7DBJ | pdb_00007dbj

Crystal structure of human LDHB in complex with NADH, oxamate, and AXKO-0046

PDB DOI: https://doi.org/10.2210/pdb7DBJ/pdb

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

Deposited: 2020-10-20 Released: 2021-10-20
Deposition Author(s): Sogabe, S., Miwa, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free:
0.192 (Depositor), 0.197 (DCC)
R-Value Work:
0.170 (Depositor), 0.179 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Identification of the first highly selective inhibitor of human lactate dehydrogenase B.

Shibata, S., Sogabe, S., Miwa, M., Fujimoto, T., Takakura, N., Naotsuka, A., Kitamura, S., Kawamoto, T., Soga, T.

(2021) Sci Rep 11: 21353-21353

PubMed: 34725423 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41598-021-00820-7
Primary Citation Related Structures:
7DBJ, 7DBK

PubMed Abstract:
Lactate dehydrogenase (LDH) catalyses the conversion of pyruvate to lactate and NADH to NAD ⁺; it has two isoforms, LDHA and LDHB. LDHA is a promising target for cancer therapy, whereas LDHB is necessary for basal autophagy and cancer cell proliferation in oxidative and glycolytic cancer cells. To the best of our knowledge, selective inhibitors for LDHB have not yet been reported. Here, we developed a high-throughput mass spectrometry screening system using an LDHB enzyme assay by detecting NADH and NAD ⁺. As a result, we identified a small-molecule LDHB selective inhibitor AXKO-0046, an indole derivative. This compound exhibited uncompetitive LDHB inhibition (EC ₅₀ = 42 nM). X-ray crystallography revealed that AXKO-0046 bound to the potential allosteric site away from the LDHB catalytic active site, suggesting that targeting the tetramerisation interface of the two dimers is critical for the enzymatic activity. AXKO-0046 and its derivatives can be used to validate LDHB-associated pathways in cancer metabolism.

Organizational Affiliation

Discovery Biology, Discovery Science, Axcelead Drug Discovery Partners, Inc., 2-26-1 Muraoka-Higashi, Fujisawa, Kanagawa, Japan. sachio.shibata@axcelead.com.

Macromolecule Content

Total Structure Weight: 150.4 kDa
Atom Count: 11,302
Modeled Residue Count: 1,332
Deposited Residue Count: 1,332
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-lactate dehydrogenase B chain	A, B, C, D	333	Homo sapiens	Mutation(s): 0 Gene Names: LDHB EC: 1.1.1.27
UniProt & NIH Common Fund Data Resources
Find proteins for P07195 (Homo sapiens) Explore P07195 Go to UniProtKB: P07195
PHAROS: P07195 GTEx: ENSG00000111716
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P07195
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAI Query on NAI Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] SDF format, chain L [auth C] SDF format, chain Q [auth D] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain L [auth C] MOL2 format, chain Q [auth D] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain L [auth C] mmCIF format, chain Q [auth D]	E [auth A], H [auth B], L [auth C], Q [auth D]	1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE C₂₁ H₂₉ N₇ O₁₄ P₂ BOPGDPNILDQYTO-NNYOXOHSSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain L [auth C] Focus chain Q [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain L [auth C] Focus chain Q [auth D]
H1U Query on H1U Download:Ideal Coordinates CCD File SDF format, chain K [auth C] SDF format, chain P [auth D] MOL2 format, chain K [auth C] MOL2 format, chain P [auth D] mmCIF format, chain K [auth C] mmCIF format, chain P [auth D]	K [auth C], P [auth D]	N-[[3-[2-[(phenylmethyl)amino]ethyl]-1H-indol-2-yl]methyl]cycloheptanamine C₂₅ H₃₃ N₃ VJTXDVYRAXQJAK-UHFFFAOYSA-N		Interactions Focus chain K [auth C] Focus chain P [auth D] Interactions & Density Focus chain K [auth C] Focus chain P [auth D]
OXM Query on OXM Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain I [auth B] SDF format, chain M [auth C] SDF format, chain R [auth D] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain M [auth C] MOL2 format, chain R [auth D] mmCIF format, chain F [auth A] mmCIF format, chain I [auth B] mmCIF format, chain M [auth C] mmCIF format, chain R [auth D]	F [auth A], I [auth B], M [auth C], R [auth D]	OXAMIC ACID C₂ H₃ N O₃ SOWBFZRMHSNYGE-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain I [auth B] Focus chain M [auth C] Focus chain R [auth D] Interactions & Density Focus chain F [auth A] Focus chain I [auth B] Focus chain M [auth C] Focus chain R [auth D]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain J [auth B] SDF format, chain N [auth C] SDF format, chain O [auth C] SDF format, chain S [auth D] SDF format, chain T [auth D] SDF format, chain U [auth D] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain N [auth C] MOL2 format, chain O [auth C] MOL2 format, chain S [auth D] MOL2 format, chain T [auth D] MOL2 format, chain U [auth D] mmCIF format, chain G [auth A] mmCIF format, chain J [auth B] mmCIF format, chain N [auth C] mmCIF format, chain O [auth C] mmCIF format, chain S [auth D] mmCIF format, chain T [auth D] mmCIF format, chain U [auth D]	G [auth A] J [auth B] N [auth C] O [auth C] S [auth D] G [auth A], J [auth B], N [auth C], O [auth C], S [auth D], T [auth D], U [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain J [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain S [auth D] Focus chain T [auth D] Focus chain U [auth D] Interactions & Density Focus chain G [auth A] Focus chain J [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain S [auth D] Focus chain T [auth D] Focus chain U [auth D]

Binding Affinity Annotations
ID	Source	Binding Affinity
OXM	BindingDB: 7DBJ	Ki: 9.44e+4 (nM) from 1 assay(s)
OXM	BindingDB: 7DBJ	IC50: min: 3.38e+4, max: 1.23e+5 (nM) from 3 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free: 0.192 (Depositor), 0.197 (DCC)
R-Value Work: 0.170 (Depositor), 0.179 (DCC)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.389	α = 90
b = 137.577	β = 109.264
c = 84.909	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2021-10-20

Deposition Author(s):

Sogabe, S.

Miwa, M.

Revision History (Full details and data files)

Version 1.0: 2021-10-20
Type: Initial release
Version 1.1: 2021-11-10
Changes: Database references
Version 1.2: 2022-02-16
Changes: Database references
Version 1.3: 2023-11-29
Changes: Data collection, Derived calculations, Refinement description