6BB2

Lactate Dehydrogenase in complex with inhibitor (S)-5-((2-chlorophenyl)thio)-6'-(4-fluorophenoxy)-4-hydroxy-2-(thiophen-3-yl)-2,3-dihydro-[2,2'-bipyridin]-6(1H)-one


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.47 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.190 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history


Literature

Structure-guided optimization and in vivo activities of hydroxylactone and hydroxylactam Inhibitors of Human Lactate Dehydrogenase

Wei, B.Labadie, S.S.Robarge, K.Chen, J.Chen, Z.Corson, L.B.Ding, C.Z.DiPasquale, A.G.Dragovich, P.S.Eigenbrot, C.Evangelista, M.Fauber, B.P.Goa, Z.Ge, H.Hitz, A.Ho, Q.Lai, K.W.Liu, W.Liu, Y.Li, C.Ma, S.Malek, S.O'Brien, T.Pang, J.Peterson, D.Salphati, L.Sideris, S.Ultsch, M.Yen, I.Yue, Q.Zhang, H.Zhou, A.Purkey, H.E.

To be published.

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, E
A, B, C, D, E, F, G, H
331Homo 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 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD

Download Ideal Coordinates CCD File 
AA [auth G]
CA [auth H]
I [auth A]
L [auth B]
O [auth C]
AA [auth G],
CA [auth H],
I [auth A],
L [auth B],
O [auth C],
Q [auth D],
V [auth E],
X [auth F]
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
D4J
Query on D4J

Download Ideal Coordinates CCD File 
BA [auth G],
U [auth D],
W [auth E]
(2S)-5-[(2-chlorophenyl)sulfanyl]-6'-(4-fluorophenoxy)-4-hydroxy-2-(thiophen-3-yl)-2,3-dihydro[2,2'-bipyridin]-6(1H)-one
C26 H18 Cl F N2 O3 S2
XFNQOQKMMIFYDK-SANMLTNESA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
J [auth A]
M [auth B]
R [auth D]
S [auth D]
T [auth D]
J [auth A],
M [auth B],
R [auth D],
S [auth D],
T [auth D],
Y [auth F]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
LAC
Query on LAC

Download Ideal Coordinates CCD File 
DA [auth H],
K [auth A],
N [auth B],
P [auth C],
Z [auth F]
LACTIC ACID
C3 H6 O3
JVTAAEKCZFNVCJ-UWTATZPHSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.47 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.190 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.183α = 90
b = 158.561β = 90
c = 264.978γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-10-24
    Type: Initial release
  • Version 1.1: 2023-10-04
    Changes: Data collection, Database references, Refinement description
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection