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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free:
0.204 (Depositor), 0.220 (DCC)
R-Value Work:
0.164 (Depositor), 0.180 (DCC)
R-Value Observed:
0.166 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

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 Search on PubMed
DOI: https://doi.org/10.1016/j.bmcl.2010.03.091
Primary Citation of 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).

Organizational Affiliation

Takeda San Diego, San Diego, CA 92121, USA.

Macromolecule Content

Total Structure Weight: 127.9 kDa
Atom Count: 9,584
Modelled Residue Count: 1,097
Deposited Residue Count: 1,101
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q92769
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LLX Query on LLX Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain L [auth B] SDF format, chain P [auth C] MOL2 format, chain G [auth A] MOL2 format, chain L [auth B] MOL2 format, chain P [auth C] mmCIF format, chain G [auth A] mmCIF format, chain L [auth B] mmCIF format, chain P [auth C]	G [auth A], L [auth B], P [auth C]	N-(4-aminobiphenyl-3-yl)benzamide C₁₉ H₁₆ N₂ O ZWLFHHHQRUYIBT-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain L [auth B] Focus chain P [auth C] Interactions & Density Focus chain G [auth A] Focus chain L [auth B] Focus chain P [auth C]
NHE Query on NHE Download Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID C₈ H₁₇ N O₃ S MKWKNSIESPFAQN-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain I [auth B] SDF format, chain M [auth C] MOL2 format, chain D [auth A] MOL2 format, chain I [auth B] MOL2 format, chain M [auth C] mmCIF format, chain D [auth A] mmCIF format, chain I [auth B] mmCIF format, chain M [auth C]	D [auth A], I [auth B], M [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain I [auth B] Focus chain M [auth C] Interactions & Density Focus chain D [auth A] Focus chain I [auth B] Focus chain M [auth C]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain J [auth B] SDF format, chain N [auth C] MOL2 format, chain E [auth A] MOL2 format, chain J [auth B] MOL2 format, chain N [auth C] mmCIF format, chain E [auth A] mmCIF format, chain J [auth B] mmCIF format, chain N [auth C]	E [auth A], J [auth B], N [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain J [auth B] Focus chain N [auth C] Interactions & Density Focus chain E [auth A] Focus chain J [auth B] Focus chain N [auth C]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain K [auth B] SDF format, chain O [auth C] MOL2 format, chain F [auth A] MOL2 format, chain K [auth B] MOL2 format, chain O [auth C] mmCIF format, chain F [auth A] mmCIF format, chain K [auth B] mmCIF format, chain O [auth C]	F [auth A], K [auth B], O [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain K [auth B] Focus chain O [auth C] Interactions & Density Focus chain F [auth A] Focus chain K [auth B] Focus chain O [auth C]

Binding Affinity Annotations
ID	Source	Binding Affinity
LLX	BindingDB: 3MAX	IC50: min: 27, max: 1200 (nM) from 9 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free: 0.204 (Depositor), 0.220 (DCC)
R-Value Work: 0.164 (Depositor), 0.180 (DCC)
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

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2010-04-28

Deposition Author(s):

Skene, R.J.

Jennings, A.J.

Revision History (Full details and data files)

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

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

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

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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