data_YVB
#
_chem_comp.id YVB
_chem_comp.name "(2P)-2-{3-[(2-amino-4,5-dimethylphenyl)carbamoyl]phenyl}-1H-benzimidazole-4-carboxamide"
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C23 H21 N5 O2"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2023-02-22
_chem_comp.pdbx_modified_date 2024-02-02
_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 399.445
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code YVB
_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 8FZ1
_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
YVB N1 N1 N 0 1 Y N N N N N 37.252 12.383 -8.339 -3.158 -0.081 -0.008 N1 YVB 1
YVB C7 C1 C 0 1 Y N N N N N 40.848 10.914 -10.251 0.874 1.478 0.189 C7 YVB 2
YVB C8 C2 C 0 1 Y N N N N N 39.800 11.335 -9.440 -0.405 0.931 0.123 C8 YVB 3
YVB N2 N2 N 0 1 Y N N N N N 36.631 10.277 -7.920 -4.039 1.922 0.112 N2 YVB 4
YVB C9 C3 C 0 1 Y N N N N N 38.616 10.606 -9.383 -1.517 1.770 0.157 C9 YVB 5
YVB O1 O1 O 0 1 N N N N N N 35.384 15.735 -6.271 -3.512 -2.872 -0.210 O1 YVB 6
YVB C1 C4 C 0 1 Y N N N N N 45.105 15.757 -10.926 6.644 -1.335 -0.165 C1 YVB 7
YVB C5 C5 C 0 1 Y N N N N N 43.130 13.779 -11.077 4.421 0.300 0.089 C5 YVB 8
YVB C6 C6 C 0 1 N N N N N N 42.109 11.717 -10.224 2.060 0.595 0.153 C6 YVB 9
YVB N3 N3 N 0 1 N N N N N N 36.867 15.198 -7.849 -5.515 -3.825 -0.319 N3 YVB 10
YVB C4 C7 C 0 1 Y N N N N N 42.878 14.970 -10.403 4.397 -0.991 0.594 C4 YVB 11
YVB C3 C8 C 0 1 N N N N N N 43.563 17.208 -9.521 5.478 -3.207 1.016 C3 YVB 12
YVB C2 C9 C 0 1 Y N N N N N 43.852 15.958 -10.310 5.508 -1.804 0.466 C2 YVB 13
YVB N4 N4 N 0 1 N N N N N N 44.643 12.400 -12.347 5.596 2.072 -1.070 N4 YVB 14
YVB N N5 N 0 1 N N N N N N 42.166 12.749 -11.098 3.297 1.126 0.217 N YVB 15
YVB C C10 C 0 1 N N N N N N 46.189 16.806 -10.855 7.851 -2.228 -0.301 C YVB 16
YVB O O2 O 0 1 N N N N N N 43.006 11.464 -9.421 1.919 -0.609 0.066 O YVB 17
YVB C10 C11 C 0 1 Y N N N N N 38.492 9.444 -10.132 -1.342 3.152 0.257 C10 YVB 18
YVB C11 C12 C 0 1 Y N N N N N 39.527 9.026 -10.948 -0.071 3.688 0.322 C11 YVB 19
YVB C12 C13 C 0 1 Y N N N N N 40.698 9.761 -11.015 1.035 2.862 0.283 C12 YVB 20
YVB C13 C14 C 0 1 Y N N N N N 37.504 11.098 -8.560 -2.879 1.198 0.087 C13 YVB 21
YVB C14 C15 C 0 1 Y N N N N N 36.151 12.393 -7.493 -4.490 -0.255 -0.049 C14 YVB 22
YVB C15 C16 C 0 1 Y N N N N N 35.748 11.086 -7.232 -5.082 1.019 0.027 C15 YVB 23
YVB C16 C17 C 0 1 Y N N N N N 34.645 10.792 -6.445 -6.463 1.146 0.005 C16 YVB 24
YVB C17 C18 C 0 1 Y N N N N N 33.933 11.857 -5.918 -7.262 0.023 -0.090 C17 YVB 25
YVB C18 C19 C 0 1 Y N N N N N 34.329 13.169 -6.155 -6.701 -1.238 -0.165 C18 YVB 26
YVB C19 C20 C 0 1 Y N N N N N 35.451 13.467 -6.926 -5.317 -1.395 -0.146 C19 YVB 27
YVB C20 C21 C 0 1 N N N N N N 35.898 14.892 -7.007 -4.721 -2.740 -0.227 C20 YVB 28
YVB C21 C22 C 0 1 Y N N N N N 44.374 13.568 -11.691 5.567 0.772 -0.553 C21 YVB 29
YVB C22 C23 C 0 1 Y N N N N N 45.348 14.569 -11.609 6.676 -0.051 -0.677 C22 YVB 30
YVB H2 H2 H 0 1 N N N N N N 39.906 12.234 -8.850 -0.535 -0.138 0.046 H2 YVB 31
YVB H3 H3 H 0 1 N N N N N N 36.628 9.277 -7.943 -4.115 2.887 0.178 H3 YVB 32
YVB H4 H4 H 0 1 N N N N N N 37.205 16.138 -7.903 -6.479 -3.721 -0.332 H4 YVB 33
YVB H5 H5 H 0 1 N N N N N N 37.264 14.490 -8.433 -5.123 -4.711 -0.372 H5 YVB 34
YVB H6 H6 H 0 1 N N N N N N 41.913 15.129 -9.946 3.512 -1.359 1.091 H6 YVB 35
YVB H7 H7 H 0 1 N N N N N N 43.129 17.970 -10.186 5.828 -3.200 2.049 H7 YVB 36
YVB H8 H8 H 0 1 N N N N N N 42.851 16.976 -8.715 4.459 -3.590 0.981 H8 YVB 37
YVB H9 H9 H 0 1 N N N N N N 44.498 17.591 -9.086 6.128 -3.846 0.417 H9 YVB 38
YVB H10 H10 H 0 1 N N N N N N 43.842 11.803 -12.308 6.394 2.398 -1.516 H10 YVB 39
YVB H11 H11 H 0 1 N N N N N N 44.865 12.598 -13.302 4.820 2.646 -0.983 H11 YVB 40
YVB H12 H12 H 0 1 N N N N N N 41.470 12.784 -11.815 3.409 2.080 0.352 H12 YVB 41
YVB H13 H13 H 0 1 N N N N N N 46.094 17.491 -11.711 7.785 -2.789 -1.233 H13 YVB 42
YVB H14 H14 H 0 1 N N N N N N 46.089 17.374 -9.918 8.755 -1.619 -0.306 H14 YVB 43
YVB H15 H15 H 0 1 N N N N N N 47.174 16.318 -10.884 7.886 -2.922 0.539 H15 YVB 44
YVB H16 H16 H 0 1 N N N N N N 37.583 8.864 -10.077 -2.204 3.803 0.283 H16 YVB 45
YVB H17 H17 H 0 1 N N N N N N 39.422 8.125 -11.534 0.058 4.757 0.399 H17 YVB 46
YVB H18 H18 H 0 1 N N N N N N 41.499 9.438 -11.663 2.026 3.288 0.335 H18 YVB 47
YVB H19 H19 H 0 1 N N N N N N 34.352 9.771 -6.250 -6.914 2.125 0.063 H19 YVB 48
YVB H20 H20 H 0 1 N N N N N N 33.058 11.666 -5.315 -8.337 0.132 -0.105 H20 YVB 49
YVB H21 H21 H 0 1 N N N N N N 33.752 13.978 -5.731 -7.339 -2.107 -0.238 H21 YVB 50
YVB H22 H22 H 0 1 N N N N N N 46.306 14.417 -12.084 7.564 0.311 -1.173 H22 YVB 51
#
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
YVB N4 C21 SING N N 1
YVB C21 C22 DOUB Y N 2
YVB C21 C5 SING Y N 3
YVB C22 C1 SING Y N 4
YVB N C5 SING N N 5
YVB N C6 SING N N 6
YVB C5 C4 DOUB Y N 7
YVB C12 C11 DOUB Y N 8
YVB C12 C7 SING Y N 9
YVB C11 C10 SING Y N 10
YVB C1 C SING N N 11
YVB C1 C2 DOUB Y N 12
YVB C4 C2 SING Y N 13
YVB C2 C3 SING N N 14
YVB C7 C6 SING N N 15
YVB C7 C8 DOUB Y N 16
YVB C6 O DOUB N N 17
YVB C10 C9 DOUB Y N 18
YVB C8 C9 SING Y N 19
YVB C9 C13 SING N N 20
YVB C13 N1 DOUB Y N 21
YVB C13 N2 SING Y N 22
YVB N1 C14 SING Y N 23
YVB N2 C15 SING Y N 24
YVB N3 C20 SING N N 25
YVB C14 C15 DOUB Y N 26
YVB C14 C19 SING Y N 27
YVB C15 C16 SING Y N 28
YVB C20 C19 SING N N 29
YVB C20 O1 DOUB N N 30
YVB C19 C18 DOUB Y N 31
YVB C16 C17 DOUB Y N 32
YVB C18 C17 SING Y N 33
YVB C8 H2 SING N N 34
YVB N2 H3 SING N N 35
YVB N3 H4 SING N N 36
YVB N3 H5 SING N N 37
YVB C4 H6 SING N N 38
YVB C3 H7 SING N N 39
YVB C3 H8 SING N N 40
YVB C3 H9 SING N N 41
YVB N4 H10 SING N N 42
YVB N4 H11 SING N N 43
YVB N H12 SING N N 44
YVB C H13 SING N N 45
YVB C H14 SING N N 46
YVB C H15 SING N N 47
YVB C10 H16 SING N N 48
YVB C11 H17 SING N N 49
YVB C12 H18 SING N N 50
YVB C16 H19 SING N N 51
YVB C17 H20 SING N N 52
YVB C18 H21 SING N N 53
YVB C22 H22 SING N N 54
#
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
YVB SMILES ACDLabs 12.01 "Cc1cc(NC(=O)c2cccc(c2)c2nc3c(cccc3[NH]2)C(N)=O)c(N)cc1C"
YVB InChI InChI 1.06 "InChI=1S/C23H21N5O2/c1-12-9-17(24)19(10-13(12)2)27-23(30)15-6-3-5-14(11-15)22-26-18-8-4-7-16(21(25)29)20(18)28-22/h3-11H,24H2,1-2H3,(H2,25,29)(H,26,28)(H,27,30)"
YVB InChIKey InChI 1.06 HJDGBHNQHCFQSJ-UHFFFAOYSA-N
YVB SMILES_CANONICAL CACTVS 3.385 "Cc1cc(N)c(NC(=O)c2cccc(c2)c3[nH]c4cccc(C(N)=O)c4n3)cc1C"
YVB SMILES CACTVS 3.385 "Cc1cc(N)c(NC(=O)c2cccc(c2)c3[nH]c4cccc(C(N)=O)c4n3)cc1C"
YVB SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "Cc1cc(c(cc1C)NC(=O)c2cccc(c2)c3[nH]c4cccc(c4n3)C(=O)N)N"
YVB SMILES "OpenEye OEToolkits" 2.0.7 "Cc1cc(c(cc1C)NC(=O)c2cccc(c2)c3[nH]c4cccc(c4n3)C(=O)N)N"
#
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
YVB "SYSTEMATIC NAME" ACDLabs 12.01 "(2P)-2-{3-[(2-amino-4,5-dimethylphenyl)carbamoyl]phenyl}-1H-benzimidazole-4-carboxamide"
YVB "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "2-[3-[(2-azanyl-4,5-dimethyl-phenyl)carbamoyl]phenyl]-1~{H}-benzimidazole-4-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
YVB "Create component" 2023-02-22 RCSB
YVB "Initial release" 2024-02-07 RCSB
#