9XBT | pdb_00009xbt

Crystal structure of human SIRT5 in complex with inhibitor 728

PDB DOI: https://doi.org/10.2210/pdb9XBT/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2025-10-24 Released: 2026-10-28
Deposition Author(s): Yang, L.-L., Jiang, Y.-Y.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.14 Å
R-Value Free:
0.341 (Depositor), 0.344 (DCC)
R-Value Work:
0.269 (Depositor), 0.270 (DCC)
R-Value Observed:
0.273 (Depositor)

Starting Model: experimental
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This is version 1.0 of the entry. See complete history.

Literature

Crystal structure of human SIRT5 in complex with inhibitor 728

Yang, L.-L., Jiang, Y.-Y.

To be published.

Macromolecule Content

Total Structure Weight: 59.84 kDa
Atom Count: 3,986
Modeled Residue Count: 514
Deposited Residue Count: 538
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD-dependent protein deacylase sirtuin-5, mitochondrial	A, B	269	Homo sapiens	Mutation(s): 0 Gene Names: SIRT5, SIR2L5 EC: 2.3.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NXA8 (Homo sapiens) Explore Q9NXA8 Go to UniProtKB: Q9NXA8
PHAROS: Q9NXA8 GTEx: ENSG00000124523
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9NXA8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1EZP( Subject of Investigation/LOI) Query on A1EZP Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth B] MOL2 format, chain D [auth A] MOL2 format, chain F [auth B] mmCIF format, chain D [auth A] mmCIF format, chain F [auth B]	D [auth A], F [auth B]	3-[3-[[2-[(2-chlorophenyl)amino]-5-[[(1~{S})-1-phenylpropyl]carbamoyl]pyrimidin-4-yl]amino]propylcarbamothioylamino]propanoic acid C₂₇ H₃₂ Cl N₇ O₃ S JKUFINLZPLTWFZ-NRFANRHFSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth B] mmCIF format, chain C [auth A] mmCIF format, chain E [auth B]	C [auth A], E [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.14 Å
R-Value Free: 0.341 (Depositor), 0.344 (DCC)
R-Value Work: 0.269 (Depositor), 0.270 (DCC)
R-Value Observed: 0.273 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.555	α = 90
b = 42.211	β = 91.25
c = 126.413	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
autoPX	data processing
autoPX	data reduction
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-10-28

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	82473764

Revision History (Full details and data files)

Version 1.0: 2026-10-28
Type: Initial release