data_A1ATD
#
_chem_comp.id A1ATD
_chem_comp.name "(3S,5R)-1-[4-(2-carbamimidamidoethyl)piperazine-1-carbonyl]-N-(4-chloro-3-fluorophenyl)-5-(hydroxymethyl)piperidine-3-carboxamide"
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C21 H31 Cl F N7 O3"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2024-05-28
_chem_comp.pdbx_modified_date 2025-03-28
_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 483.967
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code A1ATD
_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 9BXW
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site RCSB
_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
A1ATD C10 C1 C 0 1 N N N N N N -3.231 17.424 -15.154 -3.200 0.803 -0.278 C10 A1ATD 1
A1ATD CD C2 C 0 1 N N N N N N -1.371 11.599 -8.867 7.348 -0.614 0.468 CD A1ATD 2
A1ATD NE N1 N 0 1 N N N N N N -1.641 11.421 -7.459 8.535 -1.285 1.003 NE A1ATD 3
A1ATD CZ C3 C 0 1 N N N N N N -2.489 10.314 -7.043 9.466 -0.569 1.717 CZ A1ATD 4
A1ATD NH1 N2 N 0 1 N N N N N N -2.732 10.140 -5.823 10.581 -1.199 2.220 NH1 A1ATD 5
A1ATD NH2 N3 N 0 1 N N N N N N -2.982 9.536 -7.896 9.293 0.707 1.919 NH2 A1ATD 6
A1ATD C01 C4 C 0 1 N N N N N N -0.800 12.975 -9.188 6.482 -1.630 -0.280 C01 A1ATD 7
A1ATD C03 C5 C 0 1 N N N N N N 1.143 13.555 -9.888 4.424 -0.478 0.268 C03 A1ATD 8
A1ATD C04 C6 C 0 1 N N N N N N 1.276 14.866 -10.654 3.293 0.371 -0.324 C04 A1ATD 9
A1ATD C06 C7 C 0 1 N N N N N N 0.029 16.904 -11.356 1.273 -0.559 -1.357 C06 A1ATD 10
A1ATD C08 C8 C 0 1 N N N N N N -2.367 17.259 -12.612 -0.883 -0.085 -0.297 C08 A1ATD 11
A1ATD C09 C9 C 0 1 N N S N N N -2.099 17.595 -14.086 -1.783 1.085 -0.706 C09 A1ATD 12
A1ATD C13 C10 C 0 1 Y N N N N N -3.696 17.326 -17.699 -5.120 -0.603 -0.270 C13 A1ATD 13
A1ATD C14 C11 C 0 1 Y N N N N N -5.075 17.255 -17.585 -6.019 0.410 0.036 C14 A1ATD 14
A1ATD C15 C12 C 0 1 Y N N N N N -5.857 17.087 -18.726 -7.280 0.094 0.505 C15 A1ATD 15
A1ATD C17 C13 C 0 1 Y N N N N N -5.265 16.969 -19.972 -7.647 -1.233 0.670 C17 A1ATD 16
A1ATD C19 C14 C 0 1 Y N N N N N -3.890 17.018 -20.083 -6.752 -2.242 0.365 C19 A1ATD 17
A1ATD C20 C15 C 0 1 Y N N N N N -3.111 17.187 -18.953 -5.492 -1.931 -0.109 C20 A1ATD 18
A1ATD C21 C16 C 0 1 N N N N N N -1.734 19.038 -14.315 -1.289 2.365 -0.029 C21 A1ATD 19
A1ATD C22 C17 C 0 1 N N R N N N -0.705 19.648 -13.436 0.138 2.670 -0.489 C22 A1ATD 20
A1ATD C23 C18 C 0 1 N N N N N N -0.951 19.173 -11.965 1.060 1.518 -0.077 C23 A1ATD 21
A1ATD C25 C19 C 0 1 N N N N N N -0.830 14.514 -11.726 3.434 -1.044 -2.410 C25 A1ATD 22
A1ATD C26 C20 C 0 1 N N N N N N -0.617 13.039 -11.373 4.559 -1.837 -1.736 C26 A1ATD 23
A1ATD C27 C21 C 0 1 N N N N N N -0.611 21.203 -13.406 0.619 3.967 0.164 C27 A1ATD 24
A1ATD F16 F1 F 0 1 N N N N N N -7.213 17.034 -18.639 -8.156 1.079 0.804 F16 A1ATD 25
A1ATD N02 N4 N 0 1 N N N N N N -0.004 12.817 -10.141 5.292 -0.957 -0.817 N02 A1ATD 26
A1ATD N05 N5 N 0 1 N N N N N N 0.123 15.445 -11.247 2.613 -0.416 -1.363 N05 A1ATD 27
A1ATD N07 N6 N 0 1 N N N N N N -1.076 17.686 -11.932 0.512 0.261 -0.605 N07 A1ATD 28
A1ATD N12 N7 N 0 1 N N N N N N -2.810 17.487 -16.550 -3.842 -0.286 -0.745 N12 A1ATD 29
A1ATD O11 O1 O 0 1 N N N N N N -4.359 17.282 -14.848 -3.761 1.554 0.492 O11 A1ATD 30
A1ATD O24 O2 O 0 1 N N N N N N 0.929 17.525 -10.905 0.750 -1.426 -2.030 O24 A1ATD 31
A1ATD O28 O3 O 0 1 N N N N N N 0.655 21.473 -12.835 1.905 4.313 -0.354 O28 A1ATD 32
A1ATD CL1 CL1 CL 0 0 N N N N N N -6.254 16.748 -21.444 -9.231 -1.628 1.259 CL1 A1ATD 33
A1ATD H1 H1 H 0 1 N N N N N N -2.310 11.469 -9.424 6.775 -0.181 1.288 H1 A1ATD 34
A1ATD H2 H2 H 0 1 N N N N N N -0.647 10.835 -9.186 7.655 0.176 -0.218 H2 A1ATD 35
A1ATD H3 H3 H 0 1 N N N N N N -1.252 12.047 -6.783 8.665 -2.235 0.853 H3 A1ATD 36
A1ATD H4 H4 H 0 1 N N N N N N -2.343 10.761 -5.142 10.710 -2.148 2.070 H4 A1ATD 37
A1ATD H5 H5 H 0 1 N N N N N N -3.314 9.381 -5.532 11.237 -0.694 2.724 H5 A1ATD 38
A1ATD H6 H6 H 0 1 N N N N N N -3.545 8.826 -7.474 9.950 1.212 2.423 H6 A1ATD 39
A1ATD H7 H7 H 0 1 N N N N N N -0.270 13.380 -8.313 7.055 -2.062 -1.100 H7 A1ATD 40
A1ATD H8 H8 H 0 1 N N N N N N -1.608 13.663 -9.478 6.175 -2.420 0.405 H8 A1ATD 41
A1ATD H9 H9 H 0 1 N N N N N N 2.010 12.927 -10.142 5.008 0.127 0.961 H9 A1ATD 42
A1ATD H10 H10 H 0 1 N N N N N N 1.162 13.790 -8.813 4.000 -1.331 0.797 H10 A1ATD 43
A1ATD H11 H11 H 0 1 N N N N N N 2.000 14.692 -11.464 2.583 0.633 0.461 H11 A1ATD 44
A1ATD H12 H12 H 0 1 N N N N N N 1.682 15.608 -9.951 3.708 1.279 -0.761 H12 A1ATD 45
A1ATD H13 H13 H 0 1 N N N N N N -3.226 17.827 -12.225 -0.986 -0.269 0.772 H13 A1ATD 46
A1ATD H14 H14 H 0 1 N N N N N N -2.549 16.183 -12.477 -1.168 -0.980 -0.851 H14 A1ATD 47
A1ATD H15 H15 H 0 1 N N N N N N -1.250 16.978 -14.415 -1.748 1.209 -1.789 H15 A1ATD 48
A1ATD H16 H16 H 0 1 N N N N N N -5.543 17.330 -16.614 -5.733 1.444 -0.092 H16 A1ATD 49
A1ATD H17 H17 H 0 1 N N N N N N -3.423 16.924 -21.052 -7.039 -3.275 0.495 H17 A1ATD 50
A1ATD H18 H18 H 0 1 N N N N N N -2.035 17.211 -19.045 -4.794 -2.720 -0.347 H18 A1ATD 51
A1ATD H19 H19 H 0 1 N N N N N N -1.371 19.123 -15.350 -1.942 3.194 -0.299 H19 A1ATD 52
A1ATD H20 H20 H 0 1 N N N N N N -2.654 19.630 -14.200 -1.301 2.231 1.053 H20 A1ATD 53
A1ATD H21 H21 H 0 1 N N N N N N 0.280 19.266 -13.742 0.155 2.780 -1.573 H21 A1ATD 54
A1ATD H22 H22 H 0 1 N N N N N N -0.105 19.483 -11.334 2.056 1.682 -0.488 H22 A1ATD 55
A1ATD H23 H23 H 0 1 N N N N N N -1.878 19.627 -11.584 1.115 1.464 1.010 H23 A1ATD 56
A1ATD H24 H24 H 0 1 N N N N N N -0.844 14.592 -12.823 3.862 -0.273 -3.051 H24 A1ATD 57
A1ATD H25 H25 H 0 1 N N N N N N -1.811 14.810 -11.325 2.816 -1.717 -3.005 H25 A1ATD 58
A1ATD H26 H26 H 0 1 N N N N N N -1.599 12.544 -11.361 4.132 -2.671 -1.179 H26 A1ATD 59
A1ATD H27 H27 H 0 1 N N N N N N 0.011 12.587 -12.155 5.241 -2.218 -2.496 H27 A1ATD 60
A1ATD H28 H28 H 0 1 N N N N N N -0.674 21.616 -14.424 -0.087 4.767 -0.054 H28 A1ATD 61
A1ATD H29 H29 H 0 1 N N N N N N -1.415 21.629 -12.787 0.688 3.827 1.243 H29 A1ATD 62
A1ATD H31 H31 H 0 1 N N N N N N -1.841 17.653 -16.733 -3.418 -0.850 -1.411 H31 A1ATD 63
A1ATD H32 H32 H 0 1 N N N N N N 0.786 22.413 -12.783 2.273 5.127 0.016 H32 A1ATD 64
#
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
A1ATD CL1 C17 SING N N 1
A1ATD C19 C17 DOUB Y N 2
A1ATD C19 C20 SING Y N 3
A1ATD C17 C15 SING Y N 4
A1ATD C20 C13 DOUB Y N 5
A1ATD C15 F16 SING N N 6
A1ATD C15 C14 DOUB Y N 7
A1ATD C13 C14 SING Y N 8
A1ATD C13 N12 SING N N 9
A1ATD N12 C10 SING N N 10
A1ATD C10 O11 DOUB N N 11
A1ATD C10 C09 SING N N 12
A1ATD C21 C09 SING N N 13
A1ATD C21 C22 SING N N 14
A1ATD C09 C08 SING N N 15
A1ATD C22 C27 SING N N 16
A1ATD C22 C23 SING N N 17
A1ATD C27 O28 SING N N 18
A1ATD C08 N07 SING N N 19
A1ATD C23 N07 SING N N 20
A1ATD N07 C06 SING N N 21
A1ATD C25 C26 SING N N 22
A1ATD C25 N05 SING N N 23
A1ATD C26 N02 SING N N 24
A1ATD C06 N05 SING N N 25
A1ATD C06 O24 DOUB N N 26
A1ATD N05 C04 SING N N 27
A1ATD C04 C03 SING N N 28
A1ATD N02 C03 SING N N 29
A1ATD N02 C01 SING N N 30
A1ATD C01 CD SING N N 31
A1ATD CD NE SING N N 32
A1ATD NH2 CZ DOUB N N 33
A1ATD NE CZ SING N N 34
A1ATD CZ NH1 SING N N 35
A1ATD CD H1 SING N N 36
A1ATD CD H2 SING N N 37
A1ATD NE H3 SING N N 38
A1ATD NH1 H4 SING N N 39
A1ATD NH1 H5 SING N N 40
A1ATD NH2 H6 SING N N 41
A1ATD C01 H7 SING N N 42
A1ATD C01 H8 SING N N 43
A1ATD C03 H9 SING N N 44
A1ATD C03 H10 SING N N 45
A1ATD C04 H11 SING N N 46
A1ATD C04 H12 SING N N 47
A1ATD C08 H13 SING N N 48
A1ATD C08 H14 SING N N 49
A1ATD C09 H15 SING N N 50
A1ATD C14 H16 SING N N 51
A1ATD C19 H17 SING N N 52
A1ATD C20 H18 SING N N 53
A1ATD C21 H19 SING N N 54
A1ATD C21 H20 SING N N 55
A1ATD C22 H21 SING N N 56
A1ATD C23 H22 SING N N 57
A1ATD C23 H23 SING N N 58
A1ATD C25 H24 SING N N 59
A1ATD C25 H25 SING N N 60
A1ATD C26 H26 SING N N 61
A1ATD C26 H27 SING N N 62
A1ATD C27 H28 SING N N 63
A1ATD C27 H29 SING N N 64
A1ATD N12 H31 SING N N 65
A1ATD O28 H32 SING N N 66
#
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
A1ATD SMILES ACDLabs 12.01 "Clc1ccc(cc1F)NC(=O)C1CN(CC(CO)C1)C(=O)N1CCN(CCNC(=N)N)CC1"
A1ATD InChI InChI 1.06 "InChI=1S/C21H31ClFN7O3/c22-17-2-1-16(10-18(17)23)27-19(32)15-9-14(13-31)11-30(12-15)21(33)29-7-5-28(6-8-29)4-3-26-20(24)25/h1-2,10,14-15,31H,3-9,11-13H2,(H,27,32)(H4,24,25,26)/t14-,15+/m1/s1"
A1ATD InChIKey InChI 1.06 JNRCFZSAWRPICW-CABCVRRESA-N
A1ATD SMILES_CANONICAL CACTVS 3.385 "NC(=N)NCCN1CCN(CC1)C(=O)N2C[C@H](CO)C[C@@H](C2)C(=O)Nc3ccc(Cl)c(F)c3"
A1ATD SMILES CACTVS 3.385 "NC(=N)NCCN1CCN(CC1)C(=O)N2C[CH](CO)C[CH](C2)C(=O)Nc3ccc(Cl)c(F)c3"
A1ATD SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "[H]/N=C(/N)\NCCN1CCN(CC1)C(=O)N2C[C@@H](C[C@@H](C2)C(=O)Nc3ccc(c(c3)F)Cl)CO"
A1ATD SMILES "OpenEye OEToolkits" 2.0.7 "c1cc(c(cc1NC(=O)C2CC(CN(C2)C(=O)N3CCN(CC3)CCNC(=N)N)CO)F)Cl"
#
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
A1ATD "SYSTEMATIC NAME" ACDLabs 12.01 "(3S,5R)-1-[4-(2-carbamimidamidoethyl)piperazine-1-carbonyl]-N-(4-chloro-3-fluorophenyl)-5-(hydroxymethyl)piperidine-3-carboxamide"
A1ATD "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "(3~{S},5~{R})-1-[4-(2-carbamimidamidoethyl)piperazin-1-yl]carbonyl-~{N}-(4-chloranyl-3-fluoranyl-phenyl)-5-(hydroxymethyl)piperidine-3-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
A1ATD "Create component" 2024-05-28 RCSB
A1ATD "Initial release" 2025-04-02 RCSB
#