6WNK

Macrocyclic peptides TDI5575 that selectively inhibit the Mycobacterium tuberculosis proteasome

PDB DOI: https://doi.org/10.2210/pdb6WNK/pdb

Classification: HYDROLASE/HYDROLASE INHIBITOR
Organism(s): Mycobacterium tuberculosis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2020-04-22 Released: 2021-04-28
Deposition Author(s): Hsu, H.C., Li, H.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.28 Å
R-Value Free: 0.238
R-Value Work: 0.200
R-Value Observed: 0.202

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Macrocyclic Peptides that Selectively Inhibit the Mycobacterium tuberculosis Proteasome.

Zhang, H., Hsu, H.C., Kahne, S.C., Hara, R., Zhan, W., Jiang, X., Burns-Huang, K., Ouellette, T., Imaeda, T., Okamoto, R., Kawasaki, M., Michino, M., Wong, T.T., Toita, A., Yukawa, T., Moraca, F., Vendome, J., Saha, P., Sato, K., Aso, K., Ginn, J., Meinke, P.T., Foley, M., Nathan, C.F., Darwin, K.H., Li, H., Lin, G.

(2021) J Med Chem 64: 6262-6272

PubMed: 33949190 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1021/acs.jmedchem.1c00296
Primary Citation of Related Structures:
6WNK

PubMed Abstract:
Treatment of tuberculosis (TB) currently takes at least 6 months. Latent Mycobacterium tuberculosis (Mtb) is phenotypically tolerant to most anti-TB drugs. A key hypothesis is that drugs that kill nonreplicating (NR) Mtb may shorten treatment when used in combination with conventional drugs. The Mtb proteasome (Mtb20S) could be such a target because its pharmacological inhibition kills NR Mtb and its genetic deletion renders Mtb unable to persist in mice. Here, we report a series of macrocyclic peptides that potently and selectively target the Mtb20S over human proteasomes, including macrocycle 6 . The cocrystal structure of macrocycle 6 with Mtb20S revealed structural bases for the species selectivity. Inhibition of 20S within Mtb by 6 dose dependently led to the accumulation of Pup-tagged GFP that is degradable but resistant to depupylation and death of nonreplicating Mtb under nitrosative stress. These results suggest that compounds of this class have the potential to develop as anti-TB therapeutics.

Organizational Affiliation

Department of Microbiology & Immunology, Weill Cornell Medicine, 1300 York Avenue, New York, New York 10065, United States.

Macromolecule Content

Total Structure Weight: 730 kDa
Atom Count: 48,400
Modelled Residue Count: 6,148
Deposited Residue Count: 6,720
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit alpha	A, B, C, D, E A, B, C, D, E, F, G, O, P, Q, R, S, T, U	240	Mycobacterium tuberculosis	Mutation(s): 0 Gene Names: prcA, MRA_2124 EC: 3.4.25.1
UniProt
Find proteins for P9WHU1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WHU1 Go to UniProtKB: P9WHU1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P9WHU1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit beta	AA [auth a] BA [auth b] H I J AA [auth a], BA [auth b], H, I, J, K, L, M, N, V, W, X, Y, Z	240	Mycobacterium tuberculosis	Mutation(s): 0 Gene Names: prcB, MRA_2125 EC: 3.4.25.1
UniProt
Find proteins for P9WHT9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WHT9 Go to UniProtKB: P9WHT9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P9WHT9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
U5Y (Subject of Investigation/LOI) Query on U5Y Download Ideal Coordinates CCD File SDF format, chain CA [auth H] SDF format, chain CB [auth X] SDF format, chain EA [auth I] SDF format, chain EB [auth Y] SDF format, chain GA [auth J] SDF format, chain GB [auth Z] SDF format, chain IA [auth K] SDF format, chain IB [auth a] SDF format, chain KA [auth L] SDF format, chain KB [auth b] SDF format, chain MA [auth M] SDF format, chain OA [auth N] SDF format, chain WA [auth V] SDF format, chain ZA [auth W] MOL2 format, chain CA [auth H] MOL2 format, chain CB [auth X] MOL2 format, chain EA [auth I] MOL2 format, chain EB [auth Y] MOL2 format, chain GA [auth J] MOL2 format, chain GB [auth Z] MOL2 format, chain IA [auth K] MOL2 format, chain IB [auth a] MOL2 format, chain KA [auth L] MOL2 format, chain KB [auth b] MOL2 format, chain MA [auth M] MOL2 format, chain OA [auth N] MOL2 format, chain WA [auth V] MOL2 format, chain ZA [auth W]	CA [auth H] CB [auth X] EA [auth I] EB [auth Y] GA [auth J] CA [auth H], CB [auth X], EA [auth I], EB [auth Y], GA [auth J], GB [auth Z], IA [auth K], IB [auth a], KA [auth L], KB [auth b], MA [auth M], OA [auth N], WA [auth V], ZA [auth W]	(12S,15S)-N-[(2-fluorophenyl)methyl]-10,13-dioxo-12-{2-oxo-2-[(2R)-2-phenylpyrrolidin-1-yl]ethyl}-2-oxa-11,14-diazatricyclo[15.2.2.1~3,7~]docosa-1(19),3(22),4,6,17,20-hexaene-15-carboxamide C₃₉ H₃₉ F N₄ O₅ GSMYFOQUVZHNEZ-PUPDPRJKSA-N		Interactions Focus chain CA [auth H] Focus chain CB [auth X] Focus chain EA [auth I] Focus chain EB [auth Y] Focus chain GA [auth J] Focus chain GB [auth Z] Focus chain IA [auth K] Focus chain IB [auth a] Focus chain KA [auth L] Focus chain KB [auth b] Focus chain MA [auth M] Focus chain OA [auth N] Focus chain WA [auth V] Focus chain ZA [auth W] Interactions & Density Focus chain CA [auth H] Focus chain CB [auth X] Focus chain EA [auth I] Focus chain EB [auth Y] Focus chain GA [auth J] Focus chain GB [auth Z] Focus chain IA [auth K] Focus chain IB [auth a] Focus chain KA [auth L] Focus chain KB [auth b] Focus chain MA [auth M] Focus chain OA [auth N] Focus chain WA [auth V] Focus chain ZA [auth W]
CIT Query on CIT Download Ideal Coordinates CCD File SDF format, chain AB [auth W] SDF format, chain DA [auth H] SDF format, chain DB [auth X] SDF format, chain FA [auth I] SDF format, chain FB [auth Y] SDF format, chain HA [auth J] SDF format, chain HB [auth Z] SDF format, chain JA [auth K] SDF format, chain JB [auth a] SDF format, chain LA [auth L] SDF format, chain LB [auth b] SDF format, chain NA [auth M] SDF format, chain PA [auth N] SDF format, chain XA [auth V] MOL2 format, chain AB [auth W] MOL2 format, chain DA [auth H] MOL2 format, chain DB [auth X] MOL2 format, chain FA [auth I] MOL2 format, chain FB [auth Y] MOL2 format, chain HA [auth J] MOL2 format, chain HB [auth Z] MOL2 format, chain JA [auth K] MOL2 format, chain JB [auth a] MOL2 format, chain LA [auth L] MOL2 format, chain LB [auth b] MOL2 format, chain NA [auth M] MOL2 format, chain PA [auth N] MOL2 format, chain XA [auth V]	AB [auth W] DA [auth H] DB [auth X] FA [auth I] FB [auth Y] AB [auth W], DA [auth H], DB [auth X], FA [auth I], FB [auth Y], HA [auth J], HB [auth Z], JA [auth K], JB [auth a], LA [auth L], LB [auth b], NA [auth M], PA [auth N], XA [auth V]	CITRIC ACID C₆ H₈ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-N		Interactions Focus chain AB [auth W] Focus chain DA [auth H] Focus chain DB [auth X] Focus chain FA [auth I] Focus chain FB [auth Y] Focus chain HA [auth J] Focus chain HB [auth Z] Focus chain JA [auth K] Focus chain JB [auth a] Focus chain LA [auth L] Focus chain LB [auth b] Focus chain NA [auth M] Focus chain PA [auth N] Focus chain XA [auth V] Interactions & Density Focus chain AB [auth W] Focus chain DA [auth H] Focus chain DB [auth X] Focus chain FA [auth I] Focus chain FB [auth Y] Focus chain HA [auth J] Focus chain HB [auth Z] Focus chain JA [auth K] Focus chain JB [auth a] Focus chain LA [auth L] Focus chain LB [auth b] Focus chain NA [auth M] Focus chain PA [auth N] Focus chain XA [auth V]
DMF Query on DMF Download Ideal Coordinates CCD File SDF format, chain BB [auth X] SDF format, chain QA [auth O] SDF format, chain RA [auth P] SDF format, chain SA [auth Q] SDF format, chain TA [auth R] SDF format, chain UA [auth R] SDF format, chain VA [auth S] SDF format, chain YA [auth W] MOL2 format, chain BB [auth X] MOL2 format, chain QA [auth O] MOL2 format, chain RA [auth P] MOL2 format, chain SA [auth Q] MOL2 format, chain TA [auth R] MOL2 format, chain UA [auth R] MOL2 format, chain VA [auth S] MOL2 format, chain YA [auth W]	BB [auth X] QA [auth O] RA [auth P] SA [auth Q] TA [auth R] BB [auth X], QA [auth O], RA [auth P], SA [auth Q], TA [auth R], UA [auth R], VA [auth S], YA [auth W]	DIMETHYLFORMAMIDE C₃ H₇ N O ZMXDDKWLCZADIW-UHFFFAOYSA-N		Interactions Focus chain BB [auth X] Focus chain QA [auth O] Focus chain RA [auth P] Focus chain SA [auth Q] Focus chain TA [auth R] Focus chain UA [auth R] Focus chain VA [auth S] Focus chain YA [auth W] Interactions & Density Focus chain BB [auth X] Focus chain QA [auth O] Focus chain RA [auth P] Focus chain SA [auth Q] Focus chain TA [auth R] Focus chain UA [auth R] Focus chain VA [auth S] Focus chain YA [auth W]

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_002377 (U5Y) Query on PRD_002377	CA [auth H] CB [auth X] EA [auth I] EB [auth Y] GA [auth J] CA [auth H], CB [auth X], EA [auth I], EB [auth Y], GA [auth J], GB [auth Z], IA [auth K], IB [auth a], KA [auth L], KB [auth b], MA [auth M], OA [auth N], WA [auth V], ZA [auth W]	Macrocyclic peptide TDI5575	Cyclic peptide / Inhibitor		Interactions Focus chain CA [auth H] Focus chain CB [auth X] Focus chain EA [auth I] Focus chain EB [auth Y] Focus chain GA [auth J] Focus chain GB [auth Z] Focus chain IA [auth K] Focus chain IB [auth a] Focus chain KA [auth L] Focus chain KB [auth b] Focus chain MA [auth M] Focus chain OA [auth N] Focus chain WA [auth V] Focus chain ZA [auth W] Interactions & Density Focus chain CA [auth H] Focus chain CB [auth X] Focus chain EA [auth I] Focus chain EB [auth Y] Focus chain GA [auth J] Focus chain GB [auth Z] Focus chain IA [auth K] Focus chain IB [auth a] Focus chain KA [auth L] Focus chain KB [auth b] Focus chain MA [auth M] Focus chain OA [auth N] Focus chain WA [auth V] Focus chain ZA [auth W]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.28 Å
R-Value Free: 0.238
R-Value Work: 0.200
R-Value Observed: 0.202
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 155.635	α = 90
b = 115.949	β = 91.58
c = 208.113	γ = 90

Software Package:

Software Name	Purpose
Coot	model building
PHENIX	refinement
iMOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2021-04-28

Deposition Author(s):

Hsu, H.C.

Li, H.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01 AI070285

Revision History (Full details and data files)

Version 1.0: 2021-04-28
Type: Initial release
Version 1.1: 2021-05-19
Changes: Database references
Version 1.2: 2021-05-26
Changes: Database references
Version 1.3: 2023-10-18
Changes: Data collection, Database references, Refinement description