2XH1 | pdb_00002xh1

Crystal structure of human KAT II-inhibitor complex

PDB DOI: https://doi.org/10.2210/pdb2XH1/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2010-06-08 Released: 2010-07-28
Deposition Author(s): Rossi, F., Casazza, V., Garavaglia, S., Sathyasaikumar, K.V., Schwarcz, R., Kojima, S.I., Okuwaki, K., Ono, S.I., Kajii, Y., Rizzi, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.241 (Depositor), 0.238 (DCC)
R-Value Work:
0.188 (Depositor), 0.191 (DCC)
R-Value Observed:
0.189 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Crystal Structure-Based Selective Targeting of the Pyridoxal 5'-Phsosphate Dependent Enzyme Kynurenine Aminotransferase II for Cognitive Enhancement

Rossi, F., Casazza, V., Garavaglia, S., Sathyasaikumar, K.V., Schwarcz, R., Kojima, S.I., Okuwaki, K., Ono, S.I., Kajii, Y., Rizzi, M.

(2010) J Med Chem 53: 5684

PubMed: 20684605 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1021/jm100464k
Primary Citation Related Structures:
2XH1

PubMed Abstract:
Fluctuations in the brain levels of the neuromodulator kynurenic acid may control cognitive processes and play a causative role in several catastrophic brain diseases. Elimination of the pyridoxal 5'-phosphate dependent enzyme kynurenine aminotransferase II reduces cerebral kynurenic acid synthesis and has procognitive effects. The present description of the crystal structure of human kynurenine aminotransferase II in complex with its potent and specific primary amine-bearing fluoroquinolone inhibitor (S)-(-)-9-(4-aminopiperazin-1-yl)-8-fluoro-3-methyl-6-oxo-2,3-dihydro-6H-1-oxa-3a-azaphenalene-5-carboxylic acid (BFF-122) should facilitate the structure-based development of cognition-enhancing drugs. From a medicinal chemistry perspective our results demonstrate that the issue of inhibitor specificity for highly conserved PLP-dependent enzymes could be successfully addressed.

Organizational Affiliation

University of Piemonte Orientale Amedeo Avogadro, Novara, Italy.

Macromolecule Content

Total Structure Weight: 96.23 kDa
Atom Count: 6,972
Modeled Residue Count: 824
Deposited Residue Count: 850
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
KYNURENINE/ALPHA-AMINOADIPATE AMINOTRANSFERASE, MITOCHONDRIAL	A, B	425	Homo sapiens	Mutation(s): 1 EC: 2.6.1.7 (PDB Primary Data), 2.6.1.39 (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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BF5 Query on BF5 Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain C [auth A] MOL2 format, chain F [auth B] MOL2 format, chain C [auth A] mmCIF format, chain F [auth B] mmCIF format, chain C [auth A]	C [auth A], F [auth B]	(3S)-10-(4-AMINOPIPERAZIN-1-YL)-9-FLUORO-7-HYDROXY-3-METHYL-2,3-DIHYDRO-8H-[1,4]OXAZINO[2,3,4-IJ]QUINOLINE-6-CARBOXYLATE C₁₇ H₁₉ F N₄ O₄ XSSSNYCVNIDBIB-VIFPVBQESA-M		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]
PLP Query on PLP Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain D [auth A] MOL2 format, chain G [auth B] MOL2 format, chain D [auth A] mmCIF format, chain G [auth B] mmCIF format, chain D [auth A]	D [auth A], G [auth B]	PYRIDOXAL-5'-PHOSPHATE C₈ H₁₀ N O₆ P NGVDGCNFYWLIFO-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain G [auth B] Interactions & Density Focus chain D [auth A] Focus chain G [auth B]
IOD Query on IOD 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]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain H [auth B] MOL2 format, chain H [auth B] mmCIF format, chain H [auth B]	H [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Interactions & Density Focus chain H [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.241 (Depositor), 0.238 (DCC)
R-Value Work: 0.188 (Depositor), 0.191 (DCC)
R-Value Observed: 0.189 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.323	α = 90
b = 152.857	β = 90
c = 60.8	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2010-07-28

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2010-07-28
Type: Initial release
Version 1.1: 2011-10-26
Changes: Database references, Version format compliance
Version 1.2: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Other, Refinement description