6MVA | pdb_00006mva

LDHA structure in complex with inhibitor 14

PDB DOI: https://doi.org/10.2210/pdb6MVA/pdb

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

Deposited: 2018-10-24 Released: 2019-10-30
Deposition Author(s): Eigenbrot, C.E., Ultsch, M., Wei, B.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.02 Å
R-Value Free:
0.209 (Depositor), 0.214 (DCC)
R-Value Work:
0.190 (Depositor), 0.195 (DCC)
R-Value Observed:
0.190 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 6MVA

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Structure-based Optimization of Potent, Cell-Active Hydroxylactam Inhibitors of Lactate Dehydrogenase

Wei, B., Robarge, K., Labadie, S.S., Chen, J., Corson, L.B., DiPasquale, A., Eigenbrot, C., Ultsch, M.

To be published.

Macromolecule Content

Total Structure Weight: 152.23 kDa
Atom Count: 11,132
Modeled Residue Count: 1,300
Deposited Residue Count: 1,328
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-lactate dehydrogenase A chain	A, B, C, D	332	Homo sapiens	Mutation(s): 0 Gene Names: LDHA, PIG19 EC: 1.1.1.27
UniProt & NIH Common Fund Data Resources
Find proteins for P00338 (Homo sapiens) Explore P00338 Go to UniProtKB: P00338
PHAROS: P00338 GTEx: ENSG00000134333
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00338
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 I [auth B] SDF format, chain L [auth C] SDF format, chain O [auth D] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain L [auth C] MOL2 format, chain O [auth D] mmCIF format, chain E [auth A] mmCIF format, chain I [auth B] mmCIF format, chain L [auth C] mmCIF format, chain O [auth D]	E [auth A], I [auth B], L [auth C], O [auth D]	1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE C₂₁ H₂₉ N₇ O₁₄ P₂ BOPGDPNILDQYTO-NNYOXOHSSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain O [auth D] Interactions & Density Focus chain E [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain O [auth D]
D4S Query on D4S Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain K [auth B] SDF format, chain N [auth C] SDF format, chain Q [auth D] MOL2 format, chain H [auth A] MOL2 format, chain K [auth B] MOL2 format, chain N [auth C] MOL2 format, chain Q [auth D] mmCIF format, chain H [auth A] mmCIF format, chain K [auth B] mmCIF format, chain N [auth C] mmCIF format, chain Q [auth D]	H [auth A], K [auth B], N [auth C], Q [auth D]	(6R)-6-(3-aminophenyl)-3-[(2-chlorophenyl)sulfanyl]-4-hydroxy-6-(thiophen-3-yl)-5,6-dihydro-2H-pyran-2-one C₂₁ H₁₆ Cl N O₃ S₂ UHNGEDKMVUGEAD-OAQYLSRUSA-N		Interactions Focus chain H [auth A] Focus chain K [auth B] Focus chain N [auth C] Focus chain Q [auth D] Interactions & Density Focus chain H [auth A] Focus chain K [auth B] Focus chain N [auth C] Focus chain Q [auth D]
EPE Query on EPE Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain J [auth B] SDF format, chain M [auth C] MOL2 format, chain F [auth A] MOL2 format, chain J [auth B] MOL2 format, chain M [auth C] mmCIF format, chain F [auth A] mmCIF format, chain J [auth B] mmCIF format, chain M [auth C]	F [auth A], J [auth B], M [auth C]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain J [auth B] Focus chain M [auth C] Interactions & Density Focus chain F [auth A] Focus chain J [auth B] Focus chain M [auth C]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain P [auth D] MOL2 format, chain G [auth A] MOL2 format, chain P [auth D] mmCIF format, chain G [auth A] mmCIF format, chain P [auth D]	G [auth A], P [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth A] Focus chain P [auth D] Interactions & Density Focus chain G [auth A] Focus chain P [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.02 Å
R-Value Free: 0.209 (Depositor), 0.214 (DCC)
R-Value Work: 0.190 (Depositor), 0.195 (DCC)
R-Value Observed: 0.190 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.541	α = 90
b = 81.493	β = 98.55
c = 103.532	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2019-10-30

Deposition Author(s):

Eigenbrot, C.E.

Revision History (Full details and data files)

Version 1.0: 2019-10-30
Type: Initial release
Version 1.1: 2024-03-13
Changes: Data collection, Database references

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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.