9JV3 | pdb_00009jv3

Structure of Human HDAC2

PDB DOI: https://doi.org/10.2210/pdb9JV3/pdb

Classification: TRANSCRIPTION
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2024-10-08 Released: 2025-10-08
Deposition Author(s): Tojo, T., Itoh, Y., Kurohara, T., Li, Y., Singh, R., Narozny, R., Wiel, A., Miyake, Y., Yamashita, Y., Kusakabe, K., Uchida, S., Suzuki, T.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.57 Å
R-Value Free:
0.256 (Depositor), 0.256 (DCC)
R-Value Work:
0.181 (Depositor), 0.189 (DCC)
R-Value Observed:
0.183 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9JV3

This is version 1.0 of the entry. See complete history.

Literature

Discovery of an HDAC2-selective inhibitor based on enzyme-inhibitor binding thermodynamics and kinetics, and its potential as a therapeutic drug for neurological disorders

Tojo, T., Itoh, Y., Kurohara, T., Li, Y., Singh, R., Narozny, R., Wiel, A., Miyake, Y., Yamashita, Y., Kusakabe, K., Uchida, S., Suzuki, T.

To be published.

Macromolecule Content

Total Structure Weight: 140.5 kDa
Atom Count: 9,316
Modeled Residue Count: 1,102
Deposited Residue Count: 1,212
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone deacetylase 2	A, B, C	404	Homo sapiens	Mutation(s): 0 Gene Names: HDAC2 EC: 3.5.1.98 (PDB Primary Data), 3.5.1 (PDB Primary Data)
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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q92769
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
1PE Query on 1PE Download:Ideal Coordinates CCD File SDF format, chain X [auth B] MOL2 format, chain X [auth B] mmCIF format, chain X [auth B]	X [auth B]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain X [auth B] Interactions & Density Focus chain X [auth B]
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain S [auth B] MOL2 format, chain S [auth B] mmCIF format, chain S [auth B]	S [auth B]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain S [auth B] Interactions & Density Focus chain S [auth B]
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain Q [auth B] MOL2 format, chain I [auth A] MOL2 format, chain Q [auth B] mmCIF format, chain I [auth A] mmCIF format, chain Q [auth B]	I [auth A], Q [auth B]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain Q [auth B] Interactions & Density Focus chain I [auth A] Focus chain Q [auth B]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain CA [auth C] SDF format, chain H [auth A] SDF format, chain HA [auth C] SDF format, chain J [auth A] SDF format, chain R [auth B] MOL2 format, chain CA [auth C] MOL2 format, chain H [auth A] MOL2 format, chain HA [auth C] MOL2 format, chain J [auth A] MOL2 format, chain R [auth B] mmCIF format, chain CA [auth C] mmCIF format, chain H [auth A] mmCIF format, chain HA [auth C] mmCIF format, chain J [auth A] mmCIF format, chain R [auth B]	CA [auth C], H [auth A], HA [auth C], J [auth A], R [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain CA [auth C] Focus chain H [auth A] Focus chain HA [auth C] Focus chain J [auth A] Focus chain R [auth B] Interactions & Density Focus chain CA [auth C] Focus chain H [auth A] Focus chain HA [auth C] Focus chain J [auth A] Focus chain R [auth B]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain N [auth B] SDF format, chain Z [auth C] MOL2 format, chain D [auth A] MOL2 format, chain N [auth B] MOL2 format, chain Z [auth C] mmCIF format, chain D [auth A] mmCIF format, chain N [auth B] mmCIF format, chain Z [auth C]	D [auth A], N [auth B], Z [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain N [auth B] Focus chain Z [auth C] Interactions & Density Focus chain D [auth A] Focus chain N [auth B] Focus chain Z [auth C]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain EA [auth C] SDF format, chain FA [auth C] SDF format, chain G [auth A] SDF format, chain GA [auth C] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain T [auth B] SDF format, chain W [auth B] SDF format, chain Y [auth B] SDF format, chain V [auth B] SDF format, chain U [auth B] SDF format, chain M [auth A] SDF format, chain DA [auth C] MOL2 format, chain EA [auth C] MOL2 format, chain FA [auth C] MOL2 format, chain G [auth A] MOL2 format, chain GA [auth C] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain T [auth B] MOL2 format, chain W [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain V [auth B] MOL2 format, chain U [auth B] MOL2 format, chain M [auth A] MOL2 format, chain DA [auth C] mmCIF format, chain EA [auth C] mmCIF format, chain FA [auth C] mmCIF format, chain G [auth A] mmCIF format, chain GA [auth C] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain T [auth B] mmCIF format, chain W [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain V [auth B] mmCIF format, chain U [auth B] mmCIF format, chain M [auth A] mmCIF format, chain DA [auth C]	DA [auth C] EA [auth C] FA [auth C] G [auth A] GA [auth C] DA [auth C], EA [auth C], FA [auth C], G [auth A], GA [auth C], K [auth A], L [auth A], M [auth A], T [auth B], U [auth B], V [auth B], W [auth B], Y [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain DA [auth C] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain G [auth A] Focus chain GA [auth C] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain Y [auth B] Interactions & Density Focus chain DA [auth C] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain G [auth A] Focus chain GA [auth C] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain Y [auth B]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain BA [auth C] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain O [auth B] SDF format, chain P [auth B] MOL2 format, chain AA [auth C] MOL2 format, chain BA [auth C] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] mmCIF format, chain AA [auth C] mmCIF format, chain BA [auth C] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B]	AA [auth C] BA [auth C] E [auth A] F [auth A] O [auth B] AA [auth C], BA [auth C], E [auth A], F [auth A], O [auth B], P [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain BA [auth C] Focus chain E [auth A] Focus chain F [auth A] Focus chain O [auth B] Focus chain P [auth B] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth C] Focus chain E [auth A] Focus chain F [auth A] Focus chain O [auth B] Focus chain P [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.57 Å
R-Value Free: 0.256 (Depositor), 0.256 (DCC)
R-Value Work: 0.181 (Depositor), 0.189 (DCC)
R-Value Observed: 0.183 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.024	α = 90
b = 97.584	β = 90
c = 138.967	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-10-08

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2025-10-08
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.