9S48 | pdb_00009s48

Human SIRT2 in Complex with RW-80

PDB DOI: https://doi.org/10.2210/pdb9S48/pdb

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

Deposited: 2025-07-25 Released: 2025-08-20
Deposition Author(s): Wirawan, R., Frei, M., Heider, A., Papenkordt, N., Friedrich, F., Wein, T., Jung, M., Groll, M., Huber, E.M., Bracher, F.
Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free:
0.187 (Depositor), 0.191 (DCC)
R-Value Work:
0.156 (Depositor), 0.168 (DCC)
R-Value Observed:
0.158 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Tailored SirReal-type inhibitors enhance SIRT2 inhibition through ligand stabilization and disruption of NAD+ co-factor binding

Wirawan, R., Frei, M., Heider, A., Papenkordt, N., Friedrich, F., Wein, T., Jung, M., Groll, M., huber, E., Bracher, F.

(2025) RSC Med Chem

DOI: https://doi.org/10.1039/D5MD00144G

Macromolecule Content

Total Structure Weight: 35.36 kDa
Atom Count: 2,620
Modeled Residue Count: 290
Deposited Residue Count: 302
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD-dependent protein deacetylase sirtuin-2	A	302	Homo sapiens	Mutation(s): 0 Gene Names: SIRT2, SIR2L, SIR2L2 EC: 2.3.1.286 (PDB Primary Data), 2.3.1 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q8IXJ6 (Homo sapiens) Explore Q8IXJ6 Go to UniProtKB: Q8IXJ6
PHAROS: Q8IXJ6 GTEx: ENSG00000068903
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8IXJ6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1JLL (Subject of Investigation/LOI) Query on A1JLL Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	~{N}-[4-[[3-[2-(4,6-dimethylpyrimidin-2-yl)sulfanylethanoylamino]phenyl]methoxy]-2-iodanyl-phenyl]-1-methyl-pyrazole-4-carboxamide C₂₆ H₂₅ I N₆ O₃ S MCPRFXCLTXHJHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A]	D [auth A] E [auth A] F [auth A] G [auth A] H [auth A] D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain K [auth A] MOL2 format, chain K [auth A] mmCIF format, chain K [auth A]	K [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain K [auth A] Interactions & Density Focus chain K [auth A]