7M2N

Crystal structure of Human Lactate Dehydrogenase A with Inhibitor Compound 15


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.212 

Starting Model: experimental
View more details

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
L-lactate dehydrogenase A chain
A, B, C, D
338Homo sapiensMutation(s): 0 
Gene Names: LDHAPIG19
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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00338
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
YOJ (Subject of Investigation/LOI)
Query on YOJ

Download Ideal Coordinates CCD File 
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
NAI (Subject of Investigation/LOI)
Query on NAI

Download Ideal Coordinates CCD File 
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
PEG
Query on PEG

Download Ideal Coordinates CCD File 
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
SO4
Query on SO4

Download Ideal Coordinates CCD File 
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
GOL
Query on GOL

Download Ideal Coordinates CCD File 
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
EDO
Query on EDO

Download Ideal Coordinates CCD File 
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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.212 
  • Space Group: I 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.93α = 90
b = 131.05β = 99.3
c = 215.518γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-07-14
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Database references, Refinement description