Structure of PDB 3jd2 Chain C Binding Site BS03

Receptor Information
>3jd2 Chain C (length=496) Species: 9913 (Bos taurus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DPNFFKMVEGFFDRGASIVEDKLVEDLKTRETEEQKRNRVRSILRIIKPC
NHVLSLSFPIRRDDGSWEVIEGYRAQHSQHRTPCKGGIRYSTDVSVDEVK
ALASLMTYKCAVVDVPFGGAKAGVKINPKNYTDNELEKITRRFTMELAKK
GFIGPGVDVPAPDMSTGEREMSWIADTYASTIGHYDINAHACVTGKPISQ
GGIHGRISATGRGVFHGIENFINEASYMSILGMTPGFGDKTFVVQGFGNV
GLHSMRYLHRFGAKCITVGESDGSIWNPDGIDPKELEDFKLQHGTILGFP
KAKIYEGSILEVDCDILIPAASEKQLTKSNAPRVKAKIIAEGANGPTTPE
ADKIFLERNIMVIPDLYLNAGGVTVSYFEWLNNLNHVSYGRLTFKYERDS
NYHLLMSVQESLERKFGKHGGTIPIVPTAEFQDRISGASEKDIVHSGLAY
TMERSARQIMRTAMKYNLGLDLRTAAYVNAIEKVFRVYNEAGVTFT
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 chain3jd2 Chain C Residue 602 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3jd2 Using Cryo-EM to Map Small Ligands on Dynamic Metabolic Enzymes: Studies with Glutamate Dehydrogenase.
Resolution3.3 Å
Binding residue
(original residue number in PDB)		T215 Q250 G251 F252 G253 N254 V255 E275 S276 A325 A348 N374
Binding residue
(residue number reindexed from 1)		T210 Q245 G246 F247 G248 N249 V250 E270 S271 A320 A343 N369
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) K126 D168
Catalytic site (residue number reindexed from 1) K121 D163
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
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:3jd2, PDBe:3jd2, PDBj:3jd2
PDBsum3jd2
PubMed27036132
UniProtP00366|DHE3_BOVIN Glutamate dehydrogenase 1, mitochondrial (Gene Name=GLUD1)

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