6DVM | pdb_00006dvm

Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 in complex with DDK-122

PDB DOI: https://doi.org/10.2210/pdb6DVM/pdb

Classification: hydrolase/hydrolase inhibitor
Organism(s): Danio rerio
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2018-06-24 Released: 2018-08-29
Deposition Author(s): Porter, N.J., Christianson, D.W.
Funding Organization(s): National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.47 Å
R-Value Free:
0.170 (Depositor), 0.170 (DCC)
R-Value Work:
0.148 (Depositor), 0.150 (DCC)
R-Value Observed:
0.149 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Histone Deacetylase 6-Selective Inhibitors and the Influence of Capping Groups on Hydroxamate-Zinc Denticity.

Porter, N.J., Osko, J.D., Diedrich, D., Kurz, T., Hooker, J.M., Hansen, F.K., Christianson, D.W.

(2018) J Med Chem 61: 8054-8060

PubMed: 30118224 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1021/acs.jmedchem.8b01013
Primary Citation of Related Structures:
6DVL, 6DVM, 6DVN, 6DVO

PubMed Abstract:
Four crystal structures are presented of histone deacetylase 6 (HDAC6) complexes with para-substituted phenylhydromaxamate inhibitors, including bulky peptoids. These structures provide insight regarding the design of capping groups that confer selectivity for binding to HDAC6, specifically with regard to interactions in a pocket formed by the L1 loop. Capping group interactions may also influence hydroxamate-Zn ²⁺ coordination with monodentate or bidentate geometry.

Organizational Affiliation

Roy and Diana Vagelos Laboratories, Department of Chemistry , University of Pennsylvania , 231 South 34th Street , Philadelphia , Pennsylvania 19104-6323 , United States.

Macromolecule Content

Total Structure Weight: 164.57 kDa
Atom Count: 13,430
Modelled Residue Count: 1,427
Deposited Residue Count: 1,456
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hdac6 protein	A, B, C, D	364	Danio rerio	Mutation(s): 0 Gene Names: hdac6
UniProt
Find proteins for F8W4B7 (Danio rerio) Explore F8W4B7 Go to UniProtKB: F8W4B7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	F8W4B7
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HBJ Query on HBJ Download Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain H [auth A] SDF format, chain M [auth B] SDF format, chain R [auth C] MOL2 format, chain BA [auth D] MOL2 format, chain H [auth A] MOL2 format, chain M [auth B] MOL2 format, chain R [auth C] mmCIF format, chain BA [auth D] mmCIF format, chain H [auth A] mmCIF format, chain M [auth B] mmCIF format, chain R [auth C]	BA [auth D], H [auth A], M [auth B], R [auth C]	4-(dimethylamino)-N-{[4-(hydroxycarbamoyl)phenyl]methyl}-N-{2-[(4-methylphenyl)amino]-2-oxoethyl}benzamide C₂₆ H₂₈ N₄ O₄ UEKPDDMOEDHDCS-UHFFFAOYSA-N		Interactions Focus chain BA [auth D] Focus chain H [auth A] Focus chain M [auth B] Focus chain R [auth C] Interactions & Density Focus chain BA [auth D] Focus chain H [auth A] Focus chain M [auth B] Focus chain R [auth C]
BTB Query on BTB Download Ideal Coordinates CCD File SDF format, chain X [auth C] MOL2 format, chain X [auth C] mmCIF format, chain X [auth C]	X [auth C]	2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₈ H₁₉ N O₅ OWMVSZAMULFTJU-UHFFFAOYSA-N		Interactions Focus chain X [auth C] Interactions & Density Focus chain X [auth C]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain J [auth B] SDF format, chain O [auth C] SDF format, chain Y [auth D] MOL2 format, chain E [auth A] MOL2 format, chain J [auth B] MOL2 format, chain O [auth C] MOL2 format, chain Y [auth D] mmCIF format, chain E [auth A] mmCIF format, chain J [auth B] mmCIF format, chain O [auth C] mmCIF format, chain Y [auth D]	E [auth A], J [auth B], O [auth C], Y [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain J [auth B] Focus chain O [auth C] Focus chain Y [auth D] Interactions & Density Focus chain E [auth A] Focus chain J [auth B] Focus chain O [auth C] Focus chain Y [auth D]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain CA [auth D] SDF format, chain DA [auth D] SDF format, chain EA [auth D] SDF format, chain FA [auth D] SDF format, chain GA [auth D] SDF format, chain HA [auth D] SDF format, chain I [auth A] SDF format, chain N [auth B] SDF format, chain S [auth C] SDF format, chain T [auth C] SDF format, chain U [auth C] SDF format, chain V [auth C] SDF format, chain W [auth C] MOL2 format, chain CA [auth D] MOL2 format, chain DA [auth D] MOL2 format, chain EA [auth D] MOL2 format, chain FA [auth D] MOL2 format, chain GA [auth D] MOL2 format, chain HA [auth D] MOL2 format, chain I [auth A] MOL2 format, chain N [auth B] MOL2 format, chain S [auth C] MOL2 format, chain T [auth C] MOL2 format, chain U [auth C] MOL2 format, chain V [auth C] MOL2 format, chain W [auth C] mmCIF format, chain CA [auth D] mmCIF format, chain DA [auth D] mmCIF format, chain EA [auth D] mmCIF format, chain FA [auth D] mmCIF format, chain GA [auth D] mmCIF format, chain HA [auth D] mmCIF format, chain I [auth A] mmCIF format, chain N [auth B] mmCIF format, chain S [auth C] mmCIF format, chain T [auth C] mmCIF format, chain U [auth C] mmCIF format, chain V [auth C] mmCIF format, chain W [auth C]	CA [auth D] DA [auth D] EA [auth D] FA [auth D] GA [auth D] CA [auth D], DA [auth D], EA [auth D], FA [auth D], GA [auth D], HA [auth D], I [auth A], N [auth B], S [auth C], T [auth C], U [auth C], V [auth C], W [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain CA [auth D] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain GA [auth D] Focus chain HA [auth D] Focus chain I [auth A] Focus chain N [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Interactions & Density Focus chain CA [auth D] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain GA [auth D] Focus chain HA [auth D] Focus chain I [auth A] Focus chain N [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C]
K Query on K Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain P [auth C] SDF format, chain Q [auth C] SDF format, chain Z [auth D] MOL2 format, chain AA [auth D] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain Z [auth D] mmCIF format, chain AA [auth D] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain P [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain Z [auth D]	AA [auth D] F [auth A] G [auth A] K [auth B] L [auth B] AA [auth D], F [auth A], G [auth A], K [auth B], L [auth B], P [auth C], Q [auth C], Z [auth D]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth D] Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain Z [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.47 Å
R-Value Free: 0.170 (Depositor), 0.170 (DCC)
R-Value Work: 0.148 (Depositor), 0.150 (DCC)
R-Value Observed: 0.149 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.45	α = 90
b = 95.18	β = 98.87
c = 98.03	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
iMOSFLM	data reduction
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2018-08-29

Deposition Author(s):

Porter, N.J.

Christianson, D.W.

Funding Organization	Location	Grant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)	United States	GM49758

Revision History (Full details and data files)

Version 1.0: 2018-08-29
Type: Initial release
Version 1.1: 2018-09-26
Changes: Data collection, Database references
Version 1.2: 2019-12-18
Changes: Author supporting evidence
Version 1.3: 2024-03-13
Changes: Data collection, Database references, Derived calculations