Structure of PDB 5mdh Chain A Binding Site BS02

Receptor Information
>5mdh Chain A (length=333) Species: 9823 (Sus scrofa) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SEPIRVLVTGAAGQIAYSLLYSIGNGSVFGKDQPIILVLLDITPMMGVLD
GVLMELQDCALPLLKDVIATDKEEIAFKDLDVAILVGSMPRRDGMERKDL
LKANVKIFKCQGAALDKYAKKSVKVIVVGNPANTNCLTASKSAPSIPKEN
FSCLTRLDHNRAKAQIALKLGVTSDDVKNVIIWGNHSSTQYPDVNHAKVK
LQAKEVGVYEAVKDDSWLKGEFITTVQQRGAAVIKARKLSSAMSAAKAIC
DHVRDIWFGTPEGEFVSMGIISDGNSYGVPDDLLYSFPVTIKDKTWKIVE
GLPINDFSREKMDLTAKELAEEKETAFEFLSSA
Ligand information
Ligand IDMAK
InChIInChI=1S/C3H2O5/c4-1(2(5)6)3(7)8/h(H,5,6)(H,7,8)
InChIKeyXEEVLJKYYUVTRC-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=C(O)C(=O)C(=O)O
CACTVS 3.341OC(=O)C(=O)C(O)=O
OpenEye OEToolkits 1.5.0C(=O)(C(=O)O)C(=O)O
FormulaC3 H2 O5
NameALPHA-KETOMALONIC ACID
ChEMBL
DrugBankDB03589
ZINCZINC000001532759
PDB chain5mdh Chain A Residue 335 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB5mdh Structural basis of substrate specificity in malate dehydrogenases: crystal structure of a ternary complex of porcine cytoplasmic malate dehydrogenase, alpha-ketomalonate and tetrahydoNAD.
Resolution2.4 Å
Binding residue
(original residue number in PDB)		R97 N130 R161 S241
Binding residue
(residue number reindexed from 1)		R97 N130 R161 S241
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) D158 H186
Catalytic site (residue number reindexed from 1) D158 H186
Enzyme Commision number 1.1.1.37: malate dehydrogenase.
1.1.1.96: diiodophenylpyruvate reductase.
Gene Ontology
Molecular Function
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
GO:0047995 hydroxyphenylpyruvate reductase activity
GO:0051287 NAD binding
Biological Process
GO:0006099 tricarboxylic acid cycle
GO:0006107 oxaloacetate metabolic process
GO:0006108 malate metabolic process
GO:0006734 NADH metabolic process
GO:0019752 carboxylic acid metabolic process
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5mdh, PDBe:5mdh, PDBj:5mdh
PDBsum5mdh
PubMed10075524
UniProtP11708|MDHC_PIG Malate dehydrogenase, cytoplasmic (Gene Name=MDH1)

[Back to BioLiP]