8CNO

Improved complex structure of human Sirtuin 6 with its inhibitor cis-resveratrol

PDB DOI: https://doi.org/10.2210/pdb8CNO/pdb

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

Deposited: 2023-02-23 Released: 2024-03-06
Deposition Author(s): You, W., Steegborn, C.
Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.188
R-Value Work: 0.167
R-Value Observed: 0.167

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

Development of novel Sirtuin 6 inhibitors and activators based on a protein crystallography-based fragment screen

You, W., Steegborn, C.

To be published.

Macromolecule Content

Total Structure Weight: 70.62 kDa
Atom Count: 4,733
Modelled Residue Count: 559
Deposited Residue Count: 604
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD-dependent protein deacetylase sirtuin-6	A, B	302	Homo sapiens	Mutation(s): 0 Gene Names: SIRT6, SIR2L6 EC: 2.3.1.286 (PDB Primary Data), 2.4.2 (UniProt), 2.3.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q8N6T7 (Homo sapiens) Explore Q8N6T7 Go to UniProtKB: Q8N6T7
PHAROS: Q8N6T7 GTEx: ENSG00000077463
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8N6T7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 9 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AR6 Query on AR6 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain S [auth B] MOL2 format, chain C [auth A] MOL2 format, chain S [auth B] mmCIF format, chain C [auth A] mmCIF format, chain S [auth B]	C [auth A], S [auth B]	[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE C₁₅ H₂₃ N₅ O₁₄ P₂ SRNWOUGRCWSEMX-ZQSHOCFMSA-N		Interactions Focus chain C [auth A] Focus chain S [auth B] Interactions & Density Focus chain C [auth A] Focus chain S [auth B]
STL (Subject of Investigation/LOI) Query on STL Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain U [auth B] MOL2 format, chain E [auth A] MOL2 format, chain U [auth B] mmCIF format, chain E [auth A] mmCIF format, chain U [auth B]	E [auth A], U [auth B]	RESVERATROL C₁₄ H₁₂ O₃ LUKBXSAWLPMMSZ-OWOJBTEDSA-N		Interactions Focus chain E [auth A] Focus chain U [auth B] Interactions & Density Focus chain E [auth A] Focus chain U [auth B]
PG4 Query on PG4 Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain V [auth B] MOL2 format, chain V [auth B] mmCIF format, chain V [auth B]	V [auth B]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain V [auth B] Interactions & Density Focus chain V [auth B]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain R [auth B] MOL2 format, chain R [auth B] mmCIF format, chain R [auth B]	R [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain R [auth B] Interactions & Density Focus chain R [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain X [auth B] SDF format, chain Y [auth B] SDF format, chain Z [auth B] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain X [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain Z [auth B]	H [auth A] I [auth A] J [auth A] K [auth A] L [auth A] H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], X [auth B], Y [auth B], Z [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain T [auth B] MOL2 format, chain D [auth A] MOL2 format, chain T [auth B] mmCIF format, chain D [auth A] mmCIF format, chain T [auth B]	D [auth A], T [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain T [auth B] Interactions & Density Focus chain D [auth A] Focus chain T [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain W [auth B] MOL2 format, chain G [auth A] MOL2 format, chain W [auth B] mmCIF format, chain G [auth A] mmCIF format, chain W [auth B]	G [auth A], W [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain W [auth B] Interactions & Density Focus chain G [auth A] Focus chain W [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain BA [auth B] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] MOL2 format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] mmCIF format, chain AA [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A]	AA [auth B] BA [auth B] N [auth A] O [auth A] P [auth A] AA [auth B], BA [auth B], N [auth A], O [auth A], P [auth A], Q [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A]