3MAX | pdb_00003max

Crystal Structure of Human HDAC2 complexed with an N-(2-aminophenyl)benzamide

• PDB DOI: https://doi.org/10.2210/pdb3MAX/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: unidentified baculovirus
• Mutation(s): No 


• Deposited: 2010-03-24 Released: 2010-04-28 
• Deposition Author(s): Skene, R.J., Jennings, A.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 
  0.204 (Depositor) 
• R-Value Work: 
  0.164 (Depositor) 
• R-Value Observed: 
  0.166 (Depositor) 

Literature

Exploration of the HDAC2 foot pocket: Synthesis and SAR of substituted N-(2-aminophenyl)benzamides.

Bressi, J.C., Jennings, A.J., Skene, R., Wu, Y., Melkus, R., De Jong, R., O'Connell, S., Grimshaw, C.E., Navre, M., Gangloff, A.R.

(2010) Bioorg Med Chem Lett 20: 3142-3145

• PubMed: 20392638 
• DOI: https://doi.org/10.1016/j.bmcl.2010.03.091
• Primary Citation Related Structures: 
  3MAX


• PubMed Abstract: 
  

  A series of N-(2-amino-5-substituted phenyl)benzamides (3-21) were designed, synthesized and evaluated for their inhibition of HDAC2 and their cytotoxicity in HCT116 cancer cells. Multiple compounds from this series demonstrated time-dependent binding kinetics that is rationalized using a co-complex crystal structure of HDAC2 and N-(4-aminobiphenyl-3-yl)benzamide (6).

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Organizational Affiliation: 
• Takeda San Diego, San Diego, CA 92121, USA.

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: 127.9 kDa 
• Atom Count: 9,584 
• Modeled Residue Count: 1,097 
• Deposited Residue Count: 1,101 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone deacetylase 2	A, B, C	367	Homo sapiens	Mutation(s): 0  Gene Names: HDAC2 EC: 3.5.1.98 (PDB Primary Data), 3.5.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q92769 (Homo sapiens) Explore Q92769  Go to UniProtKB:  Q92769
PHAROS:  Q92769 GTEx:  ENSG00000196591

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LLX	G [auth A], L [auth B], P [auth C]	N-(4-aminobiphenyl-3-yl)benzamide C19 H16 N2 O ZWLFHHHQRUYIBT-UHFFFAOYSA-N
NHE	H [auth A]	2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID C8 H17 N O3 S MKWKNSIESPFAQN-UHFFFAOYSA-N
ZN	D [auth A], I [auth B], M [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA	E [auth A], J [auth B], N [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
NA	F [auth A], K [auth B], O [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free:  0.204 (Depositor) 
• R-Value Work:  0.164 (Depositor) 
• R-Value Observed: 0.166 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.311	α = 90
b = 97.227	β = 90
c = 138.849	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-04-28 
Deposition Author(s): Skene, R.J., Jennings, A.J.

Revision History  

• Version 1.0: 2010-04-28
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-02-21
  Changes: Data collection, Database references, Derived calculations