6V8C | pdb_00006v8c

Design, Synthesis, and Mechanism of Fluorine-substituted Cyclohexene Analogues of GAMA-Aminobutyric Acid (GABA) as Selective Ornithine Aminotransferase Inactivators

• PDB DOI: https://doi.org/10.2210/pdb6V8C/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-12-10 Released: 2020-12-16 
• Deposition Author(s): Zhu, W., Doubleday, P.T., Catlin, D.S., Weerawarna, P., Butrin, A., Shen, S., Kelleher, N.L., Liu, D., Silverman, R.B.
• Funding Organization(s): National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.268 (Depositor), 0.268 (DCC) 
• R-Value Work: 
  0.239 (Depositor), 0.239 (DCC) 
• R-Value Observed: 
  0.240 (Depositor) 

Starting Model: experimental

Literature

Design, Synthesis, and Mechanism of Fluorine-substituted Cyclohexene Analogues of GAMA-Aminobutyric Acid (GABA) as Selective Ornithine Aminotransferase Inactivators

Zhu, W., Doubleday, P.T., Catlin, D.S., Weerawarna, P., Butrin, A., Shen, S., Kelleher, N.L., Liu, D., Silverman, R.B.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: mass spectrometry, assay for oligomerization

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 135.74 kDa 
• Atom Count: 10,360 
• Modelled Residue Count: 1,212 
• Deposited Residue Count: 1,212 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ornithine aminotransferase, mitochondrial	A, B, C	404	Homo sapiens	Mutation(s): 0  Gene Names: OAT EC: 2.6.1.13
UniProt & NIH Common Fund Data Resources
Find proteins for P04181 (Homo sapiens) Explore P04181  Go to UniProtKB:  P04181
PHAROS:  P04181 GTEx:  ENSG00000065154

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PLP	D [auth A], F [auth B], H [auth C]	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N
QRM (Subject of Investigation/LOI)	E [auth A], G [auth B], I [auth C]	3-aminocyclohexa-1,3-diene-1-carboxylic acid C7 H9 N O2 CMKSBGMWHUXBKM-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.268 (Depositor), 0.268 (DCC) 
• R-Value Work:  0.239 (Depositor), 0.239 (DCC) 
• R-Value Observed: 0.240 (Depositor) 

Space Group: P 3₁ 1 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 193.782	α = 90
b = 193.782	β = 90
c = 57.2	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-12-16 
Deposition Author(s): Zhu, W., Doubleday, P.T., Catlin, D.S., Weerawarna, P., Butrin, A., Shen, S., Kelleher, N.L., Liu, D., Silverman, R.B.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)		DA030604

Revision History  

• Version 1.0: 2020-12-16
  Type: Initial release
  
• Version 2.0: 2023-10-11
  Changes: Data collection, Database references, Non-polymer description, Refinement description
• Version 3.0: 2024-12-25
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary