Structure of PDB 6dhm Chain A Binding Site BS02
Receptor Information
>6dhm Chain A (length=495) Species:
9913
(Bos taurus) [
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ADREDDPNFFKMVEGFFDRGASIVEDKLVEDLKTRETEEQKRNRVRGILR
IIKPCNHVLSLSFPIRRDDGSWEVIEGYRAQHSQHRTPCKGGIRYSTDVS
VDEVKALASLMTYKCAVVDVPFGGAKAGVKINPKNYTDNELEKITRRFTM
ELAKKGFIGPGVDVPAPDMSTGEREMSWIADTYASTIGHYDINAHACVTG
KPISQGGIHGRISATGRGVFHGIENFINEASYMSILGMTPGFGDKTFAVQ
GFGNVGLHSMRYLHRFGAKCVAVGESDGSIWNPDGIDPKELEDFKLQHGT
ILGFPKAKIYEGSILEVDCDILIPAASEKQLTKSNAPRVKAKIIAEGANG
PTTPEADKIFLERNIMVIPDLYLNAGGVTVSYFEWLKNLNHVSYGRLTFK
YERDSNYHLLMSVQESLERKFGKHGGTIPIVPTAEFQDRISGASEKDIVH
SGLAYTMERSARQIMRTAMKYNLGLDLRTAAYVNAIEKVFRVYNE
Ligand information
Ligand ID
NDP
InChI
InChI=1S/C21H30N7O17P3/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(44-46(33,34)35)14(30)11(43-21)6-41-48(38,39)45-47(36,37)40-5-10-13(29)15(31)20(42-10)27-3-1-2-9(4-27)18(23)32/h1,3-4,7-8,10-11,13-16,20-21,29-31H,2,5-6H2,(H2,23,32)(H,36,37)(H,38,39)(H2,22,24,25)(H2,33,34,35)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
InChIKey
ACFIXJIJDZMPPO-NNYOXOHSSA-N
SMILES
Software
SMILES
OpenEye OEToolkits 1.5.0
c1nc(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)OP(=O)(O)O)N
CACTVS 3.341
NC(=O)C1=CN(C=CC1)[CH]2O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O[P](O)(O)=O)[CH]3O)n4cnc5c(N)ncnc45)[CH](O)[CH]2O
CACTVS 3.341
NC(=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[P](O)(O)=O)[C@@H]3O)n4cnc5c(N)ncnc45)[C@@H](O)[C@H]2O
OpenEye OEToolkits 1.5.0
c1nc(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)OP(=O)(O)O)N
Formula
C21 H30 N7 O17 P3
Name
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
ChEMBL
CHEMBL407009
DrugBank
DB02338
ZINC
ZINC000008215411
PDB chain
6dhm Chain A Residue 602 [
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Receptor-Ligand Complex Structure
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PDB
6dhm
A novel mechanism of V-type zinc inhibition of glutamate dehydrogenase results from disruption of subunit interactions necessary for efficient catalysis.
Resolution
3.0 Å
Binding residue
(original residue number in PDB)
D168 M169 S170 R211 Q250 G251 F252 G253 N254 V255 E275 S276 A326 G347 A348 N349 N374
Binding residue
(residue number reindexed from 1)
D168 M169 S170 R211 Q250 G251 F252 G253 N254 V255 E275 S276 A326 G347 A348 N349 N374
Annotation score
4
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
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Molecular Function
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Biological Process
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Cellular Component
External links
PDB
RCSB:6dhm
,
PDBe:6dhm
,
PDBj:6dhm
PDBsum
6dhm
PubMed
21749647
UniProt
P00366
|DHE3_BOVIN Glutamate dehydrogenase 1, mitochondrial (Gene Name=GLUD1)
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