7X8X | pdb_00007x8x

structural insights into Mycobacterium tuberculosis ClpP1P2 inhibition by Cediranib: implications for developing antimicrobial agents targeting Clp protease

PDB DOI: https://doi.org/10.2210/pdb7X8X/pdb

Classification: HYDROLASE/HYDROLASE INHIBITOR
Organism(s): Mycobacterium tuberculosis CDC1551, Mycobacterium tuberculosis, synthetic construct
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2022-03-15 Released: 2023-04-12
Deposition Author(s): Bao, R., Luo, Y.F., Zhu, Y.B., Yang, Y., Zhou, Y.Z.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.24 Å
R-Value Free:
0.254 (Depositor), 0.255 (DCC)
R-Value Work:
0.179 (Depositor), 0.182 (DCC)
R-Value Observed:
0.182 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Discovery and Mechanistic Study of Novel Mycobacterium tuberculosis ClpP1P2 Inhibitors

Yang, Y., Zhao, N., Xu, X., Zhou, Y., Luo, B., Zhang, J., Sui, J., Huang, J., Qiu, Z., Zhang, X., Zeng, J., Bai, L., Bao, R., Luo, Y.

(2023) J Med Chem 66: 16597-16614

DOI: https://doi.org/10.1021/acs.jmedchem.3c01054

Macromolecule Content

Total Structure Weight: 591.97 kDa
Atom Count: 40,796
Modeled Residue Count: 5,270
Deposited Residue Count: 5,320
Unique protein chains: 3

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-dependent Clp protease proteolytic subunit 2	A B [auth O] E [auth C] F [auth Q] I [auth F] A, B [auth O], E [auth C], F [auth Q], I [auth F], J [auth S], K [auth H], L [auth T], O [auth J], P [auth V], S [auth L], T [auth X], Y [auth E], Z [auth a]	197	Mycobacterium tuberculosis CDC1551	Mutation(s): 0 Gene Names: clpP2 EC: 3.4.21.92
UniProt
Find proteins for P9WPC3 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WPC3 Go to UniProtKB: P9WPC3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P9WPC3
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-dependent Clp protease proteolytic subunit 1	AA [auth G] BA [auth b] C [auth B] D [auth P] G [auth D] AA [auth G], BA [auth b], C [auth B], D [auth P], G [auth D], H [auth R], M [auth I], N [auth U], Q [auth K], R [auth W], U [auth M], V [auth Y], W [auth N], X [auth Z]	177	Mycobacterium tuberculosis	Mutation(s): 0 Gene Names: clpP1 EC: 3.4.21.92
UniProt
Find proteins for P9WPC5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WPC5 Go to UniProtKB: P9WPC5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P9WPC5
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
4-[[3,5-bis(fluoranyl)phenyl]methyl]-N-[(4-bromophenyl)methyl]piperazine-1-carboxamide	AB [auth 1] BB [auth 2] CA [auth c] CB [auth 3] DA [auth e] AB [auth 1], BB [auth 2], CA [auth c], CB [auth 3], DA [auth e], DB [auth 4], EA [auth f], FA [auth g], GA [auth h], HA [auth i], IA [auth j], JA [auth k], KA [auth l], LA [auth m], MA [auth n], NA [auth o], OA [auth p], PA [auth q], QA [auth r], RA [auth s], SA [auth t], TA [auth u], UA [auth v], VA [auth w], WA [auth x], XA [auth y], YA [auth z], ZA [auth 0]	3	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AI4 (Subject of Investigation/LOI) Query on AI4 Download:Ideal Coordinates CCD File SDF format, chain EB [auth B] SDF format, chain FB [auth R] SDF format, chain GB [auth F] SDF format, chain HB [auth I] SDF format, chain IB [auth U] SDF format, chain JB [auth V] SDF format, chain KB [auth K] SDF format, chain LB [auth W] SDF format, chain MB [auth M] SDF format, chain NB [auth Y] SDF format, chain OB [auth N] SDF format, chain PB [auth Z] SDF format, chain QB [auth G] SDF format, chain RB [auth b] MOL2 format, chain EB [auth B] MOL2 format, chain FB [auth R] MOL2 format, chain GB [auth F] MOL2 format, chain HB [auth I] MOL2 format, chain IB [auth U] MOL2 format, chain JB [auth V] MOL2 format, chain KB [auth K] MOL2 format, chain LB [auth W] MOL2 format, chain MB [auth M] MOL2 format, chain NB [auth Y] MOL2 format, chain OB [auth N] MOL2 format, chain PB [auth Z] MOL2 format, chain QB [auth G] MOL2 format, chain RB [auth b] mmCIF format, chain EB [auth B] mmCIF format, chain FB [auth R] mmCIF format, chain GB [auth F] mmCIF format, chain HB [auth I] mmCIF format, chain IB [auth U] mmCIF format, chain JB [auth V] mmCIF format, chain KB [auth K] mmCIF format, chain LB [auth W] mmCIF format, chain MB [auth M] mmCIF format, chain NB [auth Y] mmCIF format, chain OB [auth N] mmCIF format, chain PB [auth Z] mmCIF format, chain QB [auth G] mmCIF format, chain RB [auth b]	EB [auth B] FB [auth R] GB [auth F] HB [auth I] IB [auth U] EB [auth B], FB [auth R], GB [auth F], HB [auth I], IB [auth U], JB [auth V], KB [auth K], LB [auth W], MB [auth M], NB [auth Y], OB [auth N], PB [auth Z], QB [auth G], RB [auth b]	4-[1-[3-[4-[(4-fluoranyl-2-methyl-1H-indol-5-yl)oxy]-6-methoxy-quinazolin-7-yl]oxypropyl]piperidin-4-yl]benzamide C₃₃ H₃₄ F N₅ O₄ ZUKPQXRSZJTISJ-UHFFFAOYSA-N		Interactions Focus chain EB [auth B] Focus chain FB [auth R] Focus chain GB [auth F] Focus chain HB [auth I] Focus chain IB [auth U] Focus chain JB [auth V] Focus chain KB [auth K] Focus chain LB [auth W] Focus chain MB [auth M] Focus chain NB [auth Y] Focus chain OB [auth N] Focus chain PB [auth Z] Focus chain QB [auth G] Focus chain RB [auth b] Interactions & Density Focus chain EB [auth B] Focus chain FB [auth R] Focus chain GB [auth F] Focus chain HB [auth I] Focus chain IB [auth U] Focus chain JB [auth V] Focus chain KB [auth K] Focus chain LB [auth W] Focus chain MB [auth M] Focus chain NB [auth Y] Focus chain OB [auth N] Focus chain PB [auth Z] Focus chain QB [auth G] Focus chain RB [auth b]

Binding Affinity Annotations
ID	Source	Binding Affinity
AI4	BindingDB: 7X8X	IC50: min: 2600, max: 1.00e+5 (nM) from 3 assay(s)
AI4	BindingDB: 7X8X	EC50: 1.21e+4 (nM) from 1 assay(s)