2ABJ | pdb_00002abj

Crystal structure of human branched chain amino acid transaminase in a complex with an inhibitor, C16H10N2O4F3SCl, and pyridoxal 5' phosphate.

PDB DOI: https://doi.org/10.2210/pdb2ABJ/pdb

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

Deposited: 2005-07-15 Released: 2006-06-27
Deposition Author(s): Ohren, J.F., Moreland, D.W., Rubin, J.R., Hu, H.L., McConnell, P.C., Mistry, A., Mueller, W.T., Scholten, J.D., Hasemann, C.H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.257 (Depositor), 0.252 (DCC)
R-Value Work:
0.205 (Depositor), 0.202 (DCC)
R-Value Observed:
0.205 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

The design and synthesis of human branched-chain amino acid aminotransferase inhibitors for treatment of neurodegenerative diseases.

Hu, L.Y., Boxer, P.A., Kesten, S.R., Lei, H.J., Wustrow, D.J., Moreland, D.W., Zhang, L., Ahn, K., Ryder, T.R., Liu, X., Rubin, J.R., Fahnoe, K., Carroll, R.T., Dutta, S., Fahnoe, D.C., Probert, A.W., Roof, R.L., Rafferty, M.F., Kostlan, C.R., Scholten, J.D., Hood, M., Ren, X.D., Schielke, G.P., Su, T.Z., Taylor, C.P., Mistry, A., McConnell, P., Hasemann, C., Ohren, J.

(2006) Bioorg Med Chem Lett 16: 2337-2340

PubMed: 16143519 Search on PubMed
DOI: https://doi.org/10.1016/j.bmcl.2005.07.058
Primary Citation Related Structures:
2ABJ

PubMed Abstract:
The inhibition of the cytosolic isoenzyme BCAT that is expressed specifically in neuronal tissue is likely to be useful for the treatment of neurodegenerative and other neurological disorders where glutamatergic mechanisms are implicated. Compound 2 exhibited an IC50 of 0.8 microM in the hBCATc assays; it is an active and selective inhibitor. Inhibitor 2 also blocked calcium influx into neuronal cells following inhibition of glutamate uptake, and demonstrated neuroprotective efficacy in vivo. SAR, pharmacology, and the crystal structure of hBCATc with inhibitor 2 are described.

Organizational Affiliation

Pfizer Global Research and Development, Ann Arbor, MI, USA. Lain-Yen.Hu@pfizer.com

Macromolecule Content

Total Structure Weight: 167.08 kDa
Atom Count: 13,037
Modeled Residue Count: 1,449
Deposited Residue Count: 1,464
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Branched-chain-amino-acid aminotransferase, cytosolic	A, B [auth D], C [auth G], D [auth J]	366	Homo sapiens	Mutation(s): 5 Gene Names: BCAT1, BCT1, ECA39 EC: 2.6.1.42
UniProt & NIH Common Fund Data Resources
Find proteins for P54687 (Homo sapiens) Explore P54687 Go to UniProtKB: P54687
PHAROS: P54687 GTEx: ENSG00000060982
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P54687
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CBC Query on CBC Download:Ideal Coordinates CCD File SDF format, chain K [auth J] SDF format, chain I [auth G] SDF format, chain G [auth D] SDF format, chain E [auth A] MOL2 format, chain K [auth J] MOL2 format, chain I [auth G] MOL2 format, chain G [auth D] MOL2 format, chain E [auth A] mmCIF format, chain K [auth J] mmCIF format, chain I [auth G] mmCIF format, chain G [auth D] mmCIF format, chain E [auth A]	E [auth A], G [auth D], I [auth G], K [auth J]	N'-(5-CHLOROBENZOFURAN-2-CARBONYL)-2-(TRIFLUOROMETHYL)BENZENESULFONOHYDRAZIDE C₁₆ H₁₀ Cl F₃ N₂ O₄ S ZLQBZYKAQQWOTK-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain G [auth D] Focus chain I [auth G] Focus chain K [auth J] Interactions & Density Focus chain E [auth A] Focus chain G [auth D] Focus chain I [auth G] Focus chain K [auth J]
PLP Query on PLP Download:Ideal Coordinates CCD File SDF format, chain L [auth J] SDF format, chain J [auth G] SDF format, chain H [auth D] SDF format, chain F [auth A] MOL2 format, chain L [auth J] MOL2 format, chain J [auth G] MOL2 format, chain H [auth D] MOL2 format, chain F [auth A] mmCIF format, chain L [auth J] mmCIF format, chain J [auth G] mmCIF format, chain H [auth D] mmCIF format, chain F [auth A]	F [auth A], H [auth D], J [auth G], L [auth J]	PYRIDOXAL-5'-PHOSPHATE C₈ H₁₀ N O₆ P NGVDGCNFYWLIFO-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain H [auth D] Focus chain J [auth G] Focus chain L [auth J] Interactions & Density Focus chain F [auth A] Focus chain H [auth D] Focus chain J [auth G] Focus chain L [auth J]

Binding Affinity Annotations
ID	Source	Binding Affinity
CBC	BindingDB: 2ABJ	IC50: 230 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.257 (Depositor), 0.252 (DCC)
R-Value Work: 0.205 (Depositor), 0.202 (DCC)
R-Value Observed: 0.205 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.327	α = 90
b = 114.517	β = 90
c = 148.869	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
AMoRE	phasing

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2006-06-27

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2006-06-27
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.3: 2017-10-11
Changes: Refinement description
Version 1.4: 2025-03-26
Changes: Data collection, Database references, Derived calculations, Structure summary