4JNK

Lactate Dehydrogenase A in complex with inhibitor compound 22

Structural Biology Knowledgebase: 4JNK SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.204
  • R-Value Work: 0.159

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4JNK

Classification: OXIDOREDUCTASE / OXIDOREDUCTASE INHIBITOR

Total Structure Weight: 151743.33

Macromolecule Entities
Molecule Chains Length Organism Details
L-lactate dehydrogenase A chain A, B, C, D 331 Homo sapiens EC#: 1.1.1.27 IUBMB
Gene Name(s): LDHA Gene View PIG19

Small Molecules
Ligands 5 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
NAI
Query on NAI

A, B, C, D 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
NADH (Synonym)
C21 H29 N7 O14 P2
BOPGDPNILDQYTO-NNYOXOHSSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZHK
Query on ZHK

A, C, D (2R)-2-{[5-cyano-4-(3,4-dichlorophenyl)-6- oxo-1,6-dihydropyrimidin-2-yl]sulfanyl}-N- (4-sulfamoylphenyl)propanamide
C20 H15 Cl2 N5 O4 S2
YDJOCTZRWDYNJT-SNVBAGLBSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
EPE
Query on EPE

A, B, C 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
HEPES (Synonym)
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A, C, D SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
LAC
Query on LAC

B LACTIC ACID
C3 H6 O3
JVTAAEKCZFNVCJ-UWTATZPHSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
ZHK N/A in BindingDB
Kd: 5100 nM  BindingMOAD
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.204
  • R-Value Work: 0.159
  • Space Group: C 1 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 168.25 α = 90.00
b = 81.49 β = 117.13
c = 120.41 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2013-03-15
  • Released Date: 2013-05-22
  • Deposition author(s): Eigenbrot, C., Ultsch, M.

Revision History

No revisions since initial release