6ODA | pdb_00006oda

Crystal structure of HDAC8 in complex with compound 2

• PDB DOI: https://doi.org/10.2210/pdb6ODA/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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.88 Å
• R-Value Free: 
  0.249 (Depositor), 0.231 (DCC) 
• R-Value Work: 
  0.199 (Depositor) 
• R-Value Observed: 
  0.201 (Depositor) 

Starting Model: experimental

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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 139.42 kDa 
• Atom Count: 8,516 
• Modeled Residue Count: 1,080 
• Deposited Residue Count: 1,239 
• Unique protein chains: 1

Macromolecules

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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
C7 (Subject of Investigation/LOI)	D [auth A], H [auth B], L [auth C]	N-{2-[3-(hydroxyamino)-3-oxopropyl]phenyl}-3-(trifluoromethyl)benzamide C17 H15 F3 N2 O3 QXXNUWFIASXMCG-UHFFFAOYSA-N
ZN	E [auth A], I [auth B], M [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
K	F [auth A], G [auth A], J [auth B], K [auth B], N [auth C], O [auth C]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.88 Å
• R-Value Free:  0.249 (Depositor), 0.231 (DCC) 
• R-Value Work:  0.199 (Depositor) 
• R-Value Observed: 0.201 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.75	α = 90
b = 91.29	β = 94.09
c = 92.7	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 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.

Revision History  

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