5HL1 | pdb_00005hl1

Crystal structure of glutaminase C in complex with inhibitor CB-839

• PDB DOI: https://doi.org/10.2210/pdb5HL1/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-01-14 Released: 2016-08-24 
• Deposition Author(s): Huang, Q., Cerione, R.A.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.264 (Depositor), 0.262 (DCC) 
• R-Value Work: 
  0.225 (Depositor), 0.224 (DCC) 
• R-Value Observed: 
  0.226 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the clinically relevant glutaminase inhibitot CB-839 in complex with glutaminase C

Huang, Q., Katt, W.P., McDermott, L.A., Cerione, R.A.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 238.97 kDa 
• Atom Count: 13,120 
• Modeled Residue Count: 1,620 
• Deposited Residue Count: 2,156 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutaminase kidney isoform, mitochondrial	A, B, C, D	539	Homo sapiens	Mutation(s): 0  Gene Names: GLS, GLS1, KIAA0838 EC: 3.5.1.2
UniProt & NIH Common Fund Data Resources
Find proteins for O94925 (Homo sapiens) Explore O94925  Go to UniProtKB:  O94925
PHAROS:  O94925 GTEx:  ENSG00000115419

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
63J	E [auth A], F [auth B]	2-(pyridin-2-yl)-N-(5-{4-[6-({[3-(trifluoromethoxy)phenyl]acetyl}amino)pyridazin-3-yl]butyl}-1,3,4-thiadiazol-2-yl)acetamide C26 H24 F3 N7 O3 S PRAAPINBUWJLGA-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
63J	BindingDB:  5HL1	Kd: min: 1.5, max: 106 (nM) from 4 assay(s)
		IC50: min: 2, max: 2200 (nM) from 20 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.264 (Depositor), 0.262 (DCC) 
• R-Value Work:  0.225 (Depositor), 0.224 (DCC) 
• R-Value Observed: 0.226 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.53	α = 90
b = 139.382	β = 90
c = 177.959	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-08-24 
Deposition Author(s): Huang, Q., Cerione, R.A.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM040654
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM047458

Revision History  

• Version 1.0: 2016-08-24
  Type: Initial release
  
• Version 1.1: 2017-09-20
  Changes: Advisory, Author supporting evidence, Derived calculations
• Version 1.2: 2019-12-25
  Changes: Author supporting evidence
• Version 1.3: 2023-09-27
  Changes: Advisory, Data collection, Database references, Refinement description