6WBZ | pdb_00006wbz

Structure of Human HDAC2 in complex with an ethyl ketone inhibitor containing a spiro-bicyclic group

PDB DOI: https://doi.org/10.2210/pdb6WBZ/pdb

Classification: HYDROLASE/HYDROLASE Inhibitor
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2020-03-28 Released: 2020-05-06
Deposition Author(s): Klein, D.J., Yu, W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.32 Å
R-Value Free:
0.192 (Depositor), 0.200 (DCC)
R-Value Work:
0.172 (Depositor), 0.180 (DCC)
R-Value Observed:
0.173 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Discovery of ethyl ketone-based HDACs 1, 2, and 3 selective inhibitors for HIV latency reactivation.

Yu, W., Liu, J., Yu, Y., Zhang, V., Clausen, D., Kelly, J., Wolkenberg, S., Beshore, D., Duffy, J.L., Chung, C.C., Myers, R.W., Klein, D.J., Fells, J., Holloway, K., Wu, J., Wu, G., Howell, B.J., Barnard, R.J.O., Kozlowski, J.

(2020) Bioorg Med Chem Lett 30: 127197-127197

PubMed: 32331932 Search on PubMed
DOI: https://doi.org/10.1016/j.bmcl.2020.127197
Primary Citation of Related Structures:
6WBW, 6WBZ

PubMed Abstract:
A novel series of ethyl ketone based HDACs 1, 2, and 3 selective inhibitors have been identified with good enzymatic and cellular activity and high selectivity over HDACs 6 and 8. These inhibitors contain a spirobicyclic group in the amide region. Compound 13 stands out as a lead due to its good potency, high selectivity, and reasonable rat and dog PK. Compounds 33 and 34 show good potency and rat PK profiles as well.

Organizational Affiliation

Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, NJ 07033, USA. Electronic address: wensheng.yu@merck.com.

Macromolecule Content

Total Structure Weight: 133.02 kDa
Atom Count: 10,534
Modelled Residue Count: 1,101
Deposited Residue Count: 1,128
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone deacetylase 2	A, B, C	376	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

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TV7 (Subject of Investigation/LOI) Query on TV7 Download Ideal Coordinates CCD File SDF format, chain FA [auth C] SDF format, chain N [auth A] SDF format, chain V [auth B] MOL2 format, chain FA [auth C] MOL2 format, chain N [auth A] MOL2 format, chain V [auth B] mmCIF format, chain FA [auth C] mmCIF format, chain N [auth A] mmCIF format, chain V [auth B]	FA [auth C], N [auth A], V [auth B]	(1S)-N-{(1S)-7,7-dihydroxy-1-[5-(2-methoxyquinolin-3-yl)-1H-imidazol-2-yl]nonyl}-6-ethyl-6-azaspiro[2.5]octane-1-carboxamide C₃₂ H₄₅ N₅ O₄ YPIRISRXAGVBOC-RSXGOPAZSA-N		Interactions Focus chain FA [auth C] Focus chain N [auth A] Focus chain V [auth B] Interactions & Density Focus chain FA [auth C] Focus chain N [auth A] Focus chain V [auth B]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain DA [auth C] SDF format, chain EA [auth C] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain T [auth B] SDF format, chain U [auth B] MOL2 format, chain DA [auth C] MOL2 format, chain EA [auth C] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] mmCIF format, chain DA [auth C] mmCIF format, chain EA [auth C] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B]	DA [auth C] EA [auth C] K [auth A] L [auth A] M [auth A] DA [auth C], EA [auth C], K [auth A], L [auth A], M [auth A], T [auth B], U [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain DA [auth C] Focus chain EA [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] Interactions & Density Focus chain DA [auth C] Focus chain EA [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]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain X [auth C] SDF format, chain Y [auth C] SDF format, chain Z [auth C] MOL2 format, chain AA [auth C] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain X [auth C] MOL2 format, chain Y [auth C] MOL2 format, chain Z [auth C] mmCIF format, chain AA [auth C] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain X [auth C] mmCIF format, chain Y [auth C] mmCIF format, chain Z [auth C]	AA [auth C] E [auth A] F [auth A] G [auth A] H [auth A] AA [auth C], E [auth A], F [auth A], G [auth A], H [auth A], P [auth B], Q [auth B], X [auth C], Y [auth C], Z [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth C] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain O [auth B] SDF format, chain W [auth C] MOL2 format, chain D [auth A] MOL2 format, chain O [auth B] MOL2 format, chain W [auth C] mmCIF format, chain D [auth A] mmCIF format, chain O [auth B] mmCIF format, chain W [auth C]	D [auth A], O [auth B], W [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain O [auth B] Focus chain W [auth C] Interactions & Density Focus chain D [auth A] Focus chain O [auth B] Focus chain W [auth C]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain BA [auth C] SDF format, chain CA [auth C] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain R [auth B] SDF format, chain S [auth B] MOL2 format, chain BA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] mmCIF format, chain BA [auth C] mmCIF format, chain CA [auth C] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B]	BA [auth C] CA [auth C] I [auth A] J [auth A] R [auth B] BA [auth C], CA [auth C], I [auth A], J [auth A], R [auth B], S [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain BA [auth C] Focus chain CA [auth C] Focus chain I [auth A] Focus chain J [auth A] Focus chain R [auth B] Focus chain S [auth B] Interactions & Density Focus chain BA [auth C] Focus chain CA [auth C] Focus chain I [auth A] Focus chain J [auth A] Focus chain R [auth B] Focus chain S [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.32 Å
R-Value Free: 0.192 (Depositor), 0.200 (DCC)
R-Value Work: 0.172 (Depositor), 0.180 (DCC)
R-Value Observed: 0.173 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.39	α = 90
b = 99.17	β = 90
c = 139.6	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	data scaling
BUSTER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2020-05-06

Deposition Author(s):

Klein, D.J.

Yu, W.

Revision History (Full details and data files)

Version 1.0: 2020-05-06
Type: Initial release
Version 1.1: 2020-06-03
Changes: Database references
Version 1.2: 2024-03-06
Changes: Data collection, Database references, Derived calculations