7M2N

Crystal structure of Human Lactate Dehydrogenase A with Inhibitor Compound 15

PDB DOI: https://doi.org/10.2210/pdb7M2N/pdb

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

Deposited: 2021-03-17 Released: 2021-07-14
Deposition Author(s): Gumpena, R., Ding, J., Powell, D.A., Lowther, W.T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.258 (Depositor), 0.260 (DCC)
R-Value Work:
0.209 (Depositor), 0.210 (DCC)
R-Value Observed:
0.212 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Dual Glycolate Oxidase/Lactate Dehydrogenase A Inhibitors for Primary Hyperoxaluria

Ding, J., Gumpena, R., Boily, M.O., Caron, A., Chong, O., Cox, J.H., Dumais, V., Gaudreault, S., Graff, A.H., King, A., Knight, J., Oballa, R., Surendradoss, J., Tang, T., Wu, J., Lowther, W.T., Powell, D.A.

(2021) Acs Medicinal Chemistry Letters 12: 1116-1123

DOI: https://doi.org/10.1021/acsmedchemlett.1c00196

Macromolecule Content

Total Structure Weight: 162.66 kDa
Atom Count: 11,585
Modelled Residue Count: 1,320
Deposited Residue Count: 1,352
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-lactate dehydrogenase A chain	A, B, C, D	338	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00338
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
YOJ (Subject of Investigation/LOI) Query on YOJ Download Ideal Coordinates CCD File SDF format, chain BB [auth B] SDF format, chain BD [auth D] SDF format, chain EC [auth C] SDF format, chain X [auth A] MOL2 format, chain BB [auth B] MOL2 format, chain BD [auth D] MOL2 format, chain EC [auth C] MOL2 format, chain X [auth A] mmCIF format, chain BB [auth B] mmCIF format, chain BD [auth D] mmCIF format, chain EC [auth C] mmCIF format, chain X [auth A]	BB [auth B], BD [auth D], EC [auth C], X [auth A]	5-[(5'-{1-(4-carboxy-1,3-thiazol-2-yl)-5-(cyclopropylmethyl)-4-[(3-fluoro-4-sulfamoylphenyl)methyl]-1H-pyrazol-3-yl}-2'-fluoro[1,1'-biphenyl]-4-yl)oxy]-1H-1,2,3-triazole-4-carboxylic acid C₃₃ H₂₅ F₂ N₇ O₇ S₂ OLGHHCBVTKMRAO-UHFFFAOYSA-N		Interactions Focus chain BB [auth B] Focus chain BD [auth D] Focus chain EC [auth C] Focus chain X [auth A] Interactions & Density Focus chain BB [auth B] Focus chain BD [auth D] Focus chain EC [auth C] Focus chain X [auth A]
NAI (Subject of Investigation/LOI) Query on NAI Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain JA [auth B] SDF format, chain NB [auth C] SDF format, chain RC [auth D] MOL2 format, chain E [auth A] MOL2 format, chain JA [auth B] MOL2 format, chain NB [auth C] MOL2 format, chain RC [auth D] mmCIF format, chain E [auth A] mmCIF format, chain JA [auth B] mmCIF format, chain NB [auth C] mmCIF format, chain RC [auth D]	E [auth A], JA [auth B], NB [auth C], RC [auth D]	1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE C₂₁ H₂₉ N₇ O₁₄ P₂ BOPGDPNILDQYTO-NNYOXOHSSA-N		Interactions Focus chain E [auth A] Focus chain JA [auth B] Focus chain NB [auth C] Focus chain RC [auth D] Interactions & Density Focus chain E [auth A] Focus chain JA [auth B] Focus chain NB [auth C] Focus chain RC [auth D]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain CB [auth B] SDF format, chain FA [auth A] SDF format, chain IB [auth B] SDF format, chain N [auth A] SDF format, chain RA [auth B] SDF format, chain U [auth A] MOL2 format, chain CB [auth B] MOL2 format, chain FA [auth A] MOL2 format, chain IB [auth B] MOL2 format, chain N [auth A] MOL2 format, chain RA [auth B] MOL2 format, chain U [auth A] mmCIF format, chain CB [auth B] mmCIF format, chain FA [auth A] mmCIF format, chain IB [auth B] mmCIF format, chain N [auth A] mmCIF format, chain RA [auth B] mmCIF format, chain U [auth A]	CB [auth B] FA [auth A] IB [auth B] N [auth A] RA [auth B] CB [auth B], FA [auth A], IB [auth B], N [auth A], RA [auth B], U [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain CB [auth B] Focus chain FA [auth A] Focus chain IB [auth B] Focus chain N [auth A] Focus chain RA [auth B] Focus chain U [auth A] Interactions & Density Focus chain CB [auth B] Focus chain FA [auth A] Focus chain IB [auth B] Focus chain N [auth A] Focus chain RA [auth B] Focus chain U [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain AA [auth A] SDF format, chain DD [auth D] SDF format, chain EA [auth A] SDF format, chain F [auth A] SDF format, chain HA [auth B] SDF format, chain HC [auth D] SDF format, chain IA [auth B] SDF format, chain LB [auth C] SDF format, chain NA [auth B] SDF format, chain YA [auth B] MOL2 format, chain AA [auth A] MOL2 format, chain DD [auth D] MOL2 format, chain EA [auth A] MOL2 format, chain F [auth A] MOL2 format, chain HA [auth B] MOL2 format, chain HC [auth D] MOL2 format, chain IA [auth B] MOL2 format, chain LB [auth C] MOL2 format, chain NA [auth B] MOL2 format, chain YA [auth B] mmCIF format, chain AA [auth A] mmCIF format, chain DD [auth D] mmCIF format, chain EA [auth A] mmCIF format, chain F [auth A] mmCIF format, chain HA [auth B] mmCIF format, chain HC [auth D] mmCIF format, chain IA [auth B] mmCIF format, chain LB [auth C] mmCIF format, chain NA [auth B] mmCIF format, chain YA [auth B]	AA [auth A] DD [auth D] EA [auth A] F [auth A] HA [auth B] AA [auth A], DD [auth D], EA [auth A], F [auth A], HA [auth B], HC [auth D], IA [auth B], LB [auth C], NA [auth B], YA [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth A] Focus chain DD [auth D] Focus chain EA [auth A] Focus chain F [auth A] Focus chain HA [auth B] Focus chain HC [auth D] Focus chain IA [auth B] Focus chain LB [auth C] Focus chain NA [auth B] Focus chain YA [auth B] Interactions & Density Focus chain AA [auth A] Focus chain DD [auth D] Focus chain EA [auth A] Focus chain F [auth A] Focus chain HA [auth B] Focus chain HC [auth D] Focus chain IA [auth B] Focus chain LB [auth C] Focus chain NA [auth B] Focus chain YA [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain CC [auth C] SDF format, chain DC [auth C] SDF format, chain FB [auth B] SDF format, chain GC [auth C] SDF format, chain M [auth A] SDF format, chain PC [auth D] MOL2 format, chain CC [auth C] MOL2 format, chain DC [auth C] MOL2 format, chain FB [auth B] MOL2 format, chain GC [auth C] MOL2 format, chain M [auth A] MOL2 format, chain PC [auth D] mmCIF format, chain CC [auth C] mmCIF format, chain DC [auth C] mmCIF format, chain FB [auth B] mmCIF format, chain GC [auth C] mmCIF format, chain M [auth A] mmCIF format, chain PC [auth D]	CC [auth C] DC [auth C] FB [auth B] GC [auth C] M [auth A] CC [auth C], DC [auth C], FB [auth B], GC [auth C], M [auth A], PC [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain CC [auth C] Focus chain DC [auth C] Focus chain FB [auth B] Focus chain GC [auth C] Focus chain M [auth A] Focus chain PC [auth D] Interactions & Density Focus chain CC [auth C] Focus chain DC [auth C] Focus chain FB [auth B] Focus chain GC [auth C] Focus chain M [auth A] Focus chain PC [auth D]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain AB [auth B] SDF format, chain AC [auth C] SDF format, chain AD [auth D] SDF format, chain BA [auth A] SDF format, chain BC [auth C] SDF format, chain CA [auth A] SDF format, chain CD [auth D] SDF format, chain DA [auth A] SDF format, chain DB [auth B] SDF format, chain EB [auth B] SDF format, chain ED [auth D] SDF format, chain FC [auth C] SDF format, chain G [auth A] SDF format, chain GA [auth B] SDF format, chain GB [auth B] SDF format, chain H [auth A] SDF format, chain HB [auth B] SDF format, chain I [auth A] SDF format, chain IC [auth D] SDF format, chain J [auth A] SDF format, chain JB [auth B] SDF format, chain JC [auth D] SDF format, chain K [auth A] SDF format, chain KA [auth B] SDF format, chain KB [auth C] SDF format, chain KC [auth D] SDF format, chain L [auth A] SDF format, chain LA [auth B] SDF format, chain LC [auth D] SDF format, chain MA [auth B] SDF format, chain MB [auth C] SDF format, chain MC [auth D] SDF format, chain NC [auth D] SDF format, chain O [auth A] SDF format, chain OA [auth B] SDF format, chain OB [auth C] SDF format, chain OC [auth D] SDF format, chain P [auth A] SDF format, chain PA [auth B] SDF format, chain PB [auth C] SDF format, chain Q [auth A] SDF format, chain QA [auth B] SDF format, chain QB [auth C] SDF format, chain QC [auth D] SDF format, chain R [auth A] SDF format, chain RB [auth C] SDF format, chain S [auth A] SDF format, chain SA [auth B] SDF format, chain SB [auth C] SDF format, chain SC [auth D] SDF format, chain T [auth A] SDF format, chain TA [auth B] SDF format, chain TB [auth C] SDF format, chain TC [auth D] SDF format, chain UA [auth B] SDF format, chain UB [auth C] SDF format, chain UC [auth D] SDF format, chain V [auth A] SDF format, chain VA [auth B] SDF format, chain VB [auth C] SDF format, chain VC [auth D] SDF format, chain W [auth A] SDF format, chain WA [auth B] SDF format, chain WB [auth C] SDF format, chain WC [auth D] SDF format, chain XA [auth B] SDF format, chain XB [auth C] SDF format, chain XC [auth D] SDF format, chain Y [auth A] SDF format, chain YB [auth C] SDF format, chain YC [auth D] SDF format, chain Z [auth A] SDF format, chain ZA [auth B] SDF format, chain ZB [auth C] SDF format, chain ZC [auth D] MOL2 format, chain AB [auth B] MOL2 format, chain AC [auth C] MOL2 format, chain AD [auth D] MOL2 format, chain BA [auth A] MOL2 format, chain BC [auth C] MOL2 format, chain CA [auth A] MOL2 format, chain CD [auth D] MOL2 format, chain DA [auth A] MOL2 format, chain DB [auth B] MOL2 format, chain EB [auth B] MOL2 format, chain ED [auth D] MOL2 format, chain FC [auth C] MOL2 format, chain G [auth A] MOL2 format, chain GA [auth B] MOL2 format, chain GB [auth B] MOL2 format, chain H [auth A] MOL2 format, chain HB [auth B] MOL2 format, chain I [auth A] MOL2 format, chain IC [auth D] MOL2 format, chain J [auth A] MOL2 format, chain JB [auth B] MOL2 format, chain JC [auth D] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth B] MOL2 format, chain KB [auth C] MOL2 format, chain KC [auth D] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth B] MOL2 format, chain LC [auth D] MOL2 format, chain MA [auth B] MOL2 format, chain MB [auth C] MOL2 format, chain MC [auth D] MOL2 format, chain NC [auth D] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth B] MOL2 format, chain OB [auth C] MOL2 format, chain OC [auth D] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth B] MOL2 format, chain PB [auth C] MOL2 format, chain Q [auth A] MOL2 format, chain QA [auth B] MOL2 format, chain QB [auth C] MOL2 format, chain QC [auth D] MOL2 format, chain R [auth A] MOL2 format, chain RB [auth C] MOL2 format, chain S [auth A] MOL2 format, chain SA [auth B] MOL2 format, chain SB [auth C] MOL2 format, chain SC [auth D] MOL2 format, chain T [auth A] MOL2 format, chain TA [auth B] MOL2 format, chain TB [auth C] MOL2 format, chain TC [auth D] MOL2 format, chain UA [auth B] MOL2 format, chain UB [auth C] MOL2 format, chain UC [auth D] MOL2 format, chain V [auth A] MOL2 format, chain VA [auth B] MOL2 format, chain VB [auth C] MOL2 format, chain VC [auth D] MOL2 format, chain W [auth A] MOL2 format, chain WA [auth B] MOL2 format, chain WB [auth C] MOL2 format, chain WC [auth D] MOL2 format, chain XA [auth B] MOL2 format, chain XB [auth C] MOL2 format, chain XC [auth D] MOL2 format, chain Y [auth A] MOL2 format, chain YB [auth C] MOL2 format, chain YC [auth D] MOL2 format, chain Z [auth A] MOL2 format, chain ZA [auth B] MOL2 format, chain ZB [auth C] MOL2 format, chain ZC [auth D] mmCIF format, chain AB [auth B] mmCIF format, chain AC [auth C] mmCIF format, chain AD [auth D] mmCIF format, chain BA [auth A] mmCIF format, chain BC [auth C] mmCIF format, chain CA [auth A] mmCIF format, chain CD [auth D] mmCIF format, chain DA [auth A] mmCIF format, chain DB [auth B] mmCIF format, chain EB [auth B] mmCIF format, chain ED [auth D] mmCIF format, chain FC [auth C] mmCIF format, chain G [auth A] mmCIF format, chain GA [auth B] mmCIF format, chain GB [auth B] mmCIF format, chain H [auth A] mmCIF format, chain HB [auth B] mmCIF format, chain I [auth A] mmCIF format, chain IC [auth D] mmCIF format, chain J [auth A] mmCIF format, chain JB [auth B] mmCIF format, chain JC [auth D] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth B] mmCIF format, chain KB [auth C] mmCIF format, chain KC [auth D] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth B] mmCIF format, chain LC [auth D] mmCIF format, chain MA [auth B] mmCIF format, chain MB [auth C] mmCIF format, chain MC [auth D] mmCIF format, chain NC [auth D] mmCIF format, chain O [auth A] mmCIF format, chain OA [auth B] mmCIF format, chain OB [auth C] mmCIF format, chain OC [auth D] mmCIF format, chain P [auth A] mmCIF format, chain PA [auth B] mmCIF format, chain PB [auth C] mmCIF format, chain Q [auth A] mmCIF format, chain QA [auth B] mmCIF format, chain QB [auth C] mmCIF format, chain QC [auth D] mmCIF format, chain R [auth A] mmCIF format, chain RB [auth C] mmCIF format, chain S [auth A] mmCIF format, chain SA [auth B] mmCIF format, chain SB [auth C] mmCIF format, chain SC [auth D] mmCIF format, chain T [auth A] mmCIF format, chain TA [auth B] mmCIF format, chain TB [auth C] mmCIF format, chain TC [auth D] mmCIF format, chain UA [auth B] mmCIF format, chain UB [auth C] mmCIF format, chain UC [auth D] mmCIF format, chain V [auth A] mmCIF format, chain VA [auth B] mmCIF format, chain VB [auth C] mmCIF format, chain VC [auth D] mmCIF format, chain W [auth A] mmCIF format, chain WA [auth B] mmCIF format, chain WB [auth C] mmCIF format, chain WC [auth D] mmCIF format, chain XA [auth B] mmCIF format, chain XB [auth C] mmCIF format, chain XC [auth D] mmCIF format, chain Y [auth A] mmCIF format, chain YB [auth C] mmCIF format, chain YC [auth D] mmCIF format, chain Z [auth A] mmCIF format, chain ZA [auth B] mmCIF format, chain ZB [auth C] mmCIF format, chain ZC [auth D]	AB [auth B] AC [auth C] AD [auth D] BA [auth A] BC [auth C] AB [auth B], AC [auth C], AD [auth D], BA [auth A], BC [auth C], CA [auth A], CD [auth D], DA [auth A], DB [auth B], EB [auth B], ED [auth D], FC [auth C], G [auth A], GA [auth B], GB [auth B], H [auth A], HB [auth B], I [auth A], IC [auth D], J [auth A], JB [auth B], JC [auth D], K [auth A], KA [auth B], KB [auth C], KC [auth D], L [auth A], LA [auth B], LC [auth D], MA [auth B], MB [auth C], MC [auth D], NC [auth D], O [auth A], OA [auth B], OB [auth C], OC [auth D], P [auth A], PA [auth B], PB [auth C], Q [auth A], QA [auth B], QB [auth C], QC [auth D], R [auth A], RB [auth C], S [auth A], SA [auth B], SB [auth C], SC [auth D], T [auth A], TA [auth B], TB [auth C], TC [auth D], UA [auth B], UB [auth C], UC [auth D], V [auth A], VA [auth B], VB [auth C], VC [auth D], W [auth A], WA [auth B], WB [auth C], WC [auth D], XA [auth B], XB [auth C], XC [auth D], Y [auth A], YB [auth C], YC [auth D], Z [auth A], ZA [auth B], ZB [auth C], ZC [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AB [auth B] Focus chain AC [auth C] Focus chain AD [auth D] Focus chain BA [auth A] Focus chain BC [auth C] Focus chain CA [auth A] Focus chain CD [auth D] Focus chain DA [auth A] Focus chain DB [auth B] Focus chain EB [auth B] Focus chain ED [auth D] Focus chain FC [auth C] Focus chain G [auth A] Focus chain GA [auth B] Focus chain GB [auth B] Focus chain H [auth A] Focus chain HB [auth B] Focus chain I [auth A] Focus chain IC [auth D] Focus chain J [auth A] Focus chain JB [auth B] Focus chain JC [auth D] Focus chain K [auth A] Focus chain KA [auth B] Focus chain KB [auth C] Focus chain KC [auth D] Focus chain L [auth A] Focus chain LA [auth B] Focus chain LC [auth D] Focus chain MA [auth B] Focus chain MB [auth C] Focus chain MC [auth D] Focus chain NC [auth D] Focus chain O [auth A] Focus chain OA [auth B] Focus chain OB [auth C] Focus chain OC [auth D] Focus chain P [auth A] Focus chain PA [auth B] Focus chain PB [auth C] Focus chain Q [auth A] Focus chain QA [auth B] Focus chain QB [auth C] Focus chain QC [auth D] Focus chain R [auth A] Focus chain RB [auth C] Focus chain S [auth A] Focus chain SA [auth B] Focus chain SB [auth C] Focus chain SC [auth D] Focus chain T [auth A] Focus chain TA [auth B] Focus chain TB [auth C] Focus chain TC [auth D] Focus chain UA [auth B] Focus chain UB [auth C] Focus chain UC [auth D] Focus chain V [auth A] Focus chain VA [auth B] Focus chain VB [auth C] Focus chain VC [auth D] Focus chain W [auth A] Focus chain WA [auth B] Focus chain WB [auth C] Focus chain WC [auth D] Focus chain XA [auth B] Focus chain XB [auth C] Focus chain XC [auth D] Focus chain Y [auth A] Focus chain YB [auth C] Focus chain YC [auth D] Focus chain Z [auth A] Focus chain ZA [auth B] Focus chain ZB [auth C] Focus chain ZC [auth D] Interactions & Density Focus chain AB [auth B] Focus chain AC [auth C] Focus chain AD [auth D] Focus chain BA [auth A] Focus chain BC [auth C] Focus chain CA [auth A] Focus chain CD [auth D] Focus chain DA [auth A] Focus chain DB [auth B] Focus chain EB [auth B] Focus chain ED [auth D] Focus chain FC [auth C] Focus chain G [auth A] Focus chain GA [auth B] Focus chain GB [auth B] Focus chain H [auth A] Focus chain HB [auth B] Focus chain I [auth A] Focus chain IC [auth D] Focus chain J [auth A] Focus chain JB [auth B] Focus chain JC [auth D] Focus chain K [auth A] Focus chain KA [auth B] Focus chain KB [auth C] Focus chain KC [auth D] Focus chain L [auth A] Focus chain LA [auth B] Focus chain LC [auth D] Focus chain MA [auth B] Focus chain MB [auth C] Focus chain MC [auth D] Focus chain NC [auth D] Focus chain O [auth A] Focus chain OA [auth B] Focus chain OB [auth C] Focus chain OC [auth D] Focus chain P [auth A] Focus chain PA [auth B] Focus chain PB [auth C] Focus chain Q [auth A] Focus chain QA [auth B] Focus chain QB [auth C] Focus chain QC [auth D] Focus chain R [auth A] Focus chain RB [auth C] Focus chain S [auth A] Focus chain SA [auth B] Focus chain SB [auth C] Focus chain SC [auth D] Focus chain T [auth A] Focus chain TA [auth B] Focus chain TB [auth C] Focus chain TC [auth D] Focus chain UA [auth B] Focus chain UB [auth C] Focus chain UC [auth D] Focus chain V [auth A] Focus chain VA [auth B] Focus chain VB [auth C] Focus chain VC [auth D] Focus chain W [auth A] Focus chain WA [auth B] Focus chain WB [auth C] Focus chain WC [auth D] Focus chain XA [auth B] Focus chain XB [auth C] Focus chain XC [auth D] Focus chain Y [auth A] Focus chain YB [auth C] Focus chain YC [auth D] Focus chain Z [auth A] Focus chain ZA [auth B] Focus chain ZB [auth C] Focus chain ZC [auth D]