Structure of PDB 7xdf Chain A Binding Site BS02

Receptor Information
>7xdf Chain A (length=551) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EKGKPLMLNPRTNKGMAFTLQERQMLGLQGLLPPKIETQDIQALRFHRNL
KKMTSPLEKYIYIMGIQERNEKLFYRILQDDIESLMPIVYTPTVGLACSQ
YGHIFRRPKGLFISISDRGHVRSIVDNWPENHVKAVVVTDGERILGLGDL
GVYGMGIPVGKLCLYTACAGIRPDRCLPVCIDVGTDNIALLKDPFYMGLY
QKRDRTQQYDDLIDEFMKAITDRYGRNTLIQFEDFGNHNAFRFLRKYREK
YCTFNDDIQGTAAVALAGLLAAQKVISKPISEHKILFLGAGEAALGIANL
IVMSMVENGLSEQEAQKKIWMFDKYGLLVKGRKAKIDSYQEPFTHSAPES
IPDTFEDAVNILKPSTIIGVAGAGRLFTPDVIRAMASINERPVIFALSNP
TAQAECTAEEAYTLTEGRCLFASGSPFGPVKLTDGRVFTPGQGNNVYIFP
GVALAVILCNTRHISDSVFLEAAKALTSQLTDEELAQGRLYPPLANIQEV
SINIAIKVTEYLYANKMAFRYPEPEDKAKYVKERTWRSEYDSLLPDVYEW
P
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 chain7xdf Chain A Residue 602 [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]
PDB7xdf Suppression of the human malic enzyme 2 modifies energy metabolism and inhibits cellular respiration
Resolution2.72 Å
Binding residue
(original residue number in PDB)		K156 I193 R194 R197 L480 R542 R556
Binding residue
(residue number reindexed from 1)		K134 I171 R172 R175 L458 R520 R534
Annotation score4
Enzymatic activity
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:7xdf, PDBe:7xdf, PDBj:7xdf
PDBsum7xdf
PubMed
UniProtP23368|MAOM_HUMAN NAD-dependent malic enzyme, mitochondrial (Gene Name=ME2)

[Back to BioLiP]