5WBN | pdb_00005wbn

Crystal structure of fragment 3-(3-Benzyl-2-oxo-2H-[1,2,4]triazino[2,3-c]quinazolin-6-yl)propanoic acid bound in the ubiquitin binding pocket of the HDAC6 zinc-finger domain

PDB DOI: https://doi.org/10.2210/pdb5WBN/pdb

Classification: hydrolase/hydrolase inhibitor
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2017-06-29 Released: 2017-08-02
Deposition Author(s): Harding, R.J., Walker, J.R., Ferreira de Freitas, R., Ravichandran, M., Santhakumar, V., Schapira, M., Bountra, C., Edwards, A.M., Arrowsmith, C.H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.64 Å
R-Value Free:
0.168 (Depositor), 0.178 (DCC)
R-Value Work:
0.132 (Depositor), 0.147 (DCC)
R-Value Observed:
0.134 (Depositor)

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Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of fragment 3-(3-Benzyl-2-oxo-2H-[1,2,4]triazino[2,3-c]quinazolin-6-yl)propanoic acid bound in the ubiquitin binding pocket of the HDAC6 zinc-finger domain

Harding, R.J., Walker, J.R., Ferreira de Freitas, R., Ravichandran, M., Santhakumar, V., Schapira, M., Bountra, C., Edwards, A.M., Arrowsmith, C.H.

To be published.

Macromolecule Content

Total Structure Weight: 16.26 kDa
Atom Count: 1,036
Modeled Residue Count: 103
Deposited Residue Count: 107
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone deacetylase 6	A	107	Homo sapiens	Mutation(s): 0 Gene Names: HDAC6, KIAA0901, JM21 EC: 3.5.1.98 (PDB Primary Data), 2.3.2 (UniProt), 3.5.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UBN7 (Homo sapiens) Explore Q9UBN7 Go to UniProtKB: Q9UBN7
PHAROS: Q9UBN7 GTEx: ENSG00000094631
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9UBN7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
9ZV (Subject of Investigation/LOI) Query on 9ZV Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	3-(3-benzyl-2-oxo-2H-[1,2,4]triazino[2,3-c]quinazolin-6-yl)propanoic acid C₂₀ H₁₆ N₄ O₃ RRZGYLKTEQRDCA-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A], C [auth A], D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain S [auth A] SDF format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain R [auth A] mmCIF format, chain S [auth A] mmCIF format, chain R [auth A]	R [auth A], S [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain R [auth A] Focus chain S [auth A] Interactions & Density Focus chain R [auth A] Focus chain S [auth A]
FMT Query on FMT Download:Ideal Coordinates CCD File SDF format, chain P [auth A] SDF format, chain O [auth A] SDF format, chain N [auth A] MOL2 format, chain P [auth A] MOL2 format, chain O [auth A] MOL2 format, chain N [auth A] mmCIF format, chain P [auth A] mmCIF format, chain O [auth A] mmCIF format, chain N [auth A]	N [auth A], O [auth A], P [auth A]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Interactions & Density Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain Q [auth A] MOL2 format, chain Q [auth A] mmCIF format, chain Q [auth A]	Q [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain Q [auth A] Interactions & Density Focus chain Q [auth A]
UNX Query on UNX Download:Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A] G [auth A] H [auth A] I [auth A] J [auth A] F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A]	UNKNOWN ATOM OR ION X		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
9ZV	BindingDB: 5WBN	IC50: 2.50e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.64 Å
R-Value Free: 0.168 (Depositor), 0.178 (DCC)
R-Value Work: 0.132 (Depositor), 0.147 (DCC)
R-Value Observed: 0.134 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.85	α = 90
b = 43.74	β = 90
c = 55.76	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2017-08-02

Deposition Author(s):

Ferreira de Freitas, R.

Ravichandran, M.

Santhakumar, V.

Arrowsmith, C.H.

Revision History (Full details and data files)

Version 1.0: 2017-08-02
Type: Initial release
Version 1.1: 2024-03-13
Changes: Data collection, Database references

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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.