6BB0

Lactate Dehydrogenase in complex with inhibitor (R)-3-((2-chlorophenyl)thio)-6-(3-((4-fluorophenyl)amino)phenyl)-4-hydroxy-6-(thiophen-3-yl)-5,6-dihydro-2H-pyran-2-one


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.168 

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 chainABCD331Homo 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
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD

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A, B, C, D
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
D3S
Query on D3S

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A, C, D
(6S)-3-[(2-chlorophenyl)sulfanyl]-4-hydroxy-6-(2-hydroxyphenyl)-6-phenyl-5,6-dihydro-2H-pyran-2-one
C23 H17 Cl O4 S
ARSBHTFMIZULEW-QHCPKHFHSA-N
 Ligand Interaction
EPE
Query on EPE

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A, B, C
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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A, B, C, D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
LAC
Query on LAC

Download CCD File 
B
LACTIC ACID
C3 H6 O3
JVTAAEKCZFNVCJ-UWTATZPHSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.168 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.125α = 90
b = 80.968β = 98.33
c = 103.214γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

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