Structure of PDB 3d4b Chain A Binding Site BS03

Receptor Information
>3d4b Chain A (length=233) Species: 2336 (Thermotoga maritima) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MKMKEFLDLLNESRLTVTLTGAGISTPSGIPDFNVFDIDFFYSHPEEFYR
FAKEGIFPMLQAKPNLAHVLLAKLEEKGLIEAVITQNIDRLHQRAGSKKV
IELHGNVEEYYCVRCEKKYTVEDVIKKLESSDVPLCDDCNSLIRPNIVFF
GENLPQDALREAIGLSSRASLMIVLGSSLVVYPAAELPLITVRSGGKLVI
VNLGETPFDDIATLKYNMDVVEFARRVMEEGGI
Ligand information
Ligand IDDZD
InChIInChI=1S/C24H33N7O11P2/c25-21-18-23(28-10-27-21)31(11-29-18)24-20(34)19(33)17(42-24)9-41-44(38,39)12-43(36,37)40-8-15-6-30(7-16(15)32)5-13-2-1-3-14(4-13)22(26)35/h1-4,10-11,15-17,19-20,24,32-34H,5-9,12H2,(H2,26,35)(H,36,37)(H,38,39)(H2,25,27,28)/t15-,16+,17-,19-,20-,24-/m1/s1
InChIKeyIMHBNZNABRBOGP-YZOALNMRSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1cc(cc(c1)C(=O)N)CN2CC(C(C2)O)COP(=O)(CP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)O)O)O
CACTVS 3.341NC(=O)c1cccc(CN2C[CH](O)[CH](CO[P](O)(=O)C[P](O)(=O)OC[CH]3O[CH]([CH](O)[CH]3O)n4cnc5c(N)ncnc45)C2)c1
OpenEye OEToolkits 1.5.0c1cc(cc(c1)C(=O)N)CN2C[C@@H]([C@H](C2)O)CO[P@@](=O)(C[P@@](=O)(O)OC[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4ncnc5N)O)O)O
CACTVS 3.341NC(=O)c1cccc(CN2C[C@H](O)[C@@H](CO[P@@](O)(=O)C[P@](O)(=O)OC[C@H]3O[C@H]([C@H](O)[C@@H]3O)n4cnc5c(N)ncnc45)C2)c1
ACDLabs 10.04O=C(N)c1cc(ccc1)CN2CC(O)C(C2)COP(=O)(O)CP(=O)(O)OCC5OC(n4cnc3c(ncnc34)N)C(O)C5O
FormulaC24 H33 N7 O11 P2
Name5'-O-[(R)-{[(R)-{[(3R,4R)-1-(3-carbamoylbenzyl)-4-hydroxypyrrolidin-3-yl]methoxy}(hydroxy)phosphoryl]methyl}(hydroxy)phosphoryl]adenosine
ChEMBL
DrugBank
ZINCZINC000058632707
PDB chain3d4b Chain A Residue 1002 [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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PDB3d4b Structural insights into intermediate steps in the Sir2 deacetylation reaction.
Resolution1.9 Å
Binding residue
(original residue number in PDB)		G21 A22 G23 T26 I30 P31 D32 F33 Q98 N99 I100 D101 H116 F162 S189 S190 V193 N214 L215 D231 V232
Binding residue
(residue number reindexed from 1)		G21 A22 G23 T26 I30 P31 D32 F33 Q86 N87 I88 D89 H104 F150 S177 S178 V181 N202 L203 D219 V220
Annotation score2
Enzymatic activity
Catalytic site (original residue number in PDB) P31 D32 F33 N99 D101 H116
Catalytic site (residue number reindexed from 1) P31 D32 F33 N87 D89 H104
Enzyme Commision number 2.3.1.286: protein acetyllysine N-acetyltransferase.
Gene Ontology
Molecular Function
GO:0008270 zinc ion binding
GO:0016740 transferase activity
GO:0017136 NAD-dependent histone deacetylase activity
GO:0034979 NAD-dependent protein lysine deacetylase activity
GO:0046872 metal ion binding
GO:0051287 NAD binding
GO:0070403 NAD+ binding
Biological Process
GO:0006338 chromatin remodeling
GO:0006476 protein deacetylation
Cellular Component
GO:0005737 cytoplasm

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:3d4b, PDBe:3d4b, PDBj:3d4b
PDBsum3d4b
PubMed18786399
UniProtQ9WYW0|NPD_THEMA NAD-dependent protein deacetylase (Gene Name=cobB)

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