4GDY | pdb_00004gdy

Kynurenine Aminotransferase II inhibitors

PDB DOI: https://doi.org/10.2210/pdb4GDY/pdb

Classification: TRANSFERASE/TRANSFERASE INHIBITOR
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): Yes

Deposited: 2012-08-01 Released: 2012-08-29
Deposition Author(s): Pandit, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.89 Å
R-Value Free:
0.240 (Depositor), 0.242 (DCC)
R-Value Work:
0.171 (Depositor), 0.171 (DCC)
R-Value Observed:
0.174 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

Discovery of Hydroxamate Bioisosteres as KATII Inhibitors with Improved Oral Bioavailability and Pharmacokinetics

Verhoest, P.R., Henderson, J.L., Sawant-Basak, A., Tuttle, J.B., Dounay, A.B., McAllister, L.A., Pandit, J., Rong, S., Hou, X., Bechle, B., Parikh, V., Evrard, E., Ghosh, S., Salafia, M.A., Rago, B., Obach, R., Fonseca, K.R., Chang, C.

(2012) Medchemcomm

DOI: https://doi.org/10.1039/C2MD20166F

Macromolecule Content

Total Structure Weight: 98.95 kDa
Atom Count: 6,880
Modeled Residue Count: 843
Deposited Residue Count: 878
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial	A, B	439	Homo sapiens	Mutation(s): 2 Gene Names: AADAT, KAT2 EC: 2.6.1.39 (PDB Primary Data), 2.6.1.7 (PDB Primary Data), 2.6.1.4 (UniProt), 2.6.1.63 (UniProt), 2.6.1.73 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q8N5Z0 (Homo sapiens) Explore Q8N5Z0 Go to UniProtKB: Q8N5Z0
PHAROS: Q8N5Z0 GTEx: ENSG00000109576
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8N5Z0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
0X1 Query on 0X1 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	(5-hydroxy-6-methyl-4-{[(1-oxo-7-phenoxy-1,2-dihydro[1,2,4]triazolo[4,3-a]quinolin-4-yl)amino]methyl}pyridin-3-yl)methyl dihydrogen phosphate C₂₄ H₂₂ N₅ O₇ P AMDYNPYMOMDDSQ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.89 Å
R-Value Free: 0.240 (Depositor), 0.242 (DCC)
R-Value Work: 0.171 (Depositor), 0.171 (DCC)
R-Value Observed: 0.174 (Depositor)

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 116.457	α = 90
b = 116.457	β = 90
c = 115.211	γ = 120

Software Package:

Software Name	Purpose
SCALA	data scaling
BUSTER-TNT	refinement
PDB_EXTRACT	data extraction
JDirector	data collection
XDS	data reduction
PHASER	phasing
BUSTER	refinement

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2012-08-29

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-08-29
Type: Initial release
Version 1.1: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description

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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.