data_XTP
#
_chem_comp.id XTP
_chem_comp.name "benzyl [(2S)-3-cyclopropyl-1-({(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}amino)-1-oxopropan-2-yl]carbamate"
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C21 H29 N3 O5"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2021-01-13
_chem_comp.pdbx_modified_date 2024-09-27
_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 403.472
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code XTP
_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 7LCS
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site RCSB
_chem_comp.pdbx_pcm Y
#
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
XTP C10 C1 C 0 1 N N N N N N -11.609 15.658 4.358 5.561 -1.436 -1.208 C10 XTP 1
XTP C15 C2 C 0 1 N N N N N N -16.386 12.883 -0.582 0.389 2.843 0.032 C15 XTP 2
XTP C17 C3 C 0 1 N N N N N N -18.788 13.729 -0.384 -0.265 5.193 -0.912 C17 XTP 3
XTP C20 C4 C 0 1 N N N N N N -15.041 16.307 0.224 -2.022 0.082 -0.296 C20 XTP 4
XTP C22 C5 C 0 1 N N N N N N -14.164 18.492 -0.008 -3.986 -1.233 -0.627 C22 XTP 5
XTP C24 C6 C 0 1 Y N N N N N -11.783 19.171 0.446 -5.859 -1.862 0.910 C24 XTP 6
XTP C26 C7 C 0 1 Y N N N N N -9.740 18.022 -0.383 -8.122 -1.237 0.440 C26 XTP 7
XTP C28 C8 C 0 1 Y N N N N N -12.005 17.138 -0.940 -6.369 -0.604 -1.062 C28 XTP 8
XTP C02 C9 C 0 1 N N N N N N -14.255 13.379 0.643 0.924 0.534 0.762 C02 XTP 9
XTP C04 C10 C 0 1 N N S N N N -12.637 12.439 2.365 3.118 -0.228 1.500 C04 XTP 10
XTP C05 C11 C 0 1 N N N N N N -12.279 13.281 3.595 4.467 -0.467 0.821 C05 XTP 11
XTP C06 C12 C 0 1 N N S N N N -11.956 14.758 3.190 4.259 -1.291 -0.452 C06 XTP 12
XTP C07 C13 C 0 1 N N N N N N -10.758 14.777 2.297 3.862 -2.743 -0.097 C07 XTP 13
XTP C08 C14 C 0 1 N N N N N N -10.098 16.144 2.563 4.590 -3.546 -1.198 C08 XTP 14
XTP C12 C15 C 0 1 N N N N N N -12.691 10.915 2.564 3.336 0.515 2.820 C12 XTP 15
XTP C14 C16 C 0 1 N N S N N N -15.665 13.857 0.324 0.046 1.362 -0.141 C14 XTP 16
XTP C16 C17 C 0 1 N N N N N N -17.791 12.669 -0.008 -0.401 3.671 -0.984 C16 XTP 17
XTP C18 C18 C 0 1 N N N N N N -18.869 12.355 -1.059 0.393 4.419 -2.056 C18 XTP 18
XTP C23 C19 C 0 1 Y N N N N N -12.612 18.303 -0.130 -5.445 -1.233 -0.249 C23 XTP 19
XTP C25 C20 C 0 1 Y N N N N N -10.251 19.021 0.321 -7.198 -1.867 1.253 C25 XTP 20
XTP C27 C21 C 0 1 Y N N N N N -10.682 17.010 -1.056 -7.707 -0.604 -0.716 C27 XTP 21
XTP N03 N1 N 0 1 N N N N N N -13.960 12.925 1.993 2.264 0.577 0.623 N03 XTP 22
XTP N09 N2 N 0 1 N N N N N N -10.461 16.515 3.982 5.720 -2.707 -1.614 N09 XTP 23
XTP N19 N3 N 0 1 N N N N N N -15.595 15.094 -0.385 -1.359 1.142 0.209 N19 XTP 24
XTP O01 O1 O 0 1 N N N N N N -13.394 13.358 -0.158 0.425 -0.170 1.614 O01 XTP 25
XTP O11 O2 O 0 1 N N N N N N -12.130 15.719 5.415 6.344 -0.535 -1.422 O11 XTP 26
XTP O13 O3 O 0 1 N N N N N N -11.690 10.346 2.939 4.071 1.716 2.575 O13 XTP 27
XTP O21 O4 O 0 1 N N N N N N -14.862 17.411 -0.639 -3.337 -0.068 -0.051 O21 XTP 28
XTP O29 O5 O 0 1 N N N N N N -14.728 16.369 1.391 -1.432 -0.738 -0.971 O29 XTP 29
XTP H151 H1 H 0 0 N N N N N N -15.843 11.927 -0.612 0.129 3.161 1.041 H151 XTP 30
XTP H152 H2 H 0 0 N N N N N N -16.455 13.297 -1.599 1.457 2.990 -0.132 H152 XTP 31
XTP H172 H3 H 0 0 N N N N N N -18.463 14.606 -0.964 -1.147 5.789 -1.150 H172 XTP 32
XTP H171 H4 H 0 0 N N N N N N -19.563 14.032 0.336 0.387 5.605 -0.142 H171 XTP 33
XTP H221 H5 H 0 0 N N N N N N -14.451 19.437 -0.492 -3.512 -2.138 -0.246 H221 XTP 34
XTP H222 H6 H 0 0 N N N N N N -14.440 18.526 1.056 -3.891 -1.202 -1.712 H222 XTP 35
XTP H241 H7 H 0 0 N N N N N N -12.190 19.996 1.012 -5.137 -2.353 1.545 H241 XTP 36
XTP H261 H8 H 0 0 N N N N N N -8.670 17.919 -0.484 -9.168 -1.241 0.708 H261 XTP 37
XTP H281 H9 H 0 0 N N N N N N -12.656 16.421 -1.417 -6.045 -0.112 -1.968 H281 XTP 38
XTP H041 H10 H 0 0 N N N N N N -11.919 12.664 1.562 2.636 -1.185 1.698 H041 XTP 39
XTP H052 H11 H 0 0 N N N N N N -13.129 13.277 4.293 4.919 0.491 0.563 H052 XTP 40
XTP H051 H12 H 0 0 N N N N N N -11.398 12.842 4.087 5.126 -1.008 1.500 H051 XTP 41
XTP H061 H13 H 0 0 N N N N N N -12.822 15.174 2.655 3.500 -0.830 -1.084 H061 XTP 42
XTP H071 H14 H 0 0 N N N N N N -11.058 14.689 1.242 4.232 -3.014 0.892 H071 XTP 43
XTP H072 H15 H 0 0 N N N N N N -10.070 13.957 2.552 2.783 -2.883 -0.160 H072 XTP 44
XTP H082 H16 H 0 0 N N N N N N -9.006 16.068 2.456 4.948 -4.495 -0.798 H082 XTP 45
XTP H081 H17 H 0 0 N N N N N N -10.484 16.897 1.861 3.923 -3.719 -2.042 H081 XTP 46
XTP H121 H18 H 0 0 N N N N N N -13.477 10.712 3.306 2.371 0.764 3.261 H121 XTP 47
XTP H141 H19 H 0 0 N N N N N N -16.231 13.976 1.260 0.213 1.069 -1.178 H141 XTP 48
XTP H161 H20 H 0 0 N N N N N N -17.879 12.190 0.978 -1.372 3.265 -1.267 H161 XTP 49
XTP H181 H21 H 0 0 N N N N N N -19.693 11.668 -0.819 -0.056 4.505 -3.046 H181 XTP 50
XTP H182 H22 H 0 0 N N N N N N -18.594 12.241 -2.118 1.478 4.321 -2.039 H182 XTP 51
XTP H251 H23 H 0 0 N N N N N N -9.597 19.730 0.807 -7.522 -2.362 2.157 H251 XTP 52
XTP H271 H24 H 0 0 N N N N N N -10.270 16.190 -1.626 -8.429 -0.113 -1.352 H271 XTP 53
XTP H031 H25 H 0 0 N N N N N N -14.683 12.947 2.683 2.663 1.140 -0.059 H031 XTP 54
XTP H091 H26 H 0 0 N N N N N N -10.015 17.203 4.554 6.487 -3.030 -2.112 H091 XTP 55
XTP H191 H27 H 0 0 N N N N N N -15.934 15.134 -1.325 -1.813 1.759 0.804 H191 XTP 56
XTP H1 H28 H 0 1 N Y N N N N -12.975 10.471 1.598 3.896 -0.120 3.506 H1 XTP 57
XTP H2 H29 H 0 1 N N N N N N -11.865 9.416 3.019 4.246 2.239 3.369 H2 XTP 58
#
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
XTP C18 C17 SING N N 1
XTP C18 C16 SING N N 2
XTP C27 C28 DOUB Y N 3
XTP C27 C26 SING Y N 4
XTP C28 C23 SING Y N 5
XTP O21 C22 SING N N 6
XTP O21 C20 SING N N 7
XTP C15 C16 SING N N 8
XTP C15 C14 SING N N 9
XTP N19 C20 SING N N 10
XTP N19 C14 SING N N 11
XTP C17 C16 SING N N 12
XTP C26 C25 DOUB Y N 13
XTP O01 C02 DOUB N N 14
XTP C23 C22 SING N N 15
XTP C23 C24 DOUB Y N 16
XTP C20 O29 DOUB N N 17
XTP C25 C24 SING Y N 18
XTP C14 C02 SING N N 19
XTP C02 N03 SING N N 20
XTP N03 C04 SING N N 21
XTP C07 C08 SING N N 22
XTP C07 C06 SING N N 23
XTP C04 C12 SING N N 24
XTP C04 C05 SING N N 25
XTP C08 N09 SING N N 26
XTP C12 O13 SING N N 27
XTP C06 C05 SING N N 28
XTP C06 C10 SING N N 29
XTP N09 C10 SING N N 30
XTP C10 O11 DOUB N N 31
XTP C15 H151 SING N N 32
XTP C15 H152 SING N N 33
XTP C17 H172 SING N N 34
XTP C17 H171 SING N N 35
XTP C22 H221 SING N N 36
XTP C22 H222 SING N N 37
XTP C24 H241 SING N N 38
XTP C26 H261 SING N N 39
XTP C28 H281 SING N N 40
XTP C04 H041 SING N N 41
XTP C05 H052 SING N N 42
XTP C05 H051 SING N N 43
XTP C06 H061 SING N N 44
XTP C07 H071 SING N N 45
XTP C07 H072 SING N N 46
XTP C08 H082 SING N N 47
XTP C08 H081 SING N N 48
XTP C12 H121 SING N N 49
XTP C14 H141 SING N N 50
XTP C16 H161 SING N N 51
XTP C18 H181 SING N N 52
XTP C18 H182 SING N N 53
XTP C25 H251 SING N N 54
XTP C27 H271 SING N N 55
XTP N03 H031 SING N N 56
XTP N09 H091 SING N N 57
XTP N19 H191 SING N N 58
XTP C12 H1 SING N N 59
XTP O13 H2 SING N N 60
#
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
XTP SMILES ACDLabs 12.01 "C3(=O)C(CC(CO)NC(C(CC1CC1)NC(=O)OCc2ccccc2)=O)CCN3"
XTP InChI InChI 1.03 "InChI=1S/C21H29N3O5/c25-12-17(11-16-8-9-22-19(16)26)23-20(27)18(10-14-6-7-14)24-21(28)29-13-15-4-2-1-3-5-15/h1-5,14,16-18,25H,6-13H2,(H,22,26)(H,23,27)(H,24,28)/t16-,17-,18-/m0/s1"
XTP InChIKey InChI 1.03 PJKBYKVMAKWNAK-BZSNNMDCSA-N
XTP SMILES_CANONICAL CACTVS 3.385 "OC[C@H](C[C@@H]1CCNC1=O)NC(=O)[C@H](CC2CC2)NC(=O)OCc3ccccc3"
XTP SMILES CACTVS 3.385 "OC[CH](C[CH]1CCNC1=O)NC(=O)[CH](CC2CC2)NC(=O)OCc3ccccc3"
XTP SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1ccc(cc1)COC(=O)N[C@@H](CC2CC2)C(=O)N[C@@H](C[C@@H]3CCNC3=O)CO"
XTP SMILES "OpenEye OEToolkits" 2.0.7 "c1ccc(cc1)COC(=O)NC(CC2CC2)C(=O)NC(CC3CCNC3=O)CO"
#
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
XTP "SYSTEMATIC NAME" ACDLabs 12.01 "benzyl [(2S)-3-cyclopropyl-1-({(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}amino)-1-oxopropan-2-yl]carbamate"
XTP "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "(phenylmethyl) ~{N}-[(2~{S})-3-cyclopropyl-1-oxidanylidene-1-[[(2~{S})-1-oxidanyl-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]amino]propan-2-yl]carbamate"
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
XTP "Create component" 2021-01-13 RCSB
XTP "Initial release" 2021-07-07 RCSB
XTP "Modify PCM" 2024-09-27 PDBE
#
_pdbx_chem_comp_pcm.pcm_id 1
_pdbx_chem_comp_pcm.comp_id XTP
_pdbx_chem_comp_pcm.modified_residue_id CYS
_pdbx_chem_comp_pcm.type None
_pdbx_chem_comp_pcm.category "Covalent chemical modification"
_pdbx_chem_comp_pcm.position "Amino-acid side chain"
_pdbx_chem_comp_pcm.polypeptide_position "Any position"
_pdbx_chem_comp_pcm.comp_id_linking_atom C12
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom SG
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession ?
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession ?
#