Structure of PDB 1do8 Chain A Binding Site BS03

Receptor Information
>1do8 Chain A (length=553) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
IKEKGKPLMLNPRTNKGMAFTLQERQMLGLQGLLPPKIETQDIQALRFHR
NLKKMTSPLEKYIYIMGIQERNEKLFYRILQDDIESLMPIVYTPTVGLAC
SQYGHIFRRPKGLFISISDRGHVRSIVDNWPENHVKAVVVTDGERILGLG
DLGVYGMGIPVGKLCLYTACAGIRPDRCLPVCIDVGTDNIALLKDPFYMG
LYQKRDRTQQYDDLIDEFMKAITDRYGRNTLIQFEDFGNHNAFRFLRKYR
EKYCTFNDDIQGTAAVALAGLLAAQKVISKPISEHKILFLGAGEAALGIA
NLIVMSMVENGLSEQEAQKKIWMFDKYGLLVKGRKAKIDSYQEPFTHSAP
ESIPDTFEDAVNILKPSTIIGVAGAGRLFTPDVIRAMASINERPVIFALS
NPTAQAECTAEEAYTLTEGRCLFASGSPFGPVKLTDGRVFTPGQGNNVYI
FPGVALAVILCNTRHISDSVFLEAAKALTSQLTDEELAQGRLYPPLANIQ
EVSINIAIKVTEYLYANKMAFRYPEPEDKAKYVKERTWRSEYDSLLPDVY
EWP
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 chain1do8 Chain A Residue 601 [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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PDB1do8 Structure of a closed form of human malic enzyme and implications for catalytic mechanism.
Resolution2.2 Å
Binding residue
(original residue number in PDB)		R165 L167 N259 T283 G311 A312 G313 E314 A315 D345 K346 A393 A395 L398 L419 S420 N421 G465 N466 N467
Binding residue
(residue number reindexed from 1)		R145 L147 N239 T263 G291 A292 G293 E294 A295 D325 K326 A373 A375 L378 L399 S400 N401 G445 N446 N447
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) Y112 R165 K183 E255 D256 D278 D279 N421
Catalytic site (residue number reindexed from 1) Y92 R145 K163 E235 D236 D258 D259 N401
Enzyme Commision number 1.1.1.38: malate dehydrogenase (oxaloacetate-decarboxylating).
Gene Ontology
Molecular Function
GO:0004470 malic enzyme activity
GO:0004471 malate dehydrogenase (decarboxylating) (NAD+) activity
GO:0004473 malate dehydrogenase (decarboxylating) (NADP+) activity
GO:0008948 oxaloacetate decarboxylase activity
GO:0009055 electron transfer activity
GO:0016491 oxidoreductase activity
GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
GO:0046872 metal ion binding
GO:0051287 NAD binding
Biological Process
GO:0006090 pyruvate metabolic process
GO:0006108 malate metabolic process
GO:1902031 regulation of NADP metabolic process
Cellular Component
GO:0005739 mitochondrion
GO:0005759 mitochondrial matrix
GO:0043231 intracellular membrane-bounded organelle

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:1do8, PDBe:1do8, PDBj:1do8
PDBsum1do8
PubMed10700286
UniProtP23368|MAOM_HUMAN NAD-dependent malic enzyme, mitochondrial (Gene Name=ME2)

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