Structure of PDB 2dfd Chain A Binding Site BS01

Receptor Information
>2dfd Chain A (length=314) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NAKVAVLGASGGIGQPLSLLLKNSPLVSRLTLYDIAHTPGVAADLSHIET
KAAVKGYLGPEQLPDCLKGCDVVVIPAGVPRKPGMTRDDLFNTNATIVAT
LTAACAQHCPEAMICVIANPVNSTIPITAEVFKKHGVYNPNKIFGVTTLD
IVRANTFVAELKGLDPARVNVPVIGGHAGKTIIPLISQCTPKVDFPQDQL
TALTGRIQEAGTEVVKAKAGAGSATLSMAYAGARFVFSLVDAMNGKEGVV
ECSFVKSQETECTYFSTPLLLGKKGIEKNLGIGKVSSFEEKMISDAIPEL
KASIKKGEDFVKTL
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 chain2dfd Chain A Residue 3003 [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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PDB2dfd Crystal Structure of Human Malate Dehydrogenase Type 2
Resolution1.9 Å
Binding residue
(original residue number in PDB)		G16 G17 I18 Y38 D39 I40 P81 A82 G83 V84 P85 I122 N124 H182 M233
Binding residue
(residue number reindexed from 1)		G11 G12 I13 Y33 D34 I35 P76 A77 G78 V79 P80 I117 N119 H177 M228
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) D155 H182
Catalytic site (residue number reindexed from 1) D150 H177
Enzyme Commision number 1.1.1.37: malate dehydrogenase.
Gene Ontology
Molecular Function
GO:0003723 RNA 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
GO:0042802 identical protein binding
GO:0046554 L-malate dehydrogenase (NADP+) activity
Biological Process
GO:0006094 gluconeogenesis
GO:0006099 tricarboxylic acid cycle
GO:0006108 malate metabolic process
GO:0006734 NADH metabolic process
GO:0009060 aerobic respiration
GO:0019752 carboxylic acid metabolic process
GO:0043490 malate-aspartate shuttle
Cellular Component
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005739 mitochondrion
GO:0005759 mitochondrial matrix
GO:0016020 membrane
GO:0070062 extracellular exosome

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:2dfd, PDBe:2dfd, PDBj:2dfd
PDBsum2dfd
PubMed
UniProtP40926|MDHM_HUMAN Malate dehydrogenase, mitochondrial (Gene Name=MDH2)

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