe_chem_comp_rdkit_properties.NumHBD 2
_pdbe_chem_comp_rdkit_properties.NumHBA 8
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 46
_pdbe_chem_comp_rdkit_properties.NumAtoms 89
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 11
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 2
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.486
_pdbe_chem_comp_rdkit_properties.NumRings 4
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 2
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 2
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 1
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 2
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 2
_pdbe_chem_comp_rdkit_properties.NumSpiroAtoms 0
_pdbe_chem_comp_rdkit_properties.NumBridgeheadAtoms 0
_pdbe_chem_comp_rdkit_properties.NumAtomStereoCenters 7
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 335.214
_pdbe_chem_comp_rdkit_properties.tpsa 132.560
_pdbe_chem_comp_rdkit_properties.CrippenClogP 4.162
_pdbe_chem_comp_rdkit_properties.CrippenMR 170.862
_pdbe_chem_comp_rdkit_properties.chi0v 22.794
_pdbe_chem_comp_rdkit_properties.chi1v 11.911
_pdbe_chem_comp_rdkit_properties.chi2v 4.945
_pdbe_chem_comp_rdkit_properties.chi3v 4.945
_pdbe_chem_comp_rdkit_properties.chi4v 2.935
_pdbe_chem_comp_rdkit_properties.chi0n 65.038
_pdbe_chem_comp_rdkit_properties.chi1n 32.927
_pdbe_chem_comp_rdkit_properties.chi2n 4.679
_pdbe_chem_comp_rdkit_properties.chi3n 4.679
_pdbe_chem_comp_rdkit_properties.chi4n 2.754
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -3.890
_pdbe_chem_comp_rdkit_properties.kappa1 9.167
_pdbe_chem_comp_rdkit_properties.kappa2 16.092
_pdbe_chem_comp_rdkit_properties.kappa3 9.560
_pdbe_chem_comp_rdkit_properties.Phi 3.207
#
loop_
_pdbe_chem_comp_external_mappings.comp_id
_pdbe_chem_comp_external_mappings.source
_pdbe_chem_comp_external_mappings.resource
_pdbe_chem_comp_external_mappings.resource_id
YNP UniChem ChEBI 227104
YNP UniChem ZINC ZINC000161134876
YNP UniChem PubChem 6504906
#
loop_
_pdbe_chem_comp_rdkit_conformer.comp_id
_pdbe_chem_comp_rdkit_conformer.atom_id
_pdbe_chem_comp_rdkit_conformer.Cartn_x_rdkit
_pdbe_chem_comp_rdkit_conformer.Cartn_y_rdkit
_pdbe_chem_comp_rdkit_conformer.Cartn_z_rdkit
_pdbe_chem_comp_rdkit_conformer.rdkit_method
_pdbe_chem_comp_rdkit_conformer.rdkit_ordinal
YNP N1 -3.525 2.123 -2.227 ETKDGv3 1
YNP C2 -1.541 3.588 -2.194 ETKDGv3 2
YNP C4 -3.424 0.842 -1.592 ETKDGv3 3
YNP C5 -3.894 -0.396 -2.313 ETKDGv3 4
YNP C6 -1.929 -1.925 -2.759 ETKDGv3 5
YNP O2 -2.034 -1.939 -4.014 ETKDGv3 6
YNP N2 -3.049 -1.537 -1.952 ETKDGv3 7
YNP O4 -0.433 0.703 1.261 ETKDGv3 8
YNP C7 -0.651 -2.326 -2.146 ETKDGv3 9
YNP O6 -0.232 1.580 -2.226 ETKDGv3 10
YNP C8 -0.305 -1.940 -0.915 ETKDGv3 11
YNP C10 1.303 -1.580 0.992 ETKDGv3 12
YNP C11 0.702 0.844 0.729 ETKDGv3 13
YNP C12 1.127 2.184 0.198 ETKDGv3 14
YNP C13 -0.551 2.624 -1.593 ETKDGv3 15
YNP C14 1.769 3.044 1.301 ETKDGv3 16
YNP C15 3.066 2.455 1.912 ETKDGv3 17
YNP C16 4.194 2.327 0.875 ETKDGv3 18
YNP C17 3.533 3.330 3.082 ETKDGv3 19
YNP C18 2.485 -2.223 1.766 ETKDGv3 20
YNP C19 2.460 -1.796 3.239 ETKDGv3 21
YNP C20 3.838 -1.824 1.150 ETKDGv3 22
YNP C21 4.357 -2.690 0.063 ETKDGv3 23
YNP C22 5.353 -2.036 -0.846 ETKDGv3 24
YNP C23 6.746 -2.542 -0.909 ETKDGv3 25
YNP C24 7.631 -1.972 -1.738 ETKDGv3 26
YNP C25 7.219 -0.841 -2.596 ETKDGv3 27
YNP C26 5.959 -0.391 -2.553 ETKDGv3 28
YNP C27 4.979 -1.021 -1.644 ETKDGv3 29
YNP C28 -5.383 -0.693 -2.039 ETKDGv3 30
YNP C29 -5.695 -0.946 -0.582 ETKDGv3 31
YNP C3 -2.959 3.341 -1.649 ETKDGv3 32
YNP C30 -5.986 0.072 0.246 ETKDGv3 33
YNP C31 -6.259 -0.178 1.677 ETKDGv3 34
YNP C32 -6.224 -1.430 2.167 ETKDGv3 35
YNP C33 -5.912 -2.558 1.247 ETKDGv3 36
YNP C34 -5.665 -2.327 -0.047 ETKDGv3 37
YNP C35 -6.470 -2.915 4.156 ETKDGv3 38
YNP C49 -1.103 5.034 -1.928 ETKDGv3 39
YNP C9 1.017 -2.335 -0.323 ETKDGv3 40
YNP O1 -2.974 0.752 -0.417 ETKDGv3 41
YNP O3 1.615 -0.215 0.692 ETKDGv3 42
YNP O5 0.007 2.891 -0.336 ETKDGv3 43
YNP O7 4.836 -2.791 1.387 ETKDGv3 44
YNP O8 -6.483 -1.638 3.529 ETKDGv3 45
YNP CL1 -6.619 1.189 2.722 ETKDGv3 46
YNP H1 -3.927 2.179 -3.190 ETKDGv3 47
YNP H2 -1.554 3.446 -3.298 ETKDGv3 48
YNP H3 -3.804 -0.210 -3.406 ETKDGv3 49
YNP H4 -3.105 -1.908 -0.977 ETKDGv3 50
YNP H5 0.050 -2.897 -2.743 ETKDGv3 51
YNP H6 -0.974 -1.316 -0.338 ETKDGv3 52
YNP H7 0.398 -1.644 1.638 ETKDGv3 53
YNP H8 1.865 2.034 -0.620 ETKDGv3 54
YNP H9 1.993 4.049 0.879 ETKDGv3 55
YNP H10 1.019 3.191 2.109 ETKDGv3 56
YNP H11 2.853 1.447 2.323 ETKDGv3 57
YNP H12 4.369 3.297 0.363 ETKDGv3 58
YNP H13 5.137 2.008 1.369 ETKDGv3 59
YNP H14 3.948 1.553 0.120 ETKDGv3 60
YNP H15 4.436 2.889 3.557 ETKDGv3 61
YNP H16 2.738 3.394 3.856 ETKDGv3 62
YNP H17 3.777 4.356 2.732 ETKDGv3 63
YNP H18 2.369 -3.331 1.756 ETKDGv3 64
YNP H19 2.535 -0.693 3.333 ETKDGv3 65
YNP H20 3.310 -2.259 3.786 ETKDGv3 66
YNP H21 1.518 -2.133 3.721 ETKDGv3 67
YNP H22 4.233 -0.790 1.256 ETKDGv3 68
YNP H23 3.803 -3.600 -0.249 ETKDGv3 69
YNP H24 7.052 -3.372 -0.285 ETKDGv3 70
YNP H25 8.648 -2.338 -1.782 ETKDGv3 71
YNP H26 7.938 -0.382 -3.262 ETKDGv3 72
YNP H27 5.655 0.435 -3.183 ETKDGv3 73
YNP H28 3.962 -0.650 -1.625 ETKDGv3 74
YNP H29 -5.686 -1.580 -2.637 ETKDGv3 75
YNP H30 -5.998 0.156 -2.411 ETKDGv3 76
YNP H31 -2.953 3.289 -0.538 ETKDGv3 77
YNP H32 -3.618 4.191 -1.929 ETKDGv3 78
YNP H33 -6.012 1.090 -0.125 ETKDGv3 79
YNP H34 -5.879 -3.576 1.612 ETKDGv3 80
YNP H35 -5.436 -3.157 -0.704 ETKDGv3 81
YNP H36 -5.464 -3.377 4.062 ETKDGv3 82
YNP H37 -6.705 -2.793 5.233 ETKDGv3 83
YNP H38 -7.238 -3.574 3.697 ETKDGv3 84
YNP H39 -0.069 5.196 -2.302 ETKDGv3 85
YNP H40 -1.133 5.263 -0.841 ETKDGv3 86
YNP H41 -1.776 5.740 -2.459 ETKDGv3 87
YNP H42 1.824 -2.115 -1.055 ETKDGv3 88
YNP H43 0.998 -3.431 -0.140 ETKDGv3 89
#