6ODB | pdb_00006odb

Crystal structure of HDAC8 in complex with compound 3

PDB DOI: https://doi.org/10.2210/pdb6ODB/pdb

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

Deposited: 2019-03-26 Released: 2020-04-01
Deposition Author(s): Zheng, X., Conti, C., Caravella, J., Zablocki, M.-M., Bair, K., Barczak, N., Han, B., Lancia Jr., D., Liu, C., Martin, M., Ng, P.Y., Rudnitskaya, A., Thomason, J.J., Garcia-Dancey, R., Hardy, C., Lahdenranta, J., Leng, C., Li, P., Pardo, E., Saldahna, A., Tan, T., Toms, A.V., Yao, L., Zhang, C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.241 (Depositor), 0.238 (DCC)
R-Value Work:
0.195 (Depositor)
R-Value Observed:
0.198 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structure-based Discovery of Novel N-(E)-N-Hydroxy-3-(2-(2-oxoimidazolidin-1-yl)phenyl)acrylamides as Potent and Selective HDAC8 inhibitors

Zheng, X., Conti, C., Caravella, J., Zablocki, M.-M., Bair, K., Barczak, N., Han, B., Lancia Jr., D., Liu, C., Martin, M., Ng, P.Y., Rudnitskaya, A., Thomason, J.J., Garcia-Dancey, R., Hardy, C., Lahdenranta, J., Leng, C., Li, P., Pardo, E., Saldahna, A., Tan, T., Toms, A.V., Yao, L., Zhang, C.

To be published.

Macromolecule Content

Total Structure Weight: 139.85 kDa
Atom Count: 8,647
Modeled Residue Count: 1,082
Deposited Residue Count: 1,239
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone deacetylase 8	A, B, C	413	Homo sapiens	Mutation(s): 0 Gene Names: HDAC8, HDACL1, CDA07 EC: 3.5.1.98 (PDB Primary Data), 3.5.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BY41 (Homo sapiens) Explore Q9BY41 Go to UniProtKB: Q9BY41
PHAROS: Q9BY41 GTEx: ENSG00000147099
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9BY41
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
M8G (Subject of Investigation/LOI) Query on M8G Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain P [auth C] SDF format, chain K [auth B] MOL2 format, chain D [auth A] MOL2 format, chain P [auth C] MOL2 format, chain K [auth B] mmCIF format, chain D [auth A] mmCIF format, chain P [auth C] mmCIF format, chain K [auth B]	D [auth A], K [auth B], P [auth C]	N-{2-[(1E)-3-(hydroxyamino)-3-oxoprop-1-en-1-yl]phenyl}-2-phenoxybenzamide C₂₂ H₁₈ N₂ O₄ URROCBSFNUKVTR-CCEZHUSRSA-N		Interactions Focus chain D [auth A] Focus chain K [auth B] Focus chain P [auth C] Interactions & Density Focus chain D [auth A] Focus chain K [auth B] Focus chain P [auth C]
GOL Query on GOL 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 O [auth B] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain O [auth B] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain O [auth B]	H [auth A], I [auth A], J [auth A], O [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain O [auth B] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain O [auth B]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain Q [auth C] SDF format, chain L [auth B] MOL2 format, chain E [auth A] MOL2 format, chain Q [auth C] MOL2 format, chain L [auth B] mmCIF format, chain E [auth A] mmCIF format, chain Q [auth C] mmCIF format, chain L [auth B]	E [auth A], L [auth B], Q [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain L [auth B] Focus chain Q [auth C] Interactions & Density Focus chain E [auth A] Focus chain L [auth B] Focus chain Q [auth C]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain M [auth B] SDF format, chain R [auth C] SDF format, chain S [auth C] SDF format, chain N [auth B] SDF format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain M [auth B] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C] MOL2 format, chain N [auth B] MOL2 format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain M [auth B] mmCIF format, chain R [auth C] mmCIF format, chain S [auth C] mmCIF format, chain N [auth B] mmCIF format, chain G [auth A]	F [auth A] G [auth A] M [auth B] N [auth B] R [auth C] F [auth A], G [auth A], M [auth B], N [auth B], R [auth C], S [auth C]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain R [auth C] Focus chain S [auth C] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain R [auth C] Focus chain S [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.241 (Depositor), 0.238 (DCC)
R-Value Work: 0.195 (Depositor)
R-Value Observed: 0.198 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.915	α = 90
b = 90.95	β = 94.1
c = 93.067	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2020-04-01

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2020-04-01
Type: Initial release
Version 1.1: 2023-10-11
Changes: Data collection, Database references, Derived calculations, Refinement description