6OCZ

Crystal Structure of Mycobacterium tuberculosis Proteasome in Complex with Phenylimidazole-based Inhibitor A86

PDB DOI: https://doi.org/10.2210/pdb6OCZ/pdb

Classification: HYDROLASE/HYDROLASE INHIBITOR
Organism(s): Mycobacterium tuberculosis H37Rv
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2019-03-25 Released: 2019-10-09
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: 2.65 Å
R-Value Free: 0.235
R-Value Work: 0.184
R-Value Observed: 0.187

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Selective Phenylimidazole-Based Inhibitors of theMycobacterium tuberculosisProteasome.

Zhan, W., Hsu, H.C., Morgan, T., Ouellette, T., Burns-Huang, K., Hara, R., Wright, A.G., Imaeda, T., Okamoto, R., Sato, K., Michino, M., Ramjee, M., Aso, K., Meinke, P.T., Foley, M., Nathan, C.F., Li, H., Lin, G.

(2019) J Med Chem 62: 9246-9253

PubMed: 31560200 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1021/acs.jmedchem.9b01187
Primary Citation of Related Structures:
6OCW, 6OCZ, 6ODE

PubMed Abstract:
Proteasomes of pathogenic microbes have become attractive targets for anti-infectives. Coevolving with its human host, Mycobacterium tuberculosis (Mtb) has developed mechanisms to resist host-imposed nitrosative and oxidative stresses. Genetic deletion or pharmacological inhibition of the Mtb proteasome (Mtb20S) renders nonreplicating Mtb susceptible to reactive nitrogen species in vitro and unable to survive in the lungs of mice, validating the Mtb proteasome as a promising target for anti-Mtb agents. Using a structure-guided and flow chemistry-enabled study of structure-activity relationships, we developed phenylimidazole-based peptidomimetics that are highly potent for Mtb20S. X-ray structures of selected compounds with Mtb20S shed light on their selectivity for mycobacterial over human proteasomes.

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 717.94 kDa
Atom Count: 48,025
Modelled Residue Count: 6,148
Deposited Residue Count: 6,636
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 H37Rv	Mutation(s): 0 Gene Names: prcA, Rv2109c 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	234	Mycobacterium tuberculosis H37Rv	Mutation(s): 0 Gene Names: prcB, Rv2110c 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
M6Y Query on M6Y Download Ideal Coordinates CCD File SDF format, chain KA [auth H] SDF format, chain KB [auth V] SDF format, chain MA [auth I] SDF format, chain MB [auth W] SDF format, chain OB [auth X] SDF format, chain PA [auth J] SDF format, chain QB [auth Y] SDF format, chain SB [auth Z] SDF format, chain TA [auth K] SDF format, chain UB [auth a] SDF format, chain VA [auth L] SDF format, chain WB [auth b] SDF format, chain XA [auth M] SDF format, chain ZA [auth N] MOL2 format, chain KA [auth H] MOL2 format, chain KB [auth V] MOL2 format, chain MA [auth I] MOL2 format, chain MB [auth W] MOL2 format, chain OB [auth X] MOL2 format, chain PA [auth J] MOL2 format, chain QB [auth Y] MOL2 format, chain SB [auth Z] MOL2 format, chain TA [auth K] MOL2 format, chain UB [auth a] MOL2 format, chain VA [auth L] MOL2 format, chain WB [auth b] MOL2 format, chain XA [auth M] MOL2 format, chain ZA [auth N] mmCIF format, chain KA [auth H] mmCIF format, chain KB [auth V] mmCIF format, chain MA [auth I] mmCIF format, chain MB [auth W] mmCIF format, chain OB [auth X] mmCIF format, chain PA [auth J] mmCIF format, chain QB [auth Y] mmCIF format, chain SB [auth Z] mmCIF format, chain TA [auth K] mmCIF format, chain UB [auth a] mmCIF format, chain VA [auth L] mmCIF format, chain WB [auth b] mmCIF format, chain XA [auth M] mmCIF format, chain ZA [auth N]	KA [auth H] KB [auth V] MA [auth I] MB [auth W] OB [auth X] KA [auth H], KB [auth V], MA [auth I], MB [auth W], OB [auth X], PA [auth J], QB [auth Y], SB [auth Z], TA [auth K], UB [auth a], VA [auth L], WB [auth b], XA [auth M], ZA [auth N]	N-{(2S)-1-({(2S)-1-[(2,4-difluorobenzyl)amino]-1-oxopropan-2-yl}amino)-1,4-dioxo-4-[(2R)-2-phenylpyrrolidin-1-yl]butan-2-yl}-5-methyl-1,2-oxazole-3-carboxamide (non-preferred name) C₂₉ H₃₁ F₂ N₅ O₅ ZUCKFGZJAOBNRP-VVMVZBAXSA-N		Interactions Focus chain KA [auth H] Focus chain KB [auth V] Focus chain MA [auth I] Focus chain MB [auth W] Focus chain OB [auth X] Focus chain PA [auth J] Focus chain QB [auth Y] Focus chain SB [auth Z] Focus chain TA [auth K] Focus chain UB [auth a] Focus chain VA [auth L] Focus chain WB [auth b] Focus chain XA [auth M] Focus chain ZA [auth N] Interactions & Density Focus chain KA [auth H] Focus chain KB [auth V] Focus chain MA [auth I] Focus chain MB [auth W] Focus chain OB [auth X] Focus chain PA [auth J] Focus chain QB [auth Y] Focus chain SB [auth Z] Focus chain TA [auth K] Focus chain UB [auth a] Focus chain VA [auth L] Focus chain WB [auth b] Focus chain XA [auth M] Focus chain ZA [auth N]
CIT Query on CIT Download Ideal Coordinates CCD File SDF format, chain AB [auth N] SDF format, chain LA [auth H] SDF format, chain LB [auth V] SDF format, chain NA [auth I] SDF format, chain NB [auth W] SDF format, chain PB [auth X] SDF format, chain QA [auth J] SDF format, chain RB [auth Y] SDF format, chain TB [auth Z] SDF format, chain UA [auth K] SDF format, chain VB [auth a] SDF format, chain WA [auth L] SDF format, chain XB [auth b] SDF format, chain YA [auth M] MOL2 format, chain AB [auth N] MOL2 format, chain LA [auth H] MOL2 format, chain LB [auth V] MOL2 format, chain NA [auth I] MOL2 format, chain NB [auth W] MOL2 format, chain PB [auth X] MOL2 format, chain QA [auth J] MOL2 format, chain RB [auth Y] MOL2 format, chain TB [auth Z] MOL2 format, chain UA [auth K] MOL2 format, chain VB [auth a] MOL2 format, chain WA [auth L] MOL2 format, chain XB [auth b] MOL2 format, chain YA [auth M] mmCIF format, chain AB [auth N] mmCIF format, chain LA [auth H] mmCIF format, chain LB [auth V] mmCIF format, chain NA [auth I] mmCIF format, chain NB [auth W] mmCIF format, chain PB [auth X] mmCIF format, chain QA [auth J] mmCIF format, chain RB [auth Y] mmCIF format, chain TB [auth Z] mmCIF format, chain UA [auth K] mmCIF format, chain VB [auth a] mmCIF format, chain WA [auth L] mmCIF format, chain XB [auth b] mmCIF format, chain YA [auth M]	AB [auth N] LA [auth H] LB [auth V] NA [auth I] NB [auth W] AB [auth N], LA [auth H], LB [auth V], NA [auth I], NB [auth W], PB [auth X], QA [auth J], RB [auth Y], TB [auth Z], UA [auth K], VB [auth a], WA [auth L], XB [auth b], YA [auth M]	CITRIC ACID C₆ H₈ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-N		Interactions Focus chain AB [auth N] Focus chain LA [auth H] Focus chain LB [auth V] Focus chain NA [auth I] Focus chain NB [auth W] Focus chain PB [auth X] Focus chain QA [auth J] Focus chain RB [auth Y] Focus chain TB [auth Z] Focus chain UA [auth K] Focus chain VB [auth a] Focus chain WA [auth L] Focus chain XB [auth b] Focus chain YA [auth M] Interactions & Density Focus chain AB [auth N] Focus chain LA [auth H] Focus chain LB [auth V] Focus chain NA [auth I] Focus chain NB [auth W] Focus chain PB [auth X] Focus chain QA [auth J] Focus chain RB [auth Y] Focus chain TB [auth Z] Focus chain UA [auth K] Focus chain VB [auth a] Focus chain WA [auth L] Focus chain XB [auth b] Focus chain YA [auth M]
DMF Query on DMF Download Ideal Coordinates CCD File SDF format, chain BB [auth O] SDF format, chain CA [auth A] SDF format, chain CB [auth P] SDF format, chain DA [auth B] SDF format, chain DB [auth Q] SDF format, chain EA [auth C] SDF format, chain EB [auth R] SDF format, chain FA [auth E] SDF format, chain FB [auth R] SDF format, chain GA [auth F] SDF format, chain GB [auth S] SDF format, chain HA [auth F] SDF format, chain HB [auth S] SDF format, chain IA [auth G] SDF format, chain IB [auth T] SDF format, chain JA [auth G] SDF format, chain JB [auth U] SDF format, chain OA [auth I] SDF format, chain RA [auth J] SDF format, chain SA [auth J] MOL2 format, chain BB [auth O] MOL2 format, chain CA [auth A] MOL2 format, chain CB [auth P] MOL2 format, chain DA [auth B] MOL2 format, chain DB [auth Q] MOL2 format, chain EA [auth C] MOL2 format, chain EB [auth R] MOL2 format, chain FA [auth E] MOL2 format, chain FB [auth R] MOL2 format, chain GA [auth F] MOL2 format, chain GB [auth S] MOL2 format, chain HA [auth F] MOL2 format, chain HB [auth S] MOL2 format, chain IA [auth G] MOL2 format, chain IB [auth T] MOL2 format, chain JA [auth G] MOL2 format, chain JB [auth U] MOL2 format, chain OA [auth I] MOL2 format, chain RA [auth J] MOL2 format, chain SA [auth J] mmCIF format, chain BB [auth O] mmCIF format, chain CA [auth A] mmCIF format, chain CB [auth P] mmCIF format, chain DA [auth B] mmCIF format, chain DB [auth Q] mmCIF format, chain EA [auth C] mmCIF format, chain EB [auth R] mmCIF format, chain FA [auth E] mmCIF format, chain FB [auth R] mmCIF format, chain GA [auth F] mmCIF format, chain GB [auth S] mmCIF format, chain HA [auth F] mmCIF format, chain HB [auth S] mmCIF format, chain IA [auth G] mmCIF format, chain IB [auth T] mmCIF format, chain JA [auth G] mmCIF format, chain JB [auth U] mmCIF format, chain OA [auth I] mmCIF format, chain RA [auth J] mmCIF format, chain SA [auth J]	BB [auth O] CA [auth A] CB [auth P] DA [auth B] DB [auth Q] BB [auth O], CA [auth A], CB [auth P], DA [auth B], DB [auth Q], EA [auth C], EB [auth R], FA [auth E], FB [auth R], GA [auth F], GB [auth S], HA [auth F], HB [auth S], IA [auth G], IB [auth T], JA [auth G], JB [auth U], OA [auth I], RA [auth J], SA [auth J]	DIMETHYLFORMAMIDE C₃ H₇ N O ZMXDDKWLCZADIW-UHFFFAOYSA-N		Interactions Focus chain BB [auth O] Focus chain CA [auth A] Focus chain CB [auth P] Focus chain DA [auth B] Focus chain DB [auth Q] Focus chain EA [auth C] Focus chain EB [auth R] Focus chain FA [auth E] Focus chain FB [auth R] Focus chain GA [auth F] Focus chain GB [auth S] Focus chain HA [auth F] Focus chain HB [auth S] Focus chain IA [auth G] Focus chain IB [auth T] Focus chain JA [auth G] Focus chain JB [auth U] Focus chain OA [auth I] Focus chain RA [auth J] Focus chain SA [auth J] Interactions & Density Focus chain BB [auth O] Focus chain CA [auth A] Focus chain CB [auth P] Focus chain DA [auth B] Focus chain DB [auth Q] Focus chain EA [auth C] Focus chain EB [auth R] Focus chain FA [auth E] Focus chain FB [auth R] Focus chain GA [auth F] Focus chain GB [auth S] Focus chain HA [auth F] Focus chain HB [auth S] Focus chain IA [auth G] Focus chain IB [auth T] Focus chain JA [auth G] Focus chain JB [auth U] Focus chain OA [auth I] Focus chain RA [auth J] Focus chain SA [auth J]