data_YMM
#
_chem_comp.id YMM
_chem_comp.name
'(1S,2S)-1-hydroxy-2-((S)-4-methyl-2-(((((1s,4S)-4-propylcyclohexyl)oxy)carbonyl)amino)pentanamido)-3-((S)-2-oxopyrrolidin-3-yl)propane-1-sulfonic acid'
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula 'C23 H41 N3 O8 S'
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2021-03-12
_chem_comp.pdbx_modified_date 2024-09-27
_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 519.652
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code YMM
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag Y
_chem_comp.pdbx_ideal_coordinates_details Corina
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code 7LZY
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site RCSB
_chem_comp.pdbx_pcm Y
#
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
YMM C1 C1 C 0 1 N N N N N N 10.583 7.567 22.133 2.360 -0.007 0.238 C1 YMM 1
YMM C10 C2 C 0 1 N N S N N N 7.198 6.127 19.073 -4.285 2.264 -0.448 C10 YMM 2
YMM C11 C3 C 0 1 N N N N N N 6.691 6.974 17.923 -5.344 2.889 -1.329 C11 YMM 3
YMM C12 C4 C 0 1 N N N N N N 5.506 7.655 19.809 -4.597 4.585 0.071 C12 YMM 4
YMM C13 C5 C 0 1 N N N N N N 6.115 6.305 20.131 -4.125 3.265 0.720 C13 YMM 5
YMM C14 C6 C 0 1 N N S N N N 8.026 2.367 19.614 -4.185 -0.998 1.590 C14 YMM 6
YMM C15 C7 C 0 1 N N N N N N 10.430 9.920 22.534 4.720 0.318 0.383 C15 YMM 7
YMM C16 C8 C 0 1 N N N N N N 11.332 10.847 23.315 5.373 -0.986 -0.079 C16 YMM 8
YMM C17 C9 C 0 1 N N N N N N 11.114 12.300 22.895 6.710 -0.675 -0.756 C17 YMM 9
YMM C18 C10 C 0 1 N N N N N N 9.658 12.722 23.060 7.632 0.034 0.238 C18 YMM 10
YMM C19 C11 C 0 1 N N N N N N 9.436 14.173 22.646 8.968 0.345 -0.438 C19 YMM 11
YMM C2 C12 C 0 1 N N S N N N 10.813 5.147 22.085 -0.037 -0.307 -0.086 C2 YMM 12
YMM C20 C13 C 0 1 N N N N N N 10.102 15.214 23.530 9.934 0.940 0.589 C20 YMM 13
YMM C21 C14 C 0 1 N N N N N N 9.531 16.595 23.315 11.270 1.252 -0.088 C21 YMM 14
YMM C22 C15 C 0 1 N N N N N N 8.751 11.764 22.297 6.978 1.337 0.701 C22 YMM 15
YMM C23 C16 C 0 1 N N N N N N 8.979 10.308 22.705 5.642 1.026 1.377 C23 YMM 16
YMM C3 C17 C 0 1 N N N N N N 11.448 4.092 22.985 -0.171 -1.693 -0.720 C3 YMM 17
YMM C4 C18 C 0 1 N N N N N N 12.957 4.249 23.164 1.011 -1.942 -1.658 C4 YMM 18
YMM C5 C19 C 0 1 N N N N N N 13.695 3.828 21.903 0.944 -3.373 -2.196 C5 YMM 19
YMM C6 C20 C 0 1 N N N N N N 13.451 3.451 24.356 0.952 -0.955 -2.826 C6 YMM 20
YMM C7 C21 C 0 1 N N N N N N 9.396 4.752 21.684 -1.261 -0.012 0.741 C7 YMM 21
YMM C8 C22 C 0 1 N N S N N N 7.943 3.854 19.912 -3.667 0.299 0.965 C8 YMM 22
YMM C9 C23 C 0 1 N N N N N N 7.520 4.681 18.701 -4.753 0.904 0.073 C9 YMM 23
YMM N1 N1 N 0 1 N N N N N N 10.849 6.428 22.761 1.151 -0.276 0.771 N1 YMM 24
YMM N2 N2 N 0 1 N N N N N N 9.227 4.332 20.427 -2.477 0.012 0.161 N2 YMM 25
YMM N3 N3 N 0 1 N N N N N N 5.692 7.734 18.364 -5.502 4.186 -1.013 N3 YMM 26
YMM O1 O1 O 0 1 N N N N N N 10.372 7.706 20.943 2.463 0.213 -0.953 O1 YMM 27
YMM O2 O2 O 0 1 N N N N N N 7.148 6.973 16.770 -5.960 2.305 -2.195 O2 YMM 28
YMM O3 O3 O 0 1 N N N N N N 6.749 1.832 19.322 -5.410 -0.739 2.279 O3 YMM 29
YMM O4 O4 O 0 1 N N N N N N 8.477 4.835 22.492 -1.152 0.203 1.930 O4 YMM 30
YMM O5 O5 O 0 1 N N N N N N 10.605 8.563 23.042 3.451 0.022 1.025 O5 YMM 31
YMM H1 H1 H 0 1 N N N N N N 8.120 6.590 19.454 -3.347 2.161 -0.993 H1 YMM 32
YMM H2 H2 H 0 1 N N N N N N 6.038 8.467 20.326 -5.129 5.195 0.801 H2 YMM 33
YMM H3 H3 H 0 1 N N N N N N 4.440 7.687 20.077 -3.744 5.134 -0.329 H3 YMM 34
YMM H4 H4 H 0 1 N N N N N N 5.361 5.508 20.056 -4.766 2.991 1.559 H4 YMM 35
YMM H5 H5 H 0 1 N N N N N N 6.551 6.304 21.141 -3.083 3.335 1.034 H5 YMM 36
YMM S1 S1 S 0 1 N Y N N N N 8.690 2.196 18.793 -4.472 -2.226 0.285 S1 YMM 37
YMM H7 H7 H 0 1 N N N N N N 8.369 1.893 20.545 -3.447 -1.383 2.294 H7 YMM 38
YMM H8 H8 H 0 1 N N N N N N 10.697 9.963 21.468 4.549 0.964 -0.478 H8 YMM 39
YMM H9 H9 H 0 1 N N N N N N 11.111 10.745 24.388 5.544 -1.632 0.782 H9 YMM 40
YMM H10 H10 H 0 1 N N N N N N 12.380 10.571 23.128 4.716 -1.491 -0.788 H10 YMM 41
YMM H11 H11 H 0 1 N N N N N N 11.400 12.413 21.839 7.176 -1.603 -1.085 H11 YMM 42
YMM H12 H12 H 0 1 N N N N N N 11.746 12.950 23.518 6.539 -0.029 -1.617 H12 YMM 43
YMM H13 H13 H 0 1 N N N N N N 9.407 12.639 24.128 7.803 -0.612 1.099 H13 YMM 44
YMM H14 H14 H 0 1 N N N N N N 9.824 14.297 21.624 9.392 -0.572 -0.846 H14 YMM 45
YMM H15 H15 H 0 1 N N N N N N 8.353 14.366 22.653 8.809 1.061 -1.245 H15 YMM 46
YMM H16 H16 H 0 1 N N N N N N 11.416 5.214 21.168 0.061 0.443 -0.871 H16 YMM 47
YMM H17 H17 H 0 1 N N N N N N 9.956 14.930 24.583 9.510 1.858 0.997 H17 YMM 48
YMM H18 H18 H 0 1 N N N N N N 11.178 15.236 23.302 10.093 0.224 1.395 H18 YMM 49
YMM H19 H19 H 0 1 N N N N N N 10.043 17.311 23.975 11.958 1.676 0.644 H19 YMM 50
YMM H20 H20 H 0 1 N N N N N N 9.678 16.893 22.266 11.694 0.334 -0.495 H20 YMM 51
YMM H21 H21 H 0 1 N N N N N N 8.456 16.587 23.547 11.111 1.968 -0.894 H21 YMM 52
YMM H22 H22 H 0 1 N N N N N N 8.953 11.866 21.220 7.635 1.842 1.409 H22 YMM 53
YMM H23 H23 H 0 1 N N N N N N 7.703 12.030 22.501 6.808 1.984 -0.161 H23 YMM 54
YMM H24 H24 H 0 1 N N N N N N 8.694 10.181 23.760 5.176 1.955 1.707 H24 YMM 55
YMM H25 H25 H 0 1 N N N N N N 8.355 9.656 22.076 5.812 0.380 2.238 H25 YMM 56
YMM H26 H26 H 0 1 N N N N N N 10.975 4.154 23.976 -0.180 -2.452 0.063 H26 YMM 57
YMM H27 H27 H 0 1 N N N N N N 11.254 3.102 22.547 -1.101 -1.745 -1.286 H27 YMM 58
YMM H28 H28 H 0 1 N N N N N N 13.171 5.312 23.349 1.944 -1.803 -1.112 H28 YMM 59
YMM H29 H29 H 0 1 N N N N N N 14.778 3.949 22.054 0.011 -3.512 -2.742 H29 YMM 60
YMM H30 H30 H 0 1 N N N N N N 13.471 2.774 21.682 1.786 -3.550 -2.864 H30 YMM 61
YMM H31 H31 H 0 1 N N N N N N 13.370 4.456 21.061 0.986 -4.076 -1.364 H31 YMM 62
YMM H32 H32 H 0 1 N N N N N N 12.908 3.766 25.259 1.000 0.064 -2.443 H32 YMM 63
YMM H33 H33 H 0 1 N N N N N N 13.275 2.380 24.178 1.795 -1.133 -3.495 H33 YMM 64
YMM H34 H34 H 0 1 N N N N N N 14.528 3.628 24.495 0.019 -1.094 -3.373 H34 YMM 65
YMM H35 H35 H 0 1 N N N N N N 7.182 3.996 20.693 -3.411 1.005 1.755 H35 YMM 66
YMM H36 H36 H 0 1 N N N N N N 6.625 4.223 18.254 -5.669 1.031 0.650 H36 YMM 67
YMM H37 H37 H 0 1 N N N N N N 8.339 4.678 17.967 -4.943 0.238 -0.769 H37 YMM 68
YMM H38 H38 H 0 1 N N N N N N 11.082 6.455 23.733 1.068 -0.448 1.722 H38 YMM 69
YMM H39 H39 H 0 1 N N N N N N 10.014 4.345 19.810 -2.564 -0.160 -0.790 H39 YMM 70
YMM H40 H40 H 0 1 N N N N N N 5.126 8.302 17.766 -6.132 4.782 -1.447 H40 YMM 71
YMM H41 H41 H 0 1 N N N N N N 6.828 0.903 19.140 -6.114 -0.395 1.713 H41 YMM 72
YMM O6 O6 O 0 1 N Y N N N N ? ? ? -5.489 -1.781 -0.603 O6 YMM 73
YMM O7 O7 O 0 1 N Y N N N N ? ? ? -3.238 -2.728 -0.207 O7 YMM 74
YMM O8 O8 O 0 1 N Y N N N N ? ? ? -5.098 -3.409 1.009 O8 YMM 75
YMM H6 H6 H 0 1 N Y N N N N ? ? ? -5.311 -4.155 0.431 H6 YMM 76
#
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
YMM O2 C11 DOUB N N 1
YMM C11 N3 SING N N 2
YMM C11 C10 SING N N 3
YMM N3 C12 SING N N 4
YMM C9 C10 SING N N 5
YMM C9 C8 SING N N 6
YMM C10 C13 SING N N 7
YMM O3 C14 SING N N 8
YMM C14 C8 SING N N 9
YMM C12 C13 SING N N 10
YMM C8 N2 SING N N 11
YMM N2 C7 SING N N 12
YMM O1 C1 DOUB N N 13
YMM C7 C2 SING N N 14
YMM C7 O4 DOUB N N 15
YMM C5 C4 SING N N 16
YMM C2 N1 SING N N 17
YMM C2 C3 SING N N 18
YMM C1 N1 SING N N 19
YMM C1 O5 SING N N 20
YMM C22 C23 SING N N 21
YMM C22 C18 SING N N 22
YMM C15 C23 SING N N 23
YMM C15 O5 SING N N 24
YMM C15 C16 SING N N 25
YMM C19 C18 SING N N 26
YMM C19 C20 SING N N 27
YMM C17 C18 SING N N 28
YMM C17 C16 SING N N 29
YMM C3 C4 SING N N 30
YMM C4 C6 SING N N 31
YMM C21 C20 SING N N 32
YMM C10 H1 SING N N 33
YMM C12 H2 SING N N 34
YMM C12 H3 SING N N 35
YMM C13 H4 SING N N 36
YMM C13 H5 SING N N 37
YMM C14 S1 SING N N 38
YMM C14 H7 SING N N 39
YMM C15 H8 SING N N 40
YMM C16 H9 SING N N 41
YMM C16 H10 SING N N 42
YMM C17 H11 SING N N 43
YMM C17 H12 SING N N 44
YMM C18 H13 SING N N 45
YMM C19 H14 SING N N 46
YMM C19 H15 SING N N 47
YMM C2 H16 SING N N 48
YMM C20 H17 SING N N 49
YMM C20 H18 SING N N 50
YMM C21 H19 SING N N 51
YMM C21 H20 SING N N 52
YMM C21 H21 SING N N 53
YMM C22 H22 SING N N 54
YMM C22 H23 SING N N 55
YMM C23 H24 SING N N 56
YMM C23 H25 SING N N 57
YMM C3 H26 SING N N 58
YMM C3 H27 SING N N 59
YMM C4 H28 SING N N 60
YMM C5 H29 SING N N 61
YMM C5 H30 SING N N 62
YMM C5 H31 SING N N 63
YMM C6 H32 SING N N 64
YMM C6 H33 SING N N 65
YMM C6 H34 SING N N 66
YMM C8 H35 SING N N 67
YMM C9 H36 SING N N 68
YMM C9 H37 SING N N 69
YMM N1 H38 SING N N 70
YMM N2 H39 SING N N 71
YMM N3 H40 SING N N 72
YMM O3 H41 SING N N 73
YMM S1 O6 DOUB N N 74
YMM S1 O7 DOUB N N 75
YMM S1 O8 SING N N 76
YMM O8 H6 SING N N 77
#
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
YMM SMILES ACDLabs 12.01 'CC(C)CC(NC(=O)OC1CCC(CCC)CC1)C(=O)NC(CC1CCNC1=O)C(O)S(=O)(=O)O'
YMM InChI InChI 1.03 'InChI=1S/C23H41N3O8S/c1-4-5-15-6-8-17(9-7-15)34-23(30)26-18(12-14(2)3)21(28)25-19(22(29)35(31,32)33)13-16-10-11-24-20(16)27/h14-19,22,29H,4-13H2,1-3H3,(H,24,27)(H,25,28)(H,26,30)(H,31,32,33)/t15-,16-,17-,18-,19-,22-/m0/s1'
YMM InChIKey InChI 1.03 VCQYBHSDNWQLAS-LXYCOOOUSA-N
YMM SMILES_CANONICAL CACTVS 3.385 'CCC[C@@H]1CC[C@H](CC1)OC(=O)N[C@@H](CC(C)C)C(=O)N[C@@H](C[C@@H]2CCNC2=O)[C@@H](O)[S](O)(=O)=O'
YMM SMILES CACTVS 3.385 'CCC[CH]1CC[CH](CC1)OC(=O)N[CH](CC(C)C)C(=O)N[CH](C[CH]2CCNC2=O)[CH](O)[S](O)(=O)=O'
YMM SMILES_CANONICAL 'OpenEye OEToolkits' 2.0.7 'CCCC1CCC(CC1)OC(=O)N[C@@H](CC(C)C)C(=O)N[C@@H](C[C@@H]2CCNC2=O)C(O)S(=O)(=O)O'
YMM SMILES 'OpenEye OEToolkits' 2.0.7 'CCCC1CCC(CC1)OC(=O)NC(CC(C)C)C(=O)NC(CC2CCNC2=O)C(O)S(=O)(=O)O'
#
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
YMM 'SYSTEMATIC NAME' ACDLabs 12.01 '(1S,2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]-2-{[N-({[(1s,4S)-4-propylcyclohexyl]oxy}carbonyl)-L-leucyl]amino}propane-1-sulfonic acid'
YMM 'SYSTEMATIC NAME' 'OpenEye OEToolkits' 2.0.7 '(2~{S})-2-[[(2~{S})-4-methyl-2-[(4-propylcyclohexyl)oxycarbonylamino]pentanoyl]amino]-1-oxidanyl-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propane-1-sulfonic 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
YMM 'Create component' 2021-03-12 RCSB
YMM 'Initial release' 2021-03-24 RCSB
YMM 'Modify PCM' 2024-09-27 PDBE
#
_pdbx_chem_comp_pcm.pcm_id 1
_pdbx_chem_comp_pcm.comp_id YMM
_pdbx_chem_comp_pcm.modified_residue_id CYS
_pdbx_chem_comp_pcm.type None
_pdbx_chem_comp_pcm.category 'Covalent chemical modification'
_pdbx_chem_comp_pcm.position 'Amino-acid side chain'
_pdbx_chem_comp_pcm.polypeptide_position 'Any position'
_pdbx_chem_comp_pcm.comp_id_linking_atom C14
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom SG
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession ?
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession ?
#
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
YMM C1 C -2.291 -1.359 1
YMM C10 C 2.744 1.973 2
YMM C11 C 2.816 3.471 3
YMM C12 C 5.085 2.611 4
YMM C13 C 4.146 1.440 5
YMM C14 C 2.956 -0.950 6
YMM C15 C -3.699 0.856 7
YMM C16 C -5.036 1.534 8
YMM C17 C -5.124 3.030 9
YMM C18 C -3.866 3.854 10
YMM C19 C -3.952 5.351 11
YMM C2 C -0.932 -3.608 12
YMM C20 C -5.291 6.026 13
YMM C21 C -5.375 7.524 14
YMM C22 C -2.529 3.176 15
YMM C23 C -2.441 1.680 16
YMM C3 C -0.854 -5.086 17
YMM C4 C 0.522 -5.722 18
YMM C5 C 0.664 -7.208 19
YMM C6 C 1.756 -4.849 20
YMM C7 C 0.304 -2.884 21
YMM C8 C 1.594 -0.361 22
YMM C9 C 1.472 1.133 23
YMM N1 N -2.248 -2.882 24
YMM N2 N 0.294 -1.282 25
YMM N3 N 4.264 3.863 26
YMM O1 O -1.014 -0.559 27
YMM O2 O 1.649 4.410 28
YMM O3 O 4.172 -0.088 29
YMM O4 O 1.577 -3.688 30
YMM O5 O -3.622 -0.651 31
YMM S1 S 3.051 -2.338 32
YMM O6 O 1.615 -2.291 33
YMM O7 O 4.541 -2.285 34
YMM O8 O 3.050 -3.838 35
#
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
YMM O2 C11 DOUBLE NONE 1
YMM C11 N3 SINGLE NONE 2
YMM C11 C10 SINGLE NONE 3
YMM N3 C12 SINGLE NONE 4
YMM C10 C9 SINGLE BEGINWEDGE 5
YMM C8 C9 SINGLE BEGINWEDGE 6
YMM C10 C13 SINGLE NONE 7
YMM C14 O3 SINGLE BEGINWEDGE 8
YMM C14 C8 SINGLE NONE 9
YMM C12 C13 SINGLE NONE 10
YMM C8 N2 SINGLE NONE 11
YMM N2 C7 SINGLE NONE 12
YMM O1 C1 DOUBLE NONE 13
YMM C7 C2 SINGLE NONE 14
YMM C7 O4 DOUBLE NONE 15
YMM C5 C4 SINGLE NONE 16
YMM C2 N1 SINGLE NONE 17
YMM C2 C3 SINGLE BEGINDASH 18
YMM C1 N1 SINGLE NONE 19
YMM C1 O5 SINGLE NONE 20
YMM C22 C23 SINGLE NONE 21
YMM C22 C18 SINGLE NONE 22
YMM C15 C23 SINGLE NONE 23
YMM C15 O5 SINGLE BEGINDASH 24
YMM C15 C16 SINGLE NONE 25
YMM C18 C19 SINGLE BEGINWEDGE 26
YMM C19 C20 SINGLE NONE 27
YMM C17 C18 SINGLE NONE 28
YMM C17 C16 SINGLE NONE 29
YMM C3 C4 SINGLE NONE 30
YMM C4 C6 SINGLE NONE 31
YMM C21 C20 SINGLE NONE 32
YMM C14 S1 SINGLE NONE 33
YMM S1 O6 DOUBLE NONE 34
YMM S1 O7 DOUBLE NONE 35
YMM S1 O8 SINGLE NONE 36
#
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
YMM MurckoScaffold S1 scaffold 'O=C(CNC(=O)OC1CCCCC1)NCC[C@@H]1CCNC1=O' InChI=1S/C15H25N3O4/c19-13(16-8-6-11-7-9-17-14(11)20)10-18-15(21)22-12-4-2-1-3-5-12/h11-12H,1-10H2,(H,16,19)(H,17,20)(H,18,21)/t11-/m1/s1 OILPERPINNOUDS-LLVKDONJSA-N
YMM amide F1 fragment CC(N)=O InChI=1S/C2H5NO/c1-2(3)4/h1H3,(H2,3,4) DLFVBJFMPXGRIB-UHFFFAOYSA-N
YMM cyclohexane F2 fragment C1CCCCC1 InChI=1S/C6H12/c1-2-4-6-5-3-1/h1-6H2 XDTMQSROBMDMFD-UHFFFAOYSA-N
YMM peptide F3 fragment NCC=O InChI=1S/C2H5NO/c3-1-2-4/h2H,1,3H2 LYIIBVSRGJSHAV-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
YMM C1 S1 1
YMM C10 S1 1
YMM C11 S1 1
YMM C12 S1 1
YMM C13 S1 1
YMM C15 S1 1
YMM C16 S1 1
YMM C17 S1 1
YMM C18 S1 1
YMM C2 S1 1
YMM C22 S1 1
YMM C23 S1 1
YMM C7 S1 1
YMM C8 S1 1
YMM C9 S1 1
YMM N1 S1 1
YMM N2 S1 1
YMM N3 S1 1
YMM O1 S1 1
YMM O2 S1 1
YMM O4 S1 1
YMM O5 S1 1
YMM N2 F1 1
YMM C7 F1 1
YMM O4 F1 1
YMM C2 F1 1
YMM N3 F1 2
YMM C11 F1 2
YMM O2 F1 2
YMM C10 F1 2
YMM C15 F2 1
YMM C23 F2 1
YMM C22 F2 1
YMM C18 F2 1
YMM C17 F2 1
YMM C16 F2 1
YMM O4 F3 1
YMM C7 F3 1
YMM C2 F3 1
YMM N1 F3 1
#
_pdbe_chem_comp_rdkit_properties.comp_id YMM
_pdbe_chem_comp_rdkit_properties.exactmw 519.261
_pdbe_chem_comp_rdkit_properties.amw 519.661
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 11
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 5
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 17
_pdbe_chem_comp_rdkit_properties.NumHBD 5
_pdbe_chem_comp_rdkit_properties.NumHBA 8
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 35
_pdbe_chem_comp_rdkit_properties.NumAtoms 76
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 12
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 3
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.870
_pdbe_chem_comp_rdkit_properties.NumRings 2
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 0
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 2
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 2
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumSpiroAtoms 0
_pdbe_chem_comp_rdkit_properties.NumBridgeheadAtoms 0
_pdbe_chem_comp_rdkit_properties.NumAtomStereoCenters 4
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 265.378
_pdbe_chem_comp_rdkit_properties.tpsa 171.130
_pdbe_chem_comp_rdkit_properties.CrippenClogP 1.703
_pdbe_chem_comp_rdkit_properties.CrippenMR 128.734
_pdbe_chem_comp_rdkit_properties.chi0v 17.332
_pdbe_chem_comp_rdkit_properties.chi1v 9.679
_pdbe_chem_comp_rdkit_properties.chi2v 3.705
_pdbe_chem_comp_rdkit_properties.chi3v 3.705
_pdbe_chem_comp_rdkit_properties.chi4v 2.104
_pdbe_chem_comp_rdkit_properties.chi0n 57.516
_pdbe_chem_comp_rdkit_properties.chi1n 28.429
_pdbe_chem_comp_rdkit_properties.chi2n 3.057
_pdbe_chem_comp_rdkit_properties.chi3n 3.057
_pdbe_chem_comp_rdkit_properties.chi4n 1.771
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.920
_pdbe_chem_comp_rdkit_properties.kappa1 6.039
_pdbe_chem_comp_rdkit_properties.kappa2 13.405
_pdbe_chem_comp_rdkit_properties.kappa3 9.568
_pdbe_chem_comp_rdkit_properties.Phi 2.313
#
#
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
YMM C1 0.729 1.869 1.050 ETKDGv3 1
YMM C10 -2.468 -2.481 0.744 ETKDGv3 2
YMM C11 -3.106 -1.428 1.564 ETKDGv3 3
YMM C12 -4.888 -2.851 1.040 ETKDGv3 4
YMM C13 -3.664 -3.294 0.215 ETKDGv3 5
YMM C14 -2.620 -1.321 -2.606 ETKDGv3 6
YMM C15 2.794 0.869 2.019 ETKDGv3 7
YMM C16 4.223 1.379 2.313 ETKDGv3 8
YMM C17 5.206 0.221 2.509 ETKDGv3 9
YMM C18 5.348 -0.622 1.216 ETKDGv3 10
YMM C19 5.910 -2.024 1.560 ETKDGv3 11
YMM C2 -1.251 2.735 -0.277 ETKDGv3 12
YMM C20 6.561 -2.743 0.363 ETKDGv3 13
YMM C21 7.962 -2.214 0.051 ETKDGv3 14
YMM C22 4.013 -0.707 0.419 ETKDGv3 15
YMM C23 2.786 -0.513 1.317 ETKDGv3 16
YMM C3 -1.690 4.086 -0.900 ETKDGv3 17
YMM C4 -3.216 4.358 -0.932 ETKDGv3 18
YMM C5 -3.992 3.328 -1.758 ETKDGv3 19
YMM C6 -3.822 4.502 0.471 ETKDGv3 20
YMM C7 -1.393 1.585 -1.241 ETKDGv3 21
YMM C8 -1.718 -0.931 -1.395 ETKDGv3 22
YMM C9 -1.422 -2.012 -0.304 ETKDGv3 23
YMM N1 0.153 2.812 0.139 ETKDGv3 24
YMM N2 -2.056 0.381 -0.830 ETKDGv3 25
YMM N3 -4.495 -1.623 1.707 ETKDGv3 26
YMM O1 -0.008 1.067 1.687 ETKDGv3 27
YMM O2 -2.475 -0.540 2.196 ETKDGv3 28
YMM O3 -2.561 -2.698 -2.870 ETKDGv3 29
YMM O4 -0.853 1.652 -2.380 ETKDGv3 30
YMM O5 2.118 1.840 1.217 ETKDGv3 31
YMM H1 -1.926 -3.138 1.461 ETKDGv3 32
YMM H2 -5.137 -3.619 1.804 ETKDGv3 33
YMM H3 -5.771 -2.672 0.390 ETKDGv3 34
YMM H4 -3.855 -3.096 -0.850 ETKDGv3 35
YMM H5 -3.484 -4.385 0.333 ETKDGv3 36
YMM S1 -4.339 -0.792 -2.514 ETKDGv3 37
YMM H7 -2.219 -0.783 -3.498 ETKDGv3 38
YMM H8 2.262 0.769 2.991 ETKDGv3 39
YMM H9 4.209 2.013 3.225 ETKDGv3 40
YMM H10 4.583 2.012 1.472 ETKDGv3 41
YMM H11 4.845 -0.411 3.352 ETKDGv3 42
YMM H12 6.200 0.627 2.798 ETKDGv3 43
YMM H13 6.084 -0.094 0.572 ETKDGv3 44
YMM H14 6.662 -1.946 2.377 ETKDGv3 45
YMM H15 5.084 -2.657 1.953 ETKDGv3 46
YMM H16 -1.867 2.543 0.626 ETKDGv3 47
YMM H17 5.929 -2.663 -0.546 ETKDGv3 48
YMM H18 6.650 -3.823 0.610 ETKDGv3 49
YMM H19 7.922 -1.158 -0.287 ETKDGv3 50
YMM H20 8.412 -2.821 -0.763 ETKDGv3 51
YMM H21 8.614 -2.290 0.947 ETKDGv3 52
YMM H22 4.003 0.086 -0.361 ETKDGv3 53
YMM H23 3.915 -1.677 -0.112 ETKDGv3 54
YMM H24 1.865 -0.638 0.709 ETKDGv3 55
YMM H25 2.776 -1.316 2.087 ETKDGv3 56
YMM H26 -1.222 4.910 -0.317 ETKDGv3 57
YMM H27 -1.282 4.178 -1.930 ETKDGv3 58
YMM H28 -3.346 5.340 -1.439 ETKDGv3 59
YMM H29 -4.050 2.357 -1.225 ETKDGv3 60
YMM H30 -5.029 3.687 -1.931 ETKDGv3 61
YMM H31 -3.508 3.180 -2.747 ETKDGv3 62
YMM H32 -3.225 5.213 1.081 ETKDGv3 63
YMM H33 -3.871 3.526 0.996 ETKDGv3 64
YMM H34 -4.856 4.901 0.394 ETKDGv3 65
YMM H35 -0.711 -0.821 -1.863 ETKDGv3 66
YMM H36 -1.038 -2.923 -0.813 ETKDGv3 67
YMM H37 -0.554 -1.632 0.281 ETKDGv3 68
YMM H38 0.799 3.473 -0.350 ETKDGv3 69
YMM H39 -2.800 0.468 -0.108 ETKDGv3 70
YMM H40 -5.113 -1.063 2.335 ETKDGv3 71
YMM H41 -1.665 -2.879 -3.257 ETKDGv3 72
YMM O6 -4.477 0.526 -3.222 ETKDGv3 73
YMM O7 -4.813 -0.628 -1.100 ETKDGv3 74
YMM O8 -5.315 -1.916 -3.299 ETKDGv3 75
YMM H6 -5.444 -2.650 -2.647 ETKDGv3 76
#