2VCG | pdb_00002vcg

Crystal structure of a HDAC-like protein HDAH from Bordetella sp. with the bound inhibitor ST-17

PDB DOI: https://doi.org/10.2210/pdb2VCG/pdb

Classification: HYDROLASE
Organism(s): Alcaligenes sp.
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2007-09-24 Released: 2008-01-08
Deposition Author(s): Dickmanns, A., Strasser, A., Ficner, R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.206 (Depositor), 0.206 (DCC)
R-Value Work:
0.156 (Depositor), 0.156 (DCC)
R-Value Observed:
0.159 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Phenylalanine-Containing Hydroxamic Acids as Selective Inhibitors of Class Iib Histone Deacetylases (Hdacs).

Schaefer, S., Saunders, L., Eliseeva, E., Velena, A., Jung, M., Schwienhorst, A., Strasser, A., Dickmanns, A., Ficner, R., Schlimme, S., Sippl, W., Verdin, E., Jung, M.

(2008) Bioorg Med Chem 16: 2011

PubMed: 18054239 Search on PubMed
DOI: https://doi.org/10.1016/j.bmc.2007.10.092
Primary Citation Related Structures:
2VCG

PubMed Abstract:
We synthesized biarylalanine-containing hydroxamic acids and tested them on immunoprecipitated HDAC1 and HDAC6 and show a subtype selectivity for HDAC6 that was confirmed in cells by Western blot (tubulin vs histones). We obtained an X-ray structure with a HDAC6-selective inhibitor with the bacterial deacetylase HDAH. Docking studies were carried out using HDAC1 and HDAC6 protein models. Antiproliferative activity was shown on cancer cells for selected compounds.

Organizational Affiliation

Institute of Pharmaceutical Sciences, University of Freiburg, Albertstr. 25, 79104 Freiburg, Germany.

Macromolecule Content

Total Structure Weight: 163.59 kDa
Atom Count: 12,995
Modeled Residue Count: 1,479
Deposited Residue Count: 1,500
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HISTONE DEACETYLASE-LIKE AMIDOHYDROLASE	A, B, C, D	375	Alcaligenes sp.	Mutation(s): 0 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q70I53
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
S17 Query on S17 Download:Ideal Coordinates CCD File SDF format, chain W [auth D] SDF format, chain Q [auth C] SDF format, chain L [auth B] SDF format, chain H [auth A] MOL2 format, chain W [auth D] MOL2 format, chain Q [auth C] MOL2 format, chain L [auth B] MOL2 format, chain H [auth A] mmCIF format, chain W [auth D] mmCIF format, chain Q [auth C] mmCIF format, chain L [auth B] mmCIF format, chain H [auth A]	H [auth A], L [auth B], Q [auth C], W [auth D]	methyl 4-bromo-N-[8-(hydroxyamino)-8-oxooctanoyl]-L-phenylalaninate C₁₈ H₂₅ Br N₂ O₅ UPYGSQPRAHMDPD-HNNXBMFYSA-N		Interactions Focus chain H [auth A] Focus chain L [auth B] Focus chain Q [auth C] Focus chain W [auth D] Interactions & Density Focus chain H [auth A] Focus chain L [auth B] Focus chain Q [auth C] Focus chain W [auth D]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain R [auth D] SDF format, chain M [auth C] MOL2 format, chain R [auth D] MOL2 format, chain M [auth C] mmCIF format, chain R [auth D] mmCIF format, chain M [auth C]	M [auth C], R [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain M [auth C] Focus chain R [auth D] Interactions & Density Focus chain M [auth C] Focus chain R [auth D]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain T [auth D] SDF format, chain S [auth D] SDF format, chain N [auth C] SDF format, chain I [auth B] SDF format, chain E [auth A] MOL2 format, chain T [auth D] MOL2 format, chain S [auth D] MOL2 format, chain N [auth C] MOL2 format, chain I [auth B] MOL2 format, chain E [auth A] mmCIF format, chain T [auth D] mmCIF format, chain S [auth D] mmCIF format, chain N [auth C] mmCIF format, chain I [auth B] mmCIF format, chain E [auth A]	E [auth A], I [auth B], N [auth C], S [auth D], T [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Focus chain N [auth C] Focus chain S [auth D] Focus chain T [auth D] Interactions & Density Focus chain E [auth A] Focus chain I [auth B] Focus chain N [auth C] Focus chain S [auth D] Focus chain T [auth D]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain V [auth D] SDF format, chain U [auth D] SDF format, chain P [auth C] SDF format, chain O [auth C] SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain V [auth D] MOL2 format, chain U [auth D] MOL2 format, chain P [auth C] MOL2 format, chain O [auth C] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain V [auth D] mmCIF format, chain U [auth D] mmCIF format, chain P [auth C] mmCIF format, chain O [auth C] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A] G [auth A] J [auth B] K [auth B] O [auth C] F [auth A], G [auth A], J [auth B], K [auth B], O [auth C], P [auth C], U [auth D], V [auth D]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain U [auth D] Focus chain V [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain U [auth D] Focus chain V [auth D]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain X [auth D] MOL2 format, chain X [auth D] mmCIF format, chain X [auth D]	X [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain X [auth D] Interactions & Density Focus chain X [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.206 (Depositor), 0.206 (DCC)
R-Value Work: 0.156 (Depositor), 0.156 (DCC)
R-Value Observed: 0.159 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.664	α = 90
b = 93.633	β = 103.99
c = 121.664	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2008-01-08

Deposition Author(s):

Dickmanns, A.

Strasser, A.

Ficner, R.

Revision History (Full details and data files)

Version 1.0: 2008-01-08
Type: Initial release
Version 1.1: 2011-05-08
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2019-07-24
Changes: Data collection
Version 1.4: 2023-12-13
Changes: Data collection, Database references, Derived calculations, Other, Refinement description