Structure of PDB 6dhn Chain C Binding Site BS01

Receptor Information
>6dhn Chain C (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 B Residue 604 [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]
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)		H85 R86 T87 D119 P121 K488
Binding residue
(residue number reindexed from 1)		H85 R86 T87 D119 P121 K488
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)

[Back to BioLiP]