data_A1D8L
#
_chem_comp.id A1D8L
_chem_comp.name "(S)-N1-((1H-Benzo[d]imidazol-2-yl)methyl)-N1-(5,6,7,8-tetrahydroquinolin-8-yl)butane-1,4-diamine"
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C21 H27 N5"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms AMD-070
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2024-06-04
_chem_comp.pdbx_modified_date 2025-02-21
_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 349.473
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code A1D8L
_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 8ZPM
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site PDBC
_chem_comp.pdbx_pcm ?
#
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_n_terminal_atom_flag
_chem_comp_atom.pdbx_backbone_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
A1D8L C14 C1 C 0 1 N N N N N N 125.309 136.856 119.639 -0.887 -1.324 1.539 C14 A1D8L 1
A1D8L C15 C2 C 0 1 Y N N N N N 124.032 137.541 119.989 -2.190 -0.950 0.881 C15 A1D8L 2
A1D8L C16 C3 C 0 1 Y N N N N N 121.954 137.971 120.337 -3.932 0.202 0.279 C16 A1D8L 3
A1D8L C17 C4 C 0 1 Y N N N N N 120.571 137.951 120.466 -4.932 1.152 0.061 C17 A1D8L 4
A1D8L C18 C5 C 0 1 Y N N N N N 119.941 139.107 120.845 -5.998 0.848 -0.738 C18 A1D8L 5
A1D8L C19 C6 C 0 1 Y N N N N N 120.658 140.261 121.108 -6.099 -0.399 -1.339 C19 A1D8L 6
A1D8L C20 C7 C 0 1 Y N N N N N 122.027 140.295 121.003 -5.123 -1.353 -1.137 C20 A1D8L 7
A1D8L C21 C8 C 0 1 Y N N N N N 122.659 139.133 120.608 -4.033 -1.061 -0.329 C21 A1D8L 8
A1D8L N2 N1 N 0 1 N N N N N N 126.337 137.852 119.358 0.233 -0.842 0.719 N2 A1D8L 9
A1D8L C1 C9 C 0 1 N N N N N N 129.537 135.867 119.582 1.442 2.386 2.262 C1 A1D8L 10
A1D8L C10 C10 C 0 1 N N N N N N 126.282 138.287 117.955 1.472 -1.559 1.046 C10 A1D8L 11
A1D8L C11 C11 C 0 1 N N N N N N 125.711 137.376 116.894 2.497 -1.341 -0.069 C11 A1D8L 12
A1D8L C12 C12 C 0 1 N N N N N N 126.204 137.818 115.531 3.788 -2.088 0.271 C12 A1D8L 13
A1D8L C13 C13 C 0 1 N N N N N N 125.289 138.799 114.854 4.812 -1.869 -0.845 C13 A1D8L 14
A1D8L C2 C14 C 0 1 N N N N N N 128.264 136.376 118.941 1.077 0.898 2.213 C2 A1D8L 15
A1D8L C3 C15 C 0 1 N N S N N N 127.659 137.454 119.776 0.408 0.609 0.870 C3 A1D8L 16
A1D8L C4 C16 C 0 1 Y N N N N N 128.612 138.619 119.778 1.253 1.128 -0.265 C4 A1D8L 17
A1D8L C5 C17 C 0 1 Y N N N N N 129.977 138.363 119.759 2.245 2.064 -0.076 C5 A1D8L 18
A1D8L C6 C18 C 0 1 N N N N N N 130.552 136.969 119.727 2.581 2.635 1.275 C6 A1D8L 19
A1D8L C7 C19 C 0 1 Y N N N N N 130.831 139.459 119.763 2.980 2.504 -1.172 C7 A1D8L 20
A1D8L C8 C20 C 0 1 Y N N N N N 130.326 140.737 119.773 2.694 1.981 -2.422 C8 A1D8L 21
A1D8L C9 C21 C 0 1 Y N N N N N 128.959 140.884 119.790 1.689 1.040 -2.537 C9 A1D8L 22
A1D8L N1 N2 N 0 1 Y N N N N N 128.116 139.862 119.800 1.012 0.650 -1.479 N1 A1D8L 23
A1D8L N3 N3 N 0 1 N N N N N N 126.004 139.598 113.872 6.052 -2.587 -0.518 N3 A1D8L 24
A1D8L N4 N4 N 0 1 Y N N N N N 122.842 136.973 119.954 -2.782 0.202 1.002 N4 A1D8L 25
A1D8L N5 N5 N 0 1 Y N N N N N 123.980 138.826 120.386 -2.915 -1.766 0.069 N5 A1D8L 26
A1D8L H1 H1 H 0 1 N N N N N N 125.155 136.227 118.750 -0.835 -0.869 2.528 H1 A1D8L 27
A1D8L H2 H2 H 0 1 N N N N N N 125.630 136.226 120.482 -0.826 -2.409 1.635 H2 A1D8L 28
A1D8L H3 H3 H 0 1 N N N N N N 120.008 137.050 120.273 -4.864 2.125 0.524 H3 A1D8L 29
A1D8L H4 H4 H 0 1 N N N N N N 118.865 139.118 120.940 -6.769 1.585 -0.905 H4 A1D8L 30
A1D8L H5 H5 H 0 1 N N N N N N 120.129 141.155 121.403 -6.947 -0.624 -1.968 H5 A1D8L 31
A1D8L H6 H6 H 0 1 N N N N N N 122.586 141.193 121.220 -5.207 -2.322 -1.607 H6 A1D8L 32
A1D8L H8 H8 H 0 1 N N N N N N 129.301 135.464 120.578 0.576 2.986 1.982 H8 A1D8L 33
A1D8L H9 H9 H 0 1 N N N N N N 129.961 135.069 118.954 1.764 2.653 3.269 H9 A1D8L 34
A1D8L H10 H10 H 0 1 N N N N N N 127.316 138.513 117.654 1.873 -1.182 1.987 H10 A1D8L 35
A1D8L H11 H11 H 0 1 N N N N N N 125.684 139.210 117.934 1.261 -2.624 1.141 H11 A1D8L 36
A1D8L H12 H12 H 0 1 N N N N N N 124.612 137.426 116.920 2.096 -1.717 -1.010 H12 A1D8L 37
A1D8L H13 H13 H 0 1 N N N N N N 126.036 136.343 117.084 2.708 -0.275 -0.165 H13 A1D8L 38
A1D8L H14 H14 H 0 1 N N N N N N 126.298 136.929 114.889 4.189 -1.711 1.211 H14 A1D8L 39
A1D8L H15 H15 H 0 1 N N N N N N 127.191 138.289 115.653 3.577 -3.153 0.366 H15 A1D8L 40
A1D8L H16 H16 H 0 1 N N N N N N 124.856 139.467 115.613 4.411 -2.246 -1.786 H16 A1D8L 41
A1D8L H17 H17 H 0 1 N N N N N N 124.483 138.247 114.348 5.023 -0.804 -0.940 H17 A1D8L 42
A1D8L H18 H18 H 0 1 N N N N N N 128.495 136.777 117.943 1.980 0.296 2.310 H18 A1D8L 43
A1D8L H19 H19 H 0 1 N N N N N N 127.549 135.546 118.846 0.387 0.663 3.023 H19 A1D8L 44
A1D8L H20 H20 H 0 1 N N N N N N 127.595 137.079 120.808 -0.567 1.094 0.842 H20 A1D8L 45
A1D8L H21 H21 H 0 1 N N N N N N 131.102 136.805 120.665 2.747 3.708 1.181 H21 A1D8L 46
A1D8L H22 H22 H 0 1 N N N N N N 131.248 136.906 118.878 3.490 2.163 1.649 H22 A1D8L 47
A1D8L H23 H23 H 0 1 N N N N N N 131.900 139.305 119.758 3.760 3.241 -1.051 H23 A1D8L 48
A1D8L H24 H24 H 0 1 N N N N N N 130.980 141.596 119.768 3.248 2.303 -3.292 H24 A1D8L 49
A1D8L H25 H25 H 0 1 N N N N N N 128.551 141.884 119.795 1.455 0.622 -3.505 H25 A1D8L 50
A1D8L H26 H26 H 0 1 N N N N N N 125.371 140.240 113.439 5.872 -3.567 -0.361 H26 A1D8L 51
A1D8L H27 H27 H 0 1 N N N N N N 126.736 140.107 114.325 6.745 -2.458 -1.240 H27 A1D8L 52
A1D8L H30 H30 H 0 1 N N N N N N 124.759 139.443 120.499 -2.689 -2.675 -0.183 H30 A1D8L 53
#
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
A1D8L N3 C13 SING N N 1
A1D8L C13 C12 SING N N 2
A1D8L C12 C11 SING N N 3
A1D8L C11 C10 SING N N 4
A1D8L C10 N2 SING N N 5
A1D8L C2 C1 SING N N 6
A1D8L C2 C3 SING N N 7
A1D8L N2 C14 SING N N 8
A1D8L N2 C3 SING N N 9
A1D8L C1 C6 SING N N 10
A1D8L C14 C15 SING N N 11
A1D8L C6 C5 SING N N 12
A1D8L C5 C7 DOUB Y N 13
A1D8L C5 C4 SING Y N 14
A1D8L C7 C8 SING Y N 15
A1D8L C8 C9 DOUB Y N 16
A1D8L C3 C4 SING N N 17
A1D8L C4 N1 DOUB Y N 18
A1D8L C9 N1 SING Y N 19
A1D8L N4 C15 DOUB Y N 20
A1D8L N4 C16 SING Y N 21
A1D8L C15 N5 SING Y N 22
A1D8L C16 C17 DOUB Y N 23
A1D8L C16 C21 SING Y N 24
A1D8L N5 C21 SING Y N 25
A1D8L C17 C18 SING Y N 26
A1D8L C21 C20 DOUB Y N 27
A1D8L C18 C19 DOUB Y N 28
A1D8L C20 C19 SING Y N 29
A1D8L C14 H1 SING N N 30
A1D8L C14 H2 SING N N 31
A1D8L C17 H3 SING N N 32
A1D8L C18 H4 SING N N 33
A1D8L C19 H5 SING N N 34
A1D8L C20 H6 SING N N 35
A1D8L C1 H8 SING N N 36
A1D8L C1 H9 SING N N 37
A1D8L C10 H10 SING N N 38
A1D8L C10 H11 SING N N 39
A1D8L C11 H12 SING N N 40
A1D8L C11 H13 SING N N 41
A1D8L C12 H14 SING N N 42
A1D8L C12 H15 SING N N 43
A1D8L C13 H16 SING N N 44
A1D8L C13 H17 SING N N 45
A1D8L C2 H18 SING N N 46
A1D8L C2 H19 SING N N 47
A1D8L C3 H20 SING N N 48
A1D8L C6 H21 SING N N 49
A1D8L C6 H22 SING N N 50
A1D8L C7 H23 SING N N 51
A1D8L C8 H24 SING N N 52
A1D8L C9 H25 SING N N 53
A1D8L N3 H26 SING N N 54
A1D8L N3 H27 SING N N 55
A1D8L N5 H30 SING N N 56
#
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
A1D8L InChI InChI 1.06 "InChI=1S/C21H27N5/c22-12-3-4-14-26(15-20-24-17-9-1-2-10-18(17)25-20)19-11-5-7-16-8-6-13-23-21(16)19/h1-2,6,8-10,13,19H,3-5,7,11-12,14-15,22H2,(H,24,25)/t19-/m0/s1"
A1D8L InChIKey InChI 1.06 WVLHHLRVNDMIAR-IBGZPJMESA-N
A1D8L SMILES_CANONICAL CACTVS 3.385 "NCCCCN(Cc1[nH]c2ccccc2n1)[C@H]3CCCc4cccnc34"
A1D8L SMILES CACTVS 3.385 "NCCCCN(Cc1[nH]c2ccccc2n1)[CH]3CCCc4cccnc34"
A1D8L SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1ccc2c(c1)[nH]c(n2)CN(CCCCN)[C@H]3CCCc4c3nccc4"
A1D8L SMILES "OpenEye OEToolkits" 2.0.7 "c1ccc2c(c1)[nH]c(n2)CN(CCCCN)C3CCCc4c3nccc4"
#
_pdbx_chem_comp_identifier.comp_id A1D8L
_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 "~{N}'-(1~{H}-benzimidazol-2-ylmethyl)-~{N}'-[(8~{S})-5,6,7,8-tetrahydroquinolin-8-yl]butane-1,4-diamine"
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
A1D8L "Create component" 2024-06-04 PDBC
A1D8L "Initial release" 2025-02-26 RCSB
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id A1D8L
_pdbx_chem_comp_synonyms.name AMD-070
_pdbx_chem_comp_synonyms.provenance PUBCHEM
_pdbx_chem_comp_synonyms.type ?
#