Structure of PDB 6dhn Chain D Binding Site BS05

Receptor Information
>6dhn Chain D (length=501) Species: 9913 (Bos taurus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ADREDDPNFFKMVEGFFDRGASIVEDKLVEDLKTRETEEQKRNRVRGILR
IIKPCNHVLSLSFPIRRDDGSWEVIEGYRAQHSQHRTPCKGGIRYSTDVS
VDEVKALASLMTYKCAVVDVPFGGAKAGVKINPKNYTDNELEKITRRFTM
ELAKKGFIGPGVDVPAPDMSTGEREMSWIADTYASTIGHYDINAHACVTG
KPISQGGIHGRISATGRGVFHGIENFINEASYMSILGMTPGFGDKTFAVQ
GFGNVGLHSMRYLHRFGAKCVAVGESDGSIWNPDGIDPKELEDFKLQHGT
ILGFPKAKIYEGSILEVDCDILIPAASEKQLTKSNAPRVKAKIIAEGANG
PTTPEADKIFLERNIMVIPDLYLNAGGVTVSYFEWLKNLNHVSYGRLTFK
YERDSNYHLLMSVQESLERKFGKHGGTIPIVPTAEFQDRISGASEKDIVH
SGLAYTMERSARQIMRTAMKYNLGLDLRTAAYVNAIEKVFRVYNEAGVTF
T
Ligand information
Ligand IDNAI
InChIInChI=1S/C21H29N7O14P2/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/h1,3-4,7-8,10-11,13-16,20-21,29-32H,2,5-6H2,(H2,23,33)(H,34,35)(H,36,37)(H2,22,24,25)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
InChIKeyBOPGDPNILDQYTO-NNYOXOHSSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)N5C=CCC(=C5)C(=O)N)O)O)O)O)N
CACTVS 3.341NC(=O)C1=CN(C=CC1)[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 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)N5C=CCC(=C5)C(=O)N)O)O)O)O)N
CACTVS 3.341NC(=O)C1=CN(C=CC1)[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
FormulaC21 H29 N7 O14 P2
Name1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE;
NADH
ChEMBLCHEMBL1234616
DrugBankDB00157
ZINCZINC000008215403
PDB chain6dhn Chain F 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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PDB6dhn A novel mechanism of V-type zinc inhibition of glutamate dehydrogenase results from disruption of subunit interactions necessary for efficient catalysis.
Resolution3.3 Å
Binding residue
(original residue number in PDB)		H195 K387 N388 S393
Binding residue
(residue number reindexed from 1)		H195 K387 N388 S393
Annotation score4
Enzymatic activity
Enzyme Commision number 1.4.1.3: glutamate dehydrogenase [NAD(P)(+)].
Gene Ontology
Molecular Function
GO:0004352 glutamate dehydrogenase (NAD+) activity
GO:0004353 glutamate dehydrogenase [NAD(P)+] activity
GO:0004354 glutamate dehydrogenase (NADP+) activity
GO:0005524 ATP binding
GO:0005525 GTP binding
GO:0016491 oxidoreductase activity
GO:0016639 oxidoreductase activity, acting on the CH-NH2 group of donors, NAD or NADP as acceptor
GO:0042802 identical protein binding
Biological Process
GO:0006520 amino acid metabolic process
GO:0006538 glutamate catabolic process
GO:0006541 glutamine metabolic process
GO:0072350 tricarboxylic acid metabolic process
Cellular Component
GO:0005739 mitochondrion
GO:0005743 mitochondrial inner membrane
GO:0005783 endoplasmic reticulum

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6dhn, PDBe:6dhn, PDBj:6dhn
PDBsum6dhn
PubMed21749647
UniProtP00366|DHE3_BOVIN Glutamate dehydrogenase 1, mitochondrial (Gene Name=GLUD1)

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