Structure of PDB 3jd4 Chain E Binding Site BS01

Receptor Information
>3jd4 Chain E (length=497) Species: 9913 (Bos taurus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DDPNFFKMVEGFFDRGASIVEDKLVEDLKTRETEEQKRNRVRSILRIIKP
CNHVLSLSFPIRRDDGSWEVIEGYRAQHSQHRTPCKGGIRYSTDVSVDEV
KALASLMTYKCAVVDVPFGGAKAGVKINPKNYTDNELEKITRRFTMELAK
KGFIGPGVDVPAPDMSTGEREMSWIADTYASTIGHYDINAHACVTGKPIS
QGGIHGRISATGRGVFHGIENFINEASYMSILGMTPGFGDKTFVVQGFGN
VGLHSMRYLHRFGAKCITVGESDGSIWNPDGIDPKELEDFKLQHGTILGF
PKAKIYEGSILEVDCDILIPAASEKQLTKSNAPRVKAKIIAEGANGPTTP
EADKIFLERNIMVIPDLYLNAGGVTVSYFEWLNNLNHVSYGRLTFKYERD
SNYHLLMSVQESLERKFGKHGGTIPIVPTAEFQDRISGASEKDIVHSGLA
YTMERSARQIMRTAMKYNLGLDLRTAAYVNAIEKVFRVYNEAGVTFT
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 chain3jd4 Chain E Residue 602 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3jd4 Using Cryo-EM to Map Small Ligands on Dynamic Metabolic Enzymes: Studies with Glutamate Dehydrogenase.
Resolution3.4 Å
Binding residue
(original residue number in PDB)		M169 G253 N254 V255 E275 S276 A325 A326 N349
Binding residue
(residue number reindexed from 1)		M165 G249 N250 V251 E271 S272 A321 A322 N345
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) K126 D168
Catalytic site (residue number reindexed from 1) K122 D164
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
View graph for
Cellular Component
External links
PDB RCSB:3jd4, PDBe:3jd4, PDBj:3jd4
PDBsum3jd4
PubMed27036132
UniProtP00366|DHE3_BOVIN Glutamate dehydrogenase 1, mitochondrial (Gene Name=GLUD1)

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