3ZNR

HDAC7 bound with inhibitor TMP269

Structural Biology Knowledgebase: 3ZNR SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.241
  • R-Value Work: 0.212

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3ZNR

Classification: HYDROLASE

Total Structure Weight: 137697.66

Macromolecule Entities
Molecule Chains Length Organism Details
HISTONE DEACETYLASE 7 A, B, C 423 Homo sapiens EC#: 3.5.1.98 IUBMB
Fragment: CATALYTIC DOMAIN, RESIDUES 482-903
Details: LIGAND IS A TFMO INHIBITOR
Gene Name(s): HDAC7 Gene View HDAC7A

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
NU9
Query on NU9

A N-{[4-(4-phenyl-1,3-thiazol-2-yl)tetrahydro- 2H-pyran-4-yl]methyl}-3-[5-(trifluoromethyl)- 1,2,4-oxadiazol-3-yl]benzamide
C25 H21 F3 N4 O3 S
HORXBWNTEDOVKN-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A, B, C ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
K
Query on K

A, B, C POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
NU9 N/A in BindingDB
Ki: 36 nM  BindingMOAD
Ki: 36 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.241
  • R-Value Work: 0.212
  • Space Group: P 32

Unit Cell:

Length (Å) Angle (°)
a = 81.39 α = 90.00
b = 81.39 β = 90.00
c = 149.26 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2013-02-15
  • Released Date: 2013-03-27
  • Deposition author(s): Lobera, m., madauss, k., pohlhaus, d., trump, r., nolan, m.

Revision History

  • 2013-05-01
    Type: Atom nomenclature | Details: HETATM
  • 2013-05-01
    Type: Citation | Details: JRNL
  • 2013-04-03
    Type: Citation | Details: JRNL