9K0G | pdb_00009k0g

Structure of Human HDAC2 in complex with inhibitor N-(2-aminophenyl)-4-(1-((phenylsulfonyl)methyl)-1H-1,2,3-triazol-4-yl)benzamide

PDB DOI: https://doi.org/10.2210/pdb9K0G/pdb

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

Deposited: 2024-10-15 Released: 2025-10-15
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: 1.62 Å
R-Value Free:
0.196 (Depositor), 0.197 (DCC)
R-Value Work:
0.164 (Depositor), 0.165 (DCC)
R-Value Observed:
0.165 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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: 141.39 kDa
Atom Count: 10,361
Modeled Residue Count: 1,103
Deposited Residue Count: 1,212
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

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 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1L47 (Subject of Investigation/LOI) Query on A1L47 Download:Ideal Coordinates CCD File SDF format, chain R [auth B] SDF format, chain G [auth A] SDF format, chain BA [auth C] MOL2 format, chain R [auth B] MOL2 format, chain G [auth A] MOL2 format, chain BA [auth C] mmCIF format, chain R [auth B] mmCIF format, chain G [auth A] mmCIF format, chain BA [auth C]	BA [auth C], G [auth A], R [auth B]	N-(2-aminophenyl)-4-(1-((phenylsulfonyl)methyl)-1H-1,2,3-triazol-4-yl)benzamide C₂₂ H₁₉ N₅ O₃ S SOJIATBITBDKBA-UHFFFAOYSA-N		Interactions Focus chain BA [auth C] Focus chain G [auth A] Focus chain R [auth B] Interactions & Density Focus chain BA [auth C] Focus chain G [auth A] Focus chain R [auth B]
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain X [auth B] SDF format, chain FA [auth C] MOL2 format, chain X [auth B] MOL2 format, chain FA [auth C] mmCIF format, chain X [auth B] mmCIF format, chain FA [auth C]	FA [auth C], X [auth B]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain FA [auth C] Focus chain X [auth B] Interactions & Density Focus chain FA [auth C] Focus chain X [auth B]
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain N [auth A] MOL2 format, chain N [auth A] mmCIF format, chain N [auth A]	N [auth A]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain N [auth A] Interactions & Density Focus chain N [auth A]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain W [auth B] SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain EA [auth C] MOL2 format, chain W [auth B] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain EA [auth C] mmCIF format, chain W [auth B] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain EA [auth C]	EA [auth C], K [auth A], L [auth A], M [auth A], W [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain EA [auth C] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain W [auth B] Interactions & Density Focus chain EA [auth C] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain W [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain V [auth B] MOL2 format, chain V [auth B] mmCIF format, chain V [auth B]	V [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain V [auth B] Interactions & Density Focus chain V [auth B]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain Y [auth C] SDF format, chain O [auth B] SDF format, chain D [auth A] MOL2 format, chain Y [auth C] MOL2 format, chain O [auth B] MOL2 format, chain D [auth A] mmCIF format, chain Y [auth C] mmCIF format, chain O [auth B] mmCIF format, chain D [auth A]	D [auth A], O [auth B], Y [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain O [auth B] Focus chain Y [auth C] Interactions & Density Focus chain D [auth A] Focus chain O [auth B] Focus chain Y [auth C]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain U [auth B] SDF format, chain T [auth B] SDF format, chain S [auth B] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain DA [auth C] SDF format, chain CA [auth C] MOL2 format, chain U [auth B] MOL2 format, chain T [auth B] MOL2 format, chain S [auth B] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain DA [auth C] MOL2 format, chain CA [auth C] mmCIF format, chain U [auth B] mmCIF format, chain T [auth B] mmCIF format, chain S [auth B] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain DA [auth C] mmCIF format, chain CA [auth C]	CA [auth C] DA [auth C] H [auth A] I [auth A] J [auth A] CA [auth C], DA [auth C], H [auth A], I [auth A], J [auth A], S [auth B], T [auth B], U [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain CA [auth C] Focus chain DA [auth C] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Interactions & Density Focus chain CA [auth C] Focus chain DA [auth C] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain Z [auth C] SDF format, chain Q [auth B] SDF format, chain P [auth B] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain AA [auth C] MOL2 format, chain Z [auth C] MOL2 format, chain Q [auth B] MOL2 format, chain P [auth B] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain AA [auth C] mmCIF format, chain Z [auth C] mmCIF format, chain Q [auth B] mmCIF format, chain P [auth B] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain AA [auth C]	AA [auth C] E [auth A] F [auth A] P [auth B] Q [auth B] AA [auth C], E [auth A], F [auth A], P [auth B], Q [auth B], Z [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain E [auth A] Focus chain F [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain E [auth A] Focus chain F [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain Z [auth C]