8W7E | pdb_00008w7e

Design, synthesis and biological evaluations of novel small molecular hyper-activators of human caseinolytic peptidase P (hClpP)

PDB DOI: https://doi.org/10.2210/pdb8W7E/pdb

Classification: APOPTOSIS
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-08-30 Released: 2024-09-04
Deposition Author(s): Jiang, J.-X., Ding, H., Chen, M.-R., Lu, M.-L., Sun, H.-Y., Xiao, Y.-B.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.274 (Depositor), 0.273 (DCC)
R-Value Work:
0.266 (Depositor), 0.265 (DCC)
R-Value Observed:
0.266 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Design, synthesis and biological evaluations of novel small molecular hyper-activators of human caseinolytic peptidase P (hClpP)

Jiang, J.-X., Ding, H., Chen, M.-R., Lu, M.-L., Sun, H.-Y., Xiao, Y.-B.

To be published.

Macromolecule Content

Total Structure Weight: 346.84 kDa
Atom Count: 19,090
Modeled Residue Count: 2,426
Deposited Residue Count: 3,122
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-dependent Clp protease proteolytic subunit, mitochondrial	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N	223	Homo sapiens	Mutation(s): 0 Gene Names: CLPP EC: 3.4.21.92
UniProt & NIH Common Fund Data Resources
Find proteins for Q16740 (Homo sapiens) Explore Q16740 Go to UniProtKB: Q16740
PHAROS: Q16740 GTEx: ENSG00000125656
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q16740
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
9I3 Query on 9I3 Download Ideal Coordinates CCD File SDF format, chain BA [auth N] SDF format, chain O [auth A] SDF format, chain P [auth B] SDF format, chain R [auth D] SDF format, chain U [auth F] SDF format, chain V [auth G] SDF format, chain X [auth I] SDF format, chain Y [auth K] SDF format, chain Z [auth L] SDF format, chain W [auth H] SDF format, chain T [auth E] SDF format, chain S [auth E] SDF format, chain Q [auth C] SDF format, chain AA [auth M] MOL2 format, chain BA [auth N] MOL2 format, chain O [auth A] MOL2 format, chain P [auth B] MOL2 format, chain R [auth D] MOL2 format, chain U [auth F] MOL2 format, chain V [auth G] MOL2 format, chain X [auth I] MOL2 format, chain Y [auth K] MOL2 format, chain Z [auth L] MOL2 format, chain W [auth H] MOL2 format, chain T [auth E] MOL2 format, chain S [auth E] MOL2 format, chain Q [auth C] MOL2 format, chain AA [auth M] mmCIF format, chain BA [auth N] mmCIF format, chain O [auth A] mmCIF format, chain P [auth B] mmCIF format, chain R [auth D] mmCIF format, chain U [auth F] mmCIF format, chain V [auth G] mmCIF format, chain X [auth I] mmCIF format, chain Y [auth K] mmCIF format, chain Z [auth L] mmCIF format, chain W [auth H] mmCIF format, chain T [auth E] mmCIF format, chain S [auth E] mmCIF format, chain Q [auth C] mmCIF format, chain AA [auth M]	AA [auth M] BA [auth N] O [auth A] P [auth B] Q [auth C] AA [auth M], BA [auth N], O [auth A], P [auth B], Q [auth C], R [auth D], S [auth E], T [auth E], U [auth F], V [auth G], W [auth H], X [auth I], Y [auth K], Z [auth L]	3-[(3-chlorophenyl)methyl]-6-[(4-chlorophenyl)methyl]-2,4-dihydro-1H-pyrido[2,3-c][2,7]naphthyridin-5-one C₂₅ H₂₁ Cl₂ N₃ O JCFSCDLNZWVEMF-UHFFFAOYSA-N		Interactions Focus chain AA [auth M] Focus chain BA [auth N] Focus chain O [auth A] Focus chain P [auth B] Focus chain Q [auth C] Focus chain R [auth D] Focus chain S [auth E] Focus chain T [auth E] Focus chain U [auth F] Focus chain V [auth G] Focus chain W [auth H] Focus chain X [auth I] Focus chain Y [auth K] Focus chain Z [auth L] Interactions & Density Focus chain AA [auth M] Focus chain BA [auth N] Focus chain O [auth A] Focus chain P [auth B] Focus chain Q [auth C] Focus chain R [auth D] Focus chain S [auth E] Focus chain T [auth E] Focus chain U [auth F] Focus chain V [auth G] Focus chain W [auth H] Focus chain X [auth I] Focus chain Y [auth K] Focus chain Z [auth L]