data_3D4 # _chem_comp.id 3D4 _chem_comp.name "N~2~-[4-(pyridin-3-yl)benzyl]-L-lysyl-N-[(1R,2S,3R)-1-{[(2R)-1-amino-1-oxo-3-phenylpropan-2-yl]amino}-1,3-dihydroxybutan-2-yl]glycinamide" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C33 H45 N7 O5" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2014-07-28 _chem_comp.pdbx_modified_date 2015-05-08 _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 619.754 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 3D4 _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 4U5N _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.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 3D4 N N1 N 0 1 N N N 2.745 37.356 9.104 3.545 -1.083 -0.021 N 3D4 1 3D4 CA C1 C 0 1 N N S 2.416 36.502 7.950 2.187 -1.620 -0.180 CA 3D4 2 3D4 CAA C2 C 0 1 N N N 3.250 28.756 10.544 -6.500 -2.226 2.216 CAA 3D4 3 3D4 CAI C3 C 0 1 Y N N -4.302 24.858 7.559 -6.002 -0.995 -3.934 CAI 3D4 4 3D4 CAJ C4 C 0 1 Y N N -3.561 25.230 6.449 -7.302 -0.650 -3.615 CAJ 3D4 5 3D4 CAK C5 C 0 1 Y N N -3.718 24.812 8.813 -4.951 -0.212 -3.494 CAK 3D4 6 3D4 CAL C6 C 0 1 Y N N -0.089 30.244 12.903 10.434 3.871 0.911 CAL 3D4 7 3D4 CAM C7 C 0 1 Y N N -1.317 29.846 12.405 11.519 3.244 0.327 CAM 3D4 8 3D4 CAN C8 C 0 1 Y N N -2.229 25.558 6.605 -7.552 0.480 -2.858 CAN 3D4 9 3D4 CAO C9 C 0 1 Y N N -2.378 25.140 8.965 -5.201 0.920 -2.741 CAO 3D4 10 3D4 CAP C10 C 0 1 Y N N 0.394 31.495 12.546 9.165 3.355 0.711 CAP 3D4 11 3D4 CAQ C11 C 0 1 Y N N 0.041 35.505 9.799 6.325 -0.061 -1.363 CAQ 3D4 12 3D4 CAR C12 C 0 1 Y N N 1.634 35.517 11.612 5.316 1.644 -0.010 CAR 3D4 13 3D4 CAS C13 C 0 1 Y N N -0.433 34.261 10.184 7.571 0.486 -1.133 CAS 3D4 14 3D4 CAT C14 C 0 1 Y N N 1.158 34.273 12.011 6.557 2.199 0.227 CAT 3D4 15 3D4 CAU C15 C 0 1 Y N N -1.597 31.819 11.256 10.174 1.643 -0.641 CAU 3D4 16 3D4 CAZ C16 C 0 1 N N N 2.472 32.581 7.678 -1.069 -0.109 1.149 CAZ 3D4 17 3D4 C C17 C 0 1 N N N 2.892 35.061 8.183 1.203 -0.705 0.502 C 3D4 18 3D4 O O1 O 0 1 N N N 3.810 34.823 8.897 1.594 0.296 1.064 O 3D4 19 3D4 NAC N2 N 0 1 N N N 2.181 25.912 5.083 -8.449 3.977 0.405 NAC 3D4 20 3D4 OAD O2 O 0 1 N N N 0.317 24.680 5.597 -6.595 3.690 1.588 OAD 3D4 21 3D4 OAE O3 O 0 1 N N N 0.170 32.117 7.562 -2.639 -1.694 0.378 OAE 3D4 22 3D4 OAG O4 O 0 1 N N N 0.601 28.352 9.268 -5.726 1.264 2.722 OAG 3D4 23 3D4 OAH O5 O 0 1 N N N 4.598 30.387 9.550 -4.118 -2.565 2.444 OAH 3D4 24 3D4 CB C18 C 0 1 N N N 2.908 37.030 6.605 2.112 -3.011 0.452 CB 3D4 25 3D4 CBA C19 C 0 1 N N N 1.615 37.498 10.049 3.841 -0.085 -1.058 CBA 3D4 26 3D4 CBB C20 C 0 1 N N N -0.137 25.863 8.030 -6.773 2.494 -1.594 CBB 3D4 27 3D4 CBH C21 C 0 1 N N N 0.939 25.669 5.809 -7.311 3.312 0.685 CBH 3D4 28 3D4 CBI C22 C 0 1 N N N 1.244 31.662 7.774 -2.463 -0.660 0.987 CBI 3D4 29 3D4 CBK C23 C 0 1 N N R 1.761 28.074 8.530 -5.882 0.602 1.466 CBK 3D4 30 3D4 CBL C24 C 0 1 Y N N 1.075 36.133 10.500 5.199 0.516 -0.803 CBL 3D4 31 3D4 CBM C25 C 0 1 Y N N -1.624 25.510 7.860 -6.501 1.263 -2.419 CBM 3D4 32 3D4 CBN C26 C 0 1 Y N N 0.130 33.662 11.300 7.694 1.621 -0.335 CBN 3D4 33 3D4 CBO C27 C 0 1 Y N N -0.380 32.294 11.722 9.032 2.213 -0.084 CBO 3D4 34 3D4 CBP C28 C 0 1 N N R 3.177 29.853 9.731 -5.141 -1.567 2.460 CBP 3D4 35 3D4 CBR C29 C 0 1 N N R 0.426 26.670 6.850 -6.928 2.099 -0.124 CBR 3D4 36 3D4 CBS C30 C 0 1 N N S 2.452 29.432 8.433 -4.867 -0.539 1.361 CBS 3D4 37 3D4 NBC N3 N 0 1 Y N N -2.032 30.628 11.616 11.362 2.167 -0.418 NBC 3D4 38 3D4 NBD N4 N 0 1 N N N 2.146 33.991 7.528 -0.112 -0.999 0.487 NBD 3D4 39 3D4 NBF N5 N 0 1 N N N 1.292 30.252 8.133 -3.513 -0.004 1.519 NBF 3D4 40 3D4 NBG N6 N 0 1 N N N 1.491 27.643 7.152 -5.656 1.560 0.375 NBG 3D4 41 3D4 CG C31 C 0 1 N N N 2.138 38.292 6.226 3.036 -3.966 -0.306 CG 3D4 42 3D4 CD C32 C 0 1 N N N 1.283 38.095 4.986 2.868 -5.384 0.245 CD 3D4 43 3D4 CE C33 C 0 1 N N N 0.835 39.414 4.354 3.793 -6.339 -0.513 CE 3D4 44 3D4 NZ N7 N 0 1 N N N -0.379 39.203 3.580 3.631 -7.699 0.016 NZ 3D4 45 3D4 H1 H1 H 0 1 N N N 3.520 36.952 9.590 3.676 -0.696 0.901 H1 3D4 46 3D4 H3 H3 H 0 1 N N N 1.319 36.458 7.884 1.945 -1.689 -1.240 H3 3D4 47 3D4 H4 H4 H 0 1 N N N 3.763 29.025 11.479 -6.648 -3.031 2.936 H4 3D4 48 3D4 H5 H5 H 0 1 N N N 2.234 28.401 10.772 -7.290 -1.484 2.332 H5 3D4 49 3D4 H6 H6 H 0 1 N N N 3.811 27.959 10.035 -6.530 -2.633 1.205 H6 3D4 50 3D4 H7 H7 H 0 1 N N N -5.345 24.602 7.445 -5.807 -1.880 -4.522 H7 3D4 51 3D4 H8 H8 H 0 1 N N N -4.020 25.263 5.472 -8.123 -1.262 -3.959 H8 3D4 52 3D4 H9 H9 H 0 1 N N N -4.304 24.521 9.672 -3.935 -0.485 -3.738 H9 3D4 53 3D4 H10 H10 H 0 1 N N N 0.480 29.597 13.554 10.575 4.752 1.520 H10 3D4 54 3D4 H11 H11 H 0 1 N N N -1.701 28.871 12.668 12.511 3.642 0.484 H11 3D4 55 3D4 H12 H12 H 0 1 N N N -1.649 25.855 5.744 -8.567 0.750 -2.610 H12 3D4 56 3D4 H13 H13 H 0 1 N N N -1.922 25.107 9.943 -4.380 1.533 -2.398 H13 3D4 57 3D4 H14 H14 H 0 1 N N N 1.354 31.838 12.904 8.300 3.822 1.158 H14 3D4 58 3D4 H15 H15 H 0 1 N N N -0.396 35.998 8.943 6.227 -0.938 -1.985 H15 3D4 59 3D4 H16 H16 H 0 1 N N N 2.430 35.999 12.161 4.434 2.090 0.425 H16 3D4 60 3D4 H17 H17 H 0 1 N N N -1.220 33.771 9.629 8.449 0.034 -1.571 H17 3D4 61 3D4 H18 H18 H 0 1 N N N 1.586 33.781 12.872 6.647 3.079 0.845 H18 3D4 62 3D4 H19 H19 H 0 1 N N N -2.193 32.429 10.593 10.086 0.760 -1.257 H19 3D4 63 3D4 H20 H20 H 0 1 N N N 3.070 32.270 6.809 -1.016 0.882 0.699 H20 3D4 64 3D4 H21 H21 H 0 1 N N N 3.068 32.459 8.595 -0.827 -0.040 2.210 H21 3D4 65 3D4 H22 H22 H 0 1 N N N 2.505 25.247 4.410 -8.696 4.757 0.925 H22 3D4 66 3D4 H23 H23 H 0 1 N N N 2.708 26.744 5.258 -9.022 3.675 -0.318 H23 3D4 67 3D4 H24 H24 H 0 1 N N N 0.841 28.624 10.146 -4.849 1.649 2.858 H24 3D4 68 3D4 H25 H25 H 0 1 N N N 4.960 30.619 10.397 -3.228 -2.218 2.593 H25 3D4 69 3D4 H26 H26 H 0 1 N N N 2.751 36.262 5.833 2.424 -2.955 1.495 H26 3D4 70 3D4 H27 H27 H 0 1 N N N 3.980 37.265 6.676 1.087 -3.379 0.399 H27 3D4 71 3D4 H28 H28 H 0 1 N N N 1.958 38.055 10.933 3.834 -0.565 -2.037 H28 3D4 72 3D4 H29 H29 H 0 1 N N N 0.806 38.056 9.555 3.086 0.700 -1.032 H29 3D4 73 3D4 H30 H30 H 0 1 N N N 0.437 24.929 8.122 -5.941 3.192 -1.696 H30 3D4 74 3D4 H31 H31 H 0 1 N N N -0.020 26.457 8.949 -7.690 2.970 -1.941 H31 3D4 75 3D4 H32 H32 H 0 1 N N N 2.414 27.354 9.046 -6.892 0.198 1.391 H32 3D4 76 3D4 H33 H33 H 0 1 N N N 2.577 30.641 10.210 -5.148 -1.069 3.430 H33 3D4 77 3D4 H34 H34 H 0 1 N N N -0.415 27.215 6.395 -7.705 1.341 -0.032 H34 3D4 78 3D4 H35 H35 H 0 1 N N N 3.163 29.432 7.594 -4.958 -1.017 0.386 H35 3D4 79 3D4 H36 H36 H 0 1 N N N 1.371 34.240 6.947 -0.426 -1.799 0.037 H36 3D4 80 3D4 H37 H37 H 0 1 N N N 0.408 29.786 8.179 -3.372 0.823 2.006 H37 3D4 81 3D4 H38 H38 H 0 1 N N N 2.342 27.247 6.807 -5.124 1.139 -0.371 H38 3D4 82 3D4 H40 H40 H 0 1 N N N 2.858 39.101 6.034 2.780 -3.956 -1.365 H40 3D4 83 3D4 H41 H41 H 0 1 N N N 1.485 38.573 7.065 4.071 -3.648 -0.180 H41 3D4 84 3D4 H42 H42 H 0 1 N N N 0.389 37.518 5.265 3.125 -5.394 1.304 H42 3D4 85 3D4 H43 H43 H 0 1 N N N 1.867 37.531 4.244 1.834 -5.702 0.119 H43 3D4 86 3D4 H44 H44 H 0 1 N N N 1.629 39.790 3.692 3.536 -6.328 -1.572 H44 3D4 87 3D4 H45 H45 H 0 1 N N N 0.639 40.151 5.147 4.827 -6.020 -0.387 H45 3D4 88 3D4 H46 H46 H 0 1 N N N -0.668 40.068 3.169 4.232 -8.349 -0.469 H46 3D4 89 3D4 H47 H47 H 0 1 N N N -0.202 38.534 2.858 3.801 -7.723 1.010 H47 3D4 90 # 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 3D4 NZ CE SING N N 1 3D4 CE CD SING N N 2 3D4 CD CG SING N N 3 3D4 NAC CBH SING N N 4 3D4 OAD CBH DOUB N N 5 3D4 CBH CBR SING N N 6 3D4 CG CB SING N N 7 3D4 CAJ CAN DOUB Y N 8 3D4 CAJ CAI SING Y N 9 3D4 CAN CBM SING Y N 10 3D4 CB CA SING N N 11 3D4 CBR NBG SING N N 12 3D4 CBR CBB SING N N 13 3D4 NBG CBK SING N N 14 3D4 NBD CAZ SING N N 15 3D4 NBD C SING N N 16 3D4 CAI CAK DOUB Y N 17 3D4 OAE CBI DOUB N N 18 3D4 CAZ CBI SING N N 19 3D4 CBI NBF SING N N 20 3D4 CBM CBB SING N N 21 3D4 CBM CAO DOUB Y N 22 3D4 CA C SING N N 23 3D4 CA N SING N N 24 3D4 NBF CBS SING N N 25 3D4 C O DOUB N N 26 3D4 CBS CBK SING N N 27 3D4 CBS CBP SING N N 28 3D4 CBK OAG SING N N 29 3D4 CAK CAO SING Y N 30 3D4 N CBA SING N N 31 3D4 OAH CBP SING N N 32 3D4 CBP CAA SING N N 33 3D4 CAQ CAS DOUB Y N 34 3D4 CAQ CBL SING Y N 35 3D4 CBA CBL SING N N 36 3D4 CAS CBN SING Y N 37 3D4 CBL CAR DOUB Y N 38 3D4 CAU NBC DOUB Y N 39 3D4 CAU CBO SING Y N 40 3D4 CBN CBO SING N N 41 3D4 CBN CAT DOUB Y N 42 3D4 CAR CAT SING Y N 43 3D4 NBC CAM SING Y N 44 3D4 CBO CAP DOUB Y N 45 3D4 CAM CAL DOUB Y N 46 3D4 CAP CAL SING Y N 47 3D4 N H1 SING N N 48 3D4 CA H3 SING N N 49 3D4 CAA H4 SING N N 50 3D4 CAA H5 SING N N 51 3D4 CAA H6 SING N N 52 3D4 CAI H7 SING N N 53 3D4 CAJ H8 SING N N 54 3D4 CAK H9 SING N N 55 3D4 CAL H10 SING N N 56 3D4 CAM H11 SING N N 57 3D4 CAN H12 SING N N 58 3D4 CAO H13 SING N N 59 3D4 CAP H14 SING N N 60 3D4 CAQ H15 SING N N 61 3D4 CAR H16 SING N N 62 3D4 CAS H17 SING N N 63 3D4 CAT H18 SING N N 64 3D4 CAU H19 SING N N 65 3D4 CAZ H20 SING N N 66 3D4 CAZ H21 SING N N 67 3D4 NAC H22 SING N N 68 3D4 NAC H23 SING N N 69 3D4 OAG H24 SING N N 70 3D4 OAH H25 SING N N 71 3D4 CB H26 SING N N 72 3D4 CB H27 SING N N 73 3D4 CBA H28 SING N N 74 3D4 CBA H29 SING N N 75 3D4 CBB H30 SING N N 76 3D4 CBB H31 SING N N 77 3D4 CBK H32 SING N N 78 3D4 CBP H33 SING N N 79 3D4 CBR H34 SING N N 80 3D4 CBS H35 SING N N 81 3D4 NBD H36 SING N N 82 3D4 NBF H37 SING N N 83 3D4 NBG H38 SING N N 84 3D4 CG H40 SING N N 85 3D4 CG H41 SING N N 86 3D4 CD H42 SING N N 87 3D4 CD H43 SING N N 88 3D4 CE H44 SING N N 89 3D4 CE H45 SING N N 90 3D4 NZ H46 SING N N 91 3D4 NZ H47 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 3D4 SMILES ACDLabs 12.01 "O=C(N)C(NC(O)C(NC(=O)CNC(=O)C(NCc2ccc(c1cccnc1)cc2)CCCCN)C(O)C)Cc3ccccc3" 3D4 InChI InChI 1.03 ;InChI=1S/C33H45N7O5/c1-22(41)30(33(45)39-28(31(35)43)18-23-8-3-2-4-9-23)40-29(42)21-38-32(44)27(11-5-6-16-34)37-19-24-12-14-25(15-13-24)26-10-7-17-36-20-26/h2-4,7-10,12-15,17,20,22,27-28,30,33,37,39,41,45H,5-6,11,16,18-19,21,34H2,1H3,(H2,35,43)(H,38,44)(H,40,42)/t22-,27+,28-,30+,33-/m1/s1 ; 3D4 InChIKey InChI 1.03 BRQFAWWKRPKMBL-ZQZHLTTKSA-N 3D4 SMILES_CANONICAL CACTVS 3.385 "C[C@@H](O)[C@H](NC(=O)CNC(=O)[C@H](CCCCN)NCc1ccc(cc1)c2cccnc2)[C@@H](O)N[C@H](Cc3ccccc3)C(N)=O" 3D4 SMILES CACTVS 3.385 "C[CH](O)[CH](NC(=O)CNC(=O)[CH](CCCCN)NCc1ccc(cc1)c2cccnc2)[CH](O)N[CH](Cc3ccccc3)C(N)=O" 3D4 SMILES_CANONICAL "OpenEye OEToolkits" 1.9.2 "C[C@H]([C@@H]([C@H](N[C@H](Cc1ccccc1)C(=O)N)O)NC(=O)CNC(=O)[C@H](CCCCN)NCc2ccc(cc2)c3cccnc3)O" 3D4 SMILES "OpenEye OEToolkits" 1.9.2 "CC(C(C(NC(Cc1ccccc1)C(=O)N)O)NC(=O)CNC(=O)C(CCCCN)NCc2ccc(cc2)c3cccnc3)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 3D4 "SYSTEMATIC NAME" ACDLabs 12.01 "N~2~-[4-(pyridin-3-yl)benzyl]-L-lysyl-N-[(1R,2S,3R)-1-{[(2R)-1-amino-1-oxo-3-phenylpropan-2-yl]amino}-1,3-dihydroxybutan-2-yl]glycinamide" 3D4 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.9.2 "(2S)-6-azanyl-N-[2-[[(1R,2S,3R)-1-[[(2R)-1-azanyl-1-oxidanylidene-3-phenyl-propan-2-yl]amino]-1,3-bis(oxidanyl)butan-2-yl]amino]-2-oxidanylidene-ethyl]-2-[(4-pyridin-3-ylphenyl)methylamino]hexanamide" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site 3D4 "Create component" 2014-07-28 RCSB 3D4 "Modify descriptor" 2014-09-05 RCSB 3D4 "Initial release" 2015-05-13 RCSB #