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 
# 
