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 

wwPDB Validation   3D Report Full Report



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)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
L-lactate dehydrogenase A chainABCDEFGH331Homo sapiensMutation(s): 0 
Gene Names: LDHAPIG19
EC: 1.1.1.27
Find proteins for P00338 (Homo sapiens)
Explore P00338 
Go to UniProtKB:  P00338
NIH Common Fund Data Resources
PHAROS  P00338
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD

Download CCD File 
A, B, C, D, E, F, G, H
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
D4J
Query on D4J

Download CCD File 
D, E, G
(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
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
A, B, D, F
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
LAC
Query on LAC

Download CCD File 
A, B, C, F, H
LACTIC ACID
C3 H6 O3
JVTAAEKCZFNVCJ-UWTATZPHSA-N
 Ligand Interaction
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



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-10-24
    Type: Initial release