Structure of PDB 5zi4 Chain A Binding Site BS02

Receptor Information
>5zi4 Chain A (length=339) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MVKVAILGASGGVGQPLSLLLKLSPYVSELALYDIRAAEGIGKDLSHINT
NSSCVGYDKDSIENTLSNAQVVLIPAGVPRKPGLTRDDLFKMNAGIVKSL
VTAVGKFAPNARILVISNPVNSLVPIAVETLKKMGKFKPGNVMGVTNLDL
VRAETFLVDYLMLKNPKIGQEQDKTTMHRKVTVIGGHSGETIIPIITDKS
LVFQLDKQYEHFIHRVQFGGDEIVKAKQGAGSATLSMAFAGAKFAEEVLR
SFHNEKPETESLSAFVYLPGLKNGKKAQQLVGDNSIEYFSLPIVLRNGSV
VSIDTSVLEKLSPREEQLVNTAVKELRKNIEKGKSFILD
Ligand information
Ligand IDNAD
InChIInChI=1S/C21H27N7O14P2/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(32)14(30)11(41-21)6-39-44(36,37)42-43(34,35)38-5-10-13(29)15(31)20(40-10)27-3-1-2-9(4-27)18(23)33/h1-4,7-8,10-11,13-16,20-21,29-32H,5-6H2,(H5-,22,23,24,25,33,34,35,36,37)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
InChIKeyBAWFJGJZGIEFAR-NNYOXOHSSA-N
SMILES
SoftwareSMILES
CACTVS 3.341NC(=O)c1ccc[n+](c1)[C@@H]2O[C@H](CO[P]([O-])(=O)O[P@](O)(=O)OC[C@H]3O[C@H]([C@H](O)[C@@H]3O)n4cnc5c(N)ncnc45)[C@@H](O)[C@H]2O
OpenEye OEToolkits 1.5.0c1cc(c[n+](c1)C2C(C(C(O2)COP(=O)([O-])OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)O)O)O)O)C(=O)N
CACTVS 3.341NC(=O)c1ccc[n+](c1)[CH]2O[CH](CO[P]([O-])(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O)[CH]3O)n4cnc5c(N)ncnc45)[CH](O)[CH]2O
OpenEye OEToolkits 1.5.0c1cc(c[n+](c1)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)([O-])O[P@@](=O)(O)OC[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4ncnc5N)O)O)O)O)C(=O)N
FormulaC21 H27 N7 O14 P2
NameNICOTINAMIDE-ADENINE-DINUCLEOTIDE
ChEMBLCHEMBL1234613
DrugBankDB14128
ZINC
PDB chain5zi4 Chain A Residue 402 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB5zi4 Structure of glyoxysomal malate dehydrogenase (MDH3) from Saccharomyces cerevisiae.
Resolution2.1 Å
Binding residue
(original residue number in PDB)		G11 G12 V13 Y33 D34 I35 P75 A76 G77 V78 P79 I96 I116 N118 H187 A233 M237
Binding residue
(residue number reindexed from 1)		G11 G12 V13 Y33 D34 I35 P75 A76 G77 V78 P79 I96 I116 N118 H187 A233 M237
Annotation score4
Enzymatic activity
Enzyme Commision number 1.1.1.37: malate dehydrogenase.
Gene Ontology
Molecular Function
GO:0003729 mRNA binding
GO:0003824 catalytic activity
GO:0016491 oxidoreductase activity
GO:0016615 malate dehydrogenase activity
GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
GO:0030060 L-malate dehydrogenase (NAD+) activity
Biological Process
GO:0006097 glyoxylate cycle
GO:0006099 tricarboxylic acid cycle
GO:0006108 malate metabolic process
GO:0006635 fatty acid beta-oxidation
GO:0006735 NADH regeneration
GO:0019752 carboxylic acid metabolic process
Cellular Component
GO:0005737 cytoplasm
GO:0005739 mitochondrion
GO:0005777 peroxisome
GO:0005782 peroxisomal matrix

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5zi4, PDBe:5zi4, PDBj:5zi4
PDBsum5zi4
PubMed30279312
UniProtP32419|MDHP_YEAST Malate dehydrogenase, peroxisomal (Gene Name=MDH3)

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