5BWX | pdb_00005bwx

X-RAY CRYSTAL STRUCTURE AT 1.70A RESOLUTION OF HUMAN MITOCHONDRIAL BRANCHED CHAIN AMINOTRANSFERASE (BCATM) COMPLEXED WITH A 4-CHLORO-2-FLUORO SUBSTITUTED PYRAZOLOPYRIMIDINONE COMPOUND AND AN INTERNAL ALDIMINE LINKED PLP COFACTOR.

PDB DOI: https://doi.org/10.2210/pdb5BWX/pdb

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

Deposited: 2015-06-08 Released: 2015-07-01
Deposition Author(s): Somers, D.O.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.238 (Depositor), 0.247 (DCC)
R-Value Work:
0.197 (Depositor), 0.206 (DCC)
R-Value Observed:
0.199 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

The Discovery of in Vivo Active Mitochondrial Branched-Chain Aminotransferase (BCATm) Inhibitors by Hybridizing Fragment and HTS Hits.

Bertrand, S.M., Ancellin, N., Beaufils, B., Bingham, R.P., Borthwick, J.A., Boullay, A.B., Boursier, E., Carter, P.S., Chung, C.W., Churcher, I., Dodic, N., Fouchet, M.H., Fournier, C., Francis, P.L., Gummer, L.A., Herry, K., Hobbs, A., Hobbs, C.I., Homes, P., Jamieson, C., Nicodeme, E., Pickett, S.D., Reid, I.H., Simpson, G.L., Sloan, L.A., Smith, S.E., Somers, D.O., Spitzfaden, C., Suckling, C.J., Valko, K., Washio, Y., Young, R.J.

(2015) J Med Chem 58: 7140-7163

PubMed: 26090771 Search on PubMed
DOI: https://doi.org/10.1021/acs.jmedchem.5b00313
Primary Citation Related Structures:
5BWR, 5BWT, 5BWU, 5BWV, 5BWW, 5BWX

PubMed Abstract:
The hybridization of hits, identified by complementary fragment and high throughput screens, enabled the discovery of the first series of potent inhibitors of mitochondrial branched-chain aminotransferase (BCATm) based on a 2-benzylamino-pyrazolo[1,5-a]pyrimidinone-3-carbonitrile template. Structure-guided growth enabled rapid optimization of potency with maintenance of ligand efficiency, while the focus on physicochemical properties delivered compounds with excellent pharmacokinetic exposure that enabled a proof of concept experiment in mice. Oral administration of 2-((4-chloro-2,6-difluorobenzyl)amino)-7-oxo-5-propyl-4,7-dihydropyrazolo[1,5-a]pyrimidine-3-carbonitrile 61 significantly raised the circulating levels of the branched-chain amino acids leucine, isoleucine, and valine in this acute study.

Organizational Affiliation

GlaxoSmithKline R&D, Medicines Research Centre , Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K.

Macromolecule Content

Total Structure Weight: 86.08 kDa
Atom Count: 6,930
Modeled Residue Count: 713
Deposited Residue Count: 738
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, mitochondrial	A, B	369	Homo sapiens	Mutation(s): 0 Gene Names: BCAT2, BCATM, BCT2, ECA40 EC: 2.6.1.42
UniProt & NIH Common Fund Data Resources
Find proteins for O15382 (Homo sapiens) Explore O15382 Go to UniProtKB: O15382
PHAROS: O15382 GTEx: ENSG00000105552
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O15382
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
4W4 Query on 4W4 Download:Ideal Coordinates CCD File SDF format, chain U [auth B] SDF format, chain D [auth A] MOL2 format, chain U [auth B] MOL2 format, chain D [auth A] mmCIF format, chain U [auth B] mmCIF format, chain D [auth A]	D [auth A], U [auth B]	5-butyl-2-[(4-chloro-2-fluorobenzyl)amino]-7-oxo-4,7-dihydropyrazolo[1,5-a]pyrimidine-3-carbonitrile C₁₈ H₁₇ Cl F N₅ O MRXJYWNXFPIXSE-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain U [auth B] Interactions & Density Focus chain D [auth A] Focus chain U [auth B]
PLP Query on PLP Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain T [auth B] MOL2 format, chain C [auth A] MOL2 format, chain T [auth B] mmCIF format, chain C [auth A] mmCIF format, chain T [auth B]	C [auth A], T [auth B]	PYRIDOXAL-5'-PHOSPHATE C₈ H₁₀ N O₆ P NGVDGCNFYWLIFO-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain T [auth B] Interactions & Density Focus chain C [auth A] Focus chain T [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain S [auth A] SDF format, chain BA [auth B] MOL2 format, chain S [auth A] MOL2 format, chain BA [auth B] mmCIF format, chain S [auth A] mmCIF format, chain BA [auth B]	BA [auth B], S [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain BA [auth B] Focus chain S [auth A] Interactions & Density Focus chain BA [auth B] Focus chain S [auth A]
DMS Query on DMS Download:Ideal Coordinates CCD File SDF format, chain V [auth B] MOL2 format, chain V [auth B] mmCIF format, chain V [auth B]	V [auth B]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain V [auth B] Interactions & Density Focus chain V [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain Z [auth B] SDF format, chain Y [auth B] SDF format, chain X [auth B] SDF format, chain W [auth B] SDF format, chain Q [auth A] SDF format, chain P [auth A] SDF format, chain O [auth A] SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain Z [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain X [auth B] MOL2 format, chain W [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain P [auth A] MOL2 format, chain O [auth A] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain Z [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain X [auth B] mmCIF format, chain W [auth B] mmCIF format, chain Q [auth A] mmCIF format, chain P [auth A] mmCIF format, chain O [auth A] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A] F [auth A] G [auth A] H [auth A] I [auth A] E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], W [auth B], X [auth B], Y [auth B], Z [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain R [auth A] SDF format, chain AA [auth B] MOL2 format, chain R [auth A] MOL2 format, chain AA [auth B] mmCIF format, chain R [auth A] mmCIF format, chain AA [auth B]	AA [auth B], R [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AA [auth B] Focus chain R [auth A] Interactions & Density Focus chain AA [auth B] Focus chain R [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
4W4	BindingDB: 5BWX	IC50: min: 16, max: 79 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.238 (Depositor), 0.247 (DCC)
R-Value Work: 0.197 (Depositor), 0.206 (DCC)
R-Value Observed: 0.199 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.46	α = 90
b = 106.68	β = 90
c = 107.92	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
Coot	model building

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2015-07-01

Deposition Author(s):

Somers, D.O.

Revision History (Full details and data files)

Version 1.0: 2015-07-01
Type: Initial release
Version 1.1: 2015-10-07
Changes: Database references
Version 1.2: 2019-06-12
Changes: Data collection, Structure summary
Version 1.3: 2025-04-09
Changes: Data collection, Database references, Structure summary