5WBN

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
R-Value Work: 0.132
R-Value Observed: 0.134

wwPDB Validation 3D Report Full Report

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
Modelled Residue Count: 103
Deposited Residue Count: 107
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 6	A	107	Homo sapiens	Mutation(s): 0 Gene Names: HDAC6, KIAA0901, JM21 EC: 3.5.1.98 (PDB Primary Data), 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% Identity50% Identity70% Identity90% Identity95% Identity100% 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 B [auth A] SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [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 R [auth A] SDF format, chain S [auth A] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] mmCIF format, chain R [auth A] mmCIF format, chain S [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 N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain P [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 F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [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]