data_YVP # _chem_comp.id YVP _chem_comp.name "N-{3-[(prop-2-yn-1-yl)oxy]propanoyl}-D-phenylalanyl-N-[(3S)-6-carbamimidamido-2-oxohexan-3-yl]-L-phenylalaninamide" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C31 H40 N6 O5" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2021-04-01 _chem_comp.pdbx_modified_date 2022-10-07 _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 576.686 _chem_comp.one_letter_code ? _chem_comp.three_letter_code YVP _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 7MAU _chem_comp.pdbx_subcomponent_list "YWD DPN PHE ARM" _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 YVP C10 C1 C 0 1 N N N 30.592 -2.380 7.274 8.369 2.934 1.253 C10 YWD 1 YVP C01 C10 C 0 1 N N N 30.286 -6.356 7.688 4.103 0.702 0.484 C01 YWD 2 YVP C05 C12 C 0 1 N N N 29.593 -5.565 8.793 5.128 1.655 -0.075 C05 YWD 3 YVP C08 C15 C 0 1 N N N 30.144 -4.132 8.806 6.276 1.812 0.924 C08 YWD 4 YVP C11 C16 C 0 1 N N N 32.025 -2.871 7.231 9.302 3.875 0.613 C11 YWD 5 YVP C12 C17 C 0 1 N N N 33.084 -3.362 7.281 10.047 4.625 0.103 C12 YWD 6 YVP O03 O1 O 0 1 N N N 31.207 -7.057 7.955 4.274 0.198 1.574 O03 YWD 7 YVP O09 O2 O 0 1 N N N 29.808 -3.494 7.608 7.248 2.716 0.394 O09 YWD 8 YVP N02 N1 N 0 1 N N N 29.791 -6.240 6.333 2.996 0.410 -0.227 N DPN 9 YVP C04 C11 C 0 1 N N R 30.493 -6.992 5.351 2.000 -0.516 0.317 CA DPN 10 YVP C06 C13 C 0 1 N N N 29.845 -8.370 5.130 0.655 -0.227 -0.299 C DPN 11 YVP O14 O3 O 0 1 N N N 28.623 -8.454 5.185 0.541 0.666 -1.112 O DPN 12 YVP C07 C14 C 0 1 N N N 30.224 -6.397 3.957 2.410 -1.954 -0.007 CB DPN 13 YVP C40 C29 C 0 1 Y N N 31.176 -5.402 3.333 3.694 -2.284 0.709 CG DPN 14 YVP C39 C28 C 0 1 Y N N 31.036 -5.128 1.983 4.909 -2.039 0.098 CD1 DPN 15 YVP C41 C30 C 0 1 Y N N 32.144 -4.778 4.085 3.656 -2.827 1.980 CD2 DPN 16 YVP C38 C27 C 0 1 Y N N 31.881 -4.220 1.367 6.087 -2.342 0.756 CE1 DPN 17 YVP C42 C31 C 0 1 Y N N 32.991 -3.869 3.471 4.834 -3.129 2.638 CE2 DPN 18 YVP C37 C26 C 0 1 Y N N 32.863 -3.591 2.119 6.049 -2.890 2.024 CZ DPN 19 YVP N13 N2 N 0 1 N N N 30.652 -9.542 4.798 -0.420 -0.959 0.053 N PHE 20 YVP C15 C2 C 0 1 N N S 29.996 -10.791 4.503 -1.727 -0.677 -0.546 CA PHE 21 YVP C16 C18 C 0 1 N N N 30.010 -11.894 5.517 -2.817 -1.144 0.384 C PHE 22 YVP O19 O4 O 0 1 N N N 30.535 -11.763 6.540 -2.530 -1.661 1.443 O PHE 23 YVP C17 C3 C 0 1 N N N 30.644 -11.294 3.161 -1.845 -1.414 -1.882 CB PHE 24 YVP C24 C7 C 0 1 Y N N 30.670 -10.206 2.074 -0.834 -0.861 -2.852 CG PHE 25 YVP C23 C19 C 0 1 Y N N 29.514 -10.025 1.339 0.431 -1.414 -2.923 CD1 PHE 26 YVP C25 C20 C 0 1 Y N N 31.779 -9.403 1.830 -1.173 0.196 -3.676 CD2 PHE 27 YVP C22 C6 C 0 1 Y N N 29.453 -9.047 0.362 1.359 -0.907 -3.813 CE1 PHE 28 YVP C26 C8 C 0 1 Y N N 31.725 -8.410 0.861 -0.245 0.703 -4.567 CE2 PHE 29 YVP C21 C5 C 0 1 Y N N 30.557 -8.237 0.121 1.022 0.154 -4.633 CZ PHE 30 YVP N18 N3 N 0 1 N N N 29.280 -13.072 5.094 -4.110 -0.986 0.039 N ARM 31 YVP C20 C4 C 0 1 N N S 29.109 -14.258 5.920 -5.170 -1.440 0.943 CA ARM 32 YVP C28 C9 C 0 1 N N N 30.303 -14.597 6.797 -6.446 -0.641 0.674 CB ARM 33 YVP C31 C23 C 0 1 N N N 30.250 -16.121 6.982 -6.212 0.829 1.030 CG ARM 34 YVP C32 C24 C 0 1 N N N 31.498 -16.645 7.693 -7.489 1.628 0.761 CD ARM 35 YVP N33 N4 N 0 1 N N N 31.696 -15.966 8.960 -7.265 3.035 1.102 NE ARM 36 YVP C34 C25 C 0 1 N N N 30.956 -16.342 10.157 -8.278 3.951 0.942 CZ ARM 37 YVP N35 N5 N 0 1 N N N 30.112 -17.274 10.157 -8.068 5.272 1.261 NH1 ARM 38 YVP N36 N6 N 0 1 N N N 31.207 -15.609 11.388 -9.438 3.567 0.487 NH2 ARM 39 YVP C27 C21 C 0 1 N N N 27.821 -14.009 6.764 -5.436 -2.905 0.710 C ARM 40 YVP O30 O5 O 0 1 N N N 27.581 -14.656 7.716 -5.016 -3.444 -0.286 O ARM 41 YVP C29 C22 C 0 1 N N N 26.803 -12.918 6.383 -6.225 -3.697 1.720 CM ARM 42 YVP H102 H2 H 0 0 N N N 30.294 -1.985 6.292 8.876 1.986 1.436 H102 YWD 43 YVP H101 H1 H 0 0 N N N 30.481 -1.593 8.035 8.025 3.350 2.200 H101 YWD 44 YVP H051 H14 H 0 0 N N N 29.786 -6.043 9.765 5.515 1.262 -1.015 H051 YWD 45 YVP H052 H13 H 0 0 N N N 28.509 -5.541 8.605 4.664 2.625 -0.250 H052 YWD 46 YVP H082 H18 H 0 0 N N N 29.708 -3.579 9.651 5.889 2.205 1.864 H082 YWD 47 YVP H081 H17 H 0 0 N N N 31.239 -4.161 8.912 6.740 0.841 1.100 H081 YWD 48 YVP H121 H19 H 0 0 N N N 34.045 -3.807 7.326 10.713 5.297 -0.354 H121 YWD 49 YVP H021 H34 H 0 0 N N N 29.005 -5.667 6.102 2.859 0.813 -1.098 H DPN 50 YVP H041 H12 H 0 0 N N N 31.571 -7.079 5.553 1.939 -0.391 1.398 HA DPN 51 YVP H071 H16 H 0 0 N N N 30.162 -7.247 3.262 1.626 -2.638 0.318 HB2 DPN 52 YVP H072 H15 H 0 0 N N N 29.245 -5.898 4.015 2.557 -2.056 -1.083 HB3 DPN 53 YVP H391 H31 H 0 0 N N N 30.267 -5.623 1.409 4.939 -1.612 -0.893 HD1 DPN 54 YVP H411 H32 H 0 0 N N N 32.243 -4.993 5.139 2.706 -3.014 2.460 HD2 DPN 55 YVP H381 H30 H 0 0 N N N 31.777 -4.004 0.314 7.036 -2.152 0.278 HE1 DPN 56 YVP H421 H33 H 0 0 N N N 33.756 -3.374 4.050 4.804 -3.553 3.631 HE2 DPN 57 YVP H371 H29 H 0 0 N N N 33.530 -2.883 1.650 6.969 -3.127 2.538 HZ DPN 58 YVP H131 H35 H 0 0 N N N 31.650 -9.478 4.776 -0.328 -1.673 0.703 H PHE 59 YVP H151 H3 H 0 0 N N N 28.942 -10.573 4.275 -1.826 0.396 -0.713 HA PHE 60 YVP H171 H5 H 0 0 N N N 31.677 -11.612 3.366 -1.658 -2.477 -1.728 HB2 PHE 61 YVP H172 H4 H 0 0 N N N 30.063 -12.151 2.788 -2.849 -1.277 -2.284 HB3 PHE 62 YVP H231 H20 H 0 0 N N N 28.654 -10.650 1.528 0.694 -2.243 -2.283 HD1 PHE 63 YVP H251 H21 H 0 0 N N N 32.686 -9.552 2.397 -2.162 0.626 -3.624 HD2 PHE 64 YVP H221 H8 H 0 0 N N N 28.549 -8.913 -0.213 2.347 -1.339 -3.868 HE1 PHE 65 YVP H261 H9 H 0 0 N N N 32.581 -7.777 0.682 -0.510 1.529 -5.210 HE2 PHE 66 YVP H211 H7 H 0 0 N N N 30.509 -7.473 -0.641 1.747 0.551 -5.328 HZ PHE 67 YVP H181 H36 H 0 0 N N N 28.870 -13.070 4.182 -4.339 -0.573 -0.808 H ARM 68 YVP H201 H6 H 0 0 N N N 28.913 -15.120 5.265 -4.856 -1.287 1.976 HA ARM 69 YVP H281 H11 H 0 0 N N N 30.224 -14.088 7.769 -6.710 -0.722 -0.380 HB2 ARM 70 YVP H282 H10 H 0 0 N N N 31.240 -14.301 6.303 -7.258 -1.037 1.283 HB3 ARM 71 YVP H311 H26 H 0 0 N N N 30.175 -16.598 5.994 -5.948 0.910 2.084 HG2 ARM 72 YVP H312 H25 H 0 0 N N N 29.364 -16.377 7.581 -5.400 1.225 0.420 HG3 ARM 73 YVP H321 H27 H 0 0 N N N 31.382 -17.723 7.877 -7.753 1.547 -0.294 HD2 ARM 74 YVP H322 H28 H 0 0 N N N 32.376 -16.475 7.052 -8.301 1.232 1.370 HD3 ARM 75 YVP H331 H37 H 0 0 N N N 32.359 -15.219 9.013 -6.402 3.321 1.440 HE ARM 76 YVP H5 H39 H 0 1 N N N 29.931 -17.785 9.317 -8.782 5.918 1.148 HH1 ARM 77 YVP H361 H40 H 0 0 N N N 30.648 -15.946 12.145 -10.152 4.213 0.374 HH22 ARM 78 YVP H1 H22 H 0 1 N N N 25.972 -12.923 7.104 -7.285 -3.652 1.469 HM1 ARM 79 YVP H2 H23 H 0 1 N N N 27.296 -11.935 6.399 -5.893 -4.735 1.707 HM2 ARM 80 YVP H3 H24 H 0 1 N N N 26.414 -13.116 5.374 -6.069 -3.278 2.714 HM3 ARM 81 YVP H351 H38 H 0 0 N N N 29.622 -17.504 10.997 -7.205 5.557 1.600 H351 ARM 82 # 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 YVP C21 C22 DOUB Y N 1 YVP C21 C26 SING Y N 2 YVP C22 C23 SING Y N 3 YVP C26 C25 DOUB Y N 4 YVP C23 C24 DOUB Y N 5 YVP C38 C39 DOUB Y N 6 YVP C38 C37 SING Y N 7 YVP C25 C24 SING Y N 8 YVP C39 C40 SING Y N 9 YVP C24 C17 SING N N 10 YVP C37 C42 DOUB Y N 11 YVP C17 C15 SING N N 12 YVP C40 C07 SING N N 13 YVP C40 C41 DOUB Y N 14 YVP C42 C41 SING Y N 15 YVP C07 C04 SING N N 16 YVP C15 N13 SING N N 17 YVP C15 C16 SING N N 18 YVP N13 C06 SING N N 19 YVP N18 C16 SING N N 20 YVP N18 C20 SING N N 21 YVP C06 O14 DOUB N N 22 YVP C06 C04 SING N N 23 YVP C04 N02 SING N N 24 YVP C16 O19 DOUB N N 25 YVP C20 C27 SING N N 26 YVP C20 C28 SING N N 27 YVP N02 C01 SING N N 28 YVP C29 C27 SING N N 29 YVP C27 O30 DOUB N N 30 YVP C28 C31 SING N N 31 YVP C31 C32 SING N N 32 YVP C11 C10 SING N N 33 YVP C11 C12 TRIP N N 34 YVP C10 O09 SING N N 35 YVP O09 C08 SING N N 36 YVP C01 O03 DOUB N N 37 YVP C01 C05 SING N N 38 YVP C32 N33 SING N N 39 YVP C05 C08 SING N N 40 YVP N33 C34 SING N N 41 YVP C34 N35 SING N N 42 YVP C34 N36 DOUB N N 43 YVP C10 H101 SING N N 44 YVP C10 H102 SING N N 45 YVP C15 H151 SING N N 46 YVP C17 H172 SING N N 47 YVP C17 H171 SING N N 48 YVP C20 H201 SING N N 49 YVP C21 H211 SING N N 50 YVP C22 H221 SING N N 51 YVP C26 H261 SING N N 52 YVP C28 H282 SING N N 53 YVP C28 H281 SING N N 54 YVP C04 H041 SING N N 55 YVP C05 H052 SING N N 56 YVP C05 H051 SING N N 57 YVP C07 H072 SING N N 58 YVP C07 H071 SING N N 59 YVP C08 H081 SING N N 60 YVP C08 H082 SING N N 61 YVP C12 H121 SING N N 62 YVP C23 H231 SING N N 63 YVP C25 H251 SING N N 64 YVP C29 H1 SING N N 65 YVP C29 H2 SING N N 66 YVP C29 H3 SING N N 67 YVP C31 H312 SING N N 68 YVP C31 H311 SING N N 69 YVP C32 H321 SING N N 70 YVP C32 H322 SING N N 71 YVP C37 H371 SING N N 72 YVP C38 H381 SING N N 73 YVP C39 H391 SING N N 74 YVP C41 H411 SING N N 75 YVP C42 H421 SING N N 76 YVP N02 H021 SING N N 77 YVP N13 H131 SING N N 78 YVP N18 H181 SING N N 79 YVP N33 H331 SING N N 80 YVP N35 H351 SING N N 81 YVP N35 H5 SING N N 82 YVP N36 H361 SING N N 83 # 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 YVP SMILES ACDLabs 12.01 "CC(=O)C(CCCNC(=N)N)NC(=O)C(NC(=O)C(Cc1ccccc1)NC(=O)CCOCC#C)Cc1ccccc1" YVP InChI InChI 1.03 "InChI=1S/C31H40N6O5/c1-3-18-42-19-16-28(39)35-26(20-23-11-6-4-7-12-23)29(40)37-27(21-24-13-8-5-9-14-24)30(41)36-25(22(2)38)15-10-17-34-31(32)33/h1,4-9,11-14,25-27H,10,15-21H2,2H3,(H,35,39)(H,36,41)(H,37,40)(H4,32,33,34)/t25-,26+,27-/m0/s1" YVP InChIKey InChI 1.03 JNSZEVHYEISGKR-VJGNERBWSA-N YVP SMILES_CANONICAL CACTVS 3.385 "CC(=O)[C@H](CCCNC(N)=N)NC(=O)[C@H](Cc1ccccc1)NC(=O)[C@@H](Cc2ccccc2)NC(=O)CCOCC#C" YVP SMILES CACTVS 3.385 "CC(=O)[CH](CCCNC(N)=N)NC(=O)[CH](Cc1ccccc1)NC(=O)[CH](Cc2ccccc2)NC(=O)CCOCC#C" YVP SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "[H]/N=C(/N)\NCCC[C@@H](C(=O)C)NC(=O)[C@H](Cc1ccccc1)NC(=O)[C@@H](Cc2ccccc2)NC(=O)CCOCC#C" YVP SMILES "OpenEye OEToolkits" 2.0.7 "CC(=O)C(CCCNC(=N)N)NC(=O)C(Cc1ccccc1)NC(=O)C(Cc2ccccc2)NC(=O)CCOCC#C" # 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 YVP "SYSTEMATIC NAME" ACDLabs 12.01 "N-{3-[(prop-2-yn-1-yl)oxy]propanoyl}-D-phenylalanyl-N-[(3S)-6-carbamimidamido-2-oxohexan-3-yl]-L-phenylalaninamide" YVP "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "(2~{R})-~{N}-[(2~{S})-1-[[(3~{S})-6-carbamimidamido-2-oxidanylidene-hexan-3-yl]amino]-1-oxidanylidene-3-phenyl-propan-2-yl]-3-phenyl-2-(3-prop-2-ynoxypropanoylamino)propanamide" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site YVP "Create component" 2021-04-01 RCSB YVP "Modify subcomponent list" 2021-04-01 RCSB YVP "Initial release" 2022-10-12 RCSB #