6GJK

A degradation product of PD 404182 (P2742) bound to Histone Deacetylase-like Amidohydrolase

PDB DOI: https://doi.org/10.2210/pdb6GJK/pdb

Classification: HYDROLASE
Organism(s): Alcaligenaceae bacterium FB188
Expression System: Escherichia coli BL21
Mutation(s): Yes

Deposited: 2018-05-16 Released: 2019-01-16
Deposition Author(s): Kraemer, A., Meyer-Almes, F.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.47 Å
R-Value Free: 0.174
R-Value Work: 0.144
R-Value Observed: 0.146

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Covalent inhibition of histone deacetylase 8 by 3,4-dihydro-2H-pyrimido[1,2-c][1,3]benzothiazin-6-imine.

Muth, M., Jansch, N., Kopranovic, A., Kramer, A., Wossner, N., Jung, M., Kirschhofer, F., Meyer-Almes, F.J.

(2019) Biochim Biophys Acta Gen Subj 1863: 577-585

PubMed: 30611847 Search on PubMed
DOI: https://doi.org/10.1016/j.bbagen.2019.01.001
Primary Citation of Related Structures:
6GJK

PubMed Abstract:
HDAC8 is an established target for T-cell lymphoma and childhood neuroblastoma. Benzothiazine-imines are promising HDAC8 inhibitors with unknown binding mechanism lacking a usual zinc binding group.

Organizational Affiliation

Department of Chemical Engineering and Biotechnology, University of Applied Sciences Darmstadt, Germany; Bioengineering and Biosystems, Institute of Functional Interfaces, Karlsruhe Institute of Technology, Germany.

Macromolecule Content

Total Structure Weight: 82.93 kDa
Atom Count: 6,603
Modelled Residue Count: 738
Deposited Residue Count: 750
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone deacetylase-like amidohydrolase	A, B	375	Alcaligenaceae bacterium FB188	Mutation(s): 1 Gene Names: hdaH, hdaH1 EC: 3.5.1
UniProt
Find proteins for Q70I53 (Alcaligenes sp. (strain DSM 11172)) Explore Q70I53 Go to UniProtKB: Q70I53
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q70I53
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
1PE Query on 1PE Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain P [auth B] MOL2 format, chain F [auth A] MOL2 format, chain P [auth B]	F [auth A], P [auth B]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain P [auth B] Interactions & Density Focus chain F [auth A] Focus chain P [auth B]
F0Z (Subject of Investigation/LOI) Query on F0Z Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain U [auth B] SDF format, chain V [auth B] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B]	I [auth A], J [auth A], U [auth B], V [auth B]	2-(1,4,5,6-tetrahydropyrimidin-2-yl)benzenethiol C₁₀ H₁₂ N₂ S DUHDUYRXLGSMLQ-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain U [auth B] Focus chain V [auth B] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain U [auth B] Focus chain V [auth B]
MLT Query on MLT Download Ideal Coordinates CCD File SDF format, chain L [auth A] MOL2 format, chain L [auth A]	L [auth A]	D-MALATE C₄ H₆ O₅ BJEPYKJPYRNKOW-UWTATZPHSA-N		Interactions Focus chain L [auth A] Interactions & Density Focus chain L [auth A]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain T [auth B] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B]	G [auth A] H [auth A] Q [auth B] R [auth B] S [auth B] G [auth A], H [auth A], Q [auth B], R [auth B], S [auth B], T [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain M [auth B] MOL2 format, chain C [auth A] MOL2 format, chain M [auth B]	C [auth A], M [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain M [auth B] Interactions & Density Focus chain C [auth A] Focus chain M [auth B]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain W [auth B] MOL2 format, chain K [auth A] MOL2 format, chain W [auth B]	K [auth A], W [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain K [auth A] Focus chain W [auth B] Interactions & Density Focus chain K [auth A] Focus chain W [auth B]
K Query on K Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain N [auth B] SDF format, chain O [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B]	D [auth A], E [auth A], N [auth B], O [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain N [auth B] Focus chain O [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain N [auth B] Focus chain O [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.47 Å
R-Value Free: 0.174
R-Value Work: 0.144
R-Value Observed: 0.146
Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.68	α = 90
b = 100.68	β = 90
c = 175.53	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2019-01-16

Deposition Author(s):

Kraemer, A.

Meyer-Almes, F.J.

Revision History (Full details and data files)

Version 1.0: 2019-01-16
Type: Initial release
Version 1.1: 2019-01-23
Changes: Data collection, Database references
Version 1.2: 2024-01-17
Changes: Data collection, Database references, Derived calculations, Refinement description