Structure of PDB 6eo0 Chain B Binding Site BS02

Receptor Information
>6eo0 Chain B (length=275) Species: 7955 (Danio rerio) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DPFTKMTRPSSDLTAFREHFAKAKHIAIITGAGVSAESGVPTFRGPGGFW
RKWQAQDLATPEAFSRDPSLVWEFYHYRREVMRSKMPNPAHLAIAECEAR
LGQQGRSVVIITQNIDELHHRAGSKHVYEIHGSLFKTRCMSCGEVKANHK
SPICPALDGKGAPDPNTKEARIPVELLPRCERKSCNGLLRPHVVWFGETL
DSDILTAVERELEKCDLCLVVGTSSIVYPAAMFAPQVASRGVPVAEFNME
CTPATQRFKYHFEGPCGSTLPPALE
Ligand information
Ligand IDBVT
InChIInChI=1S/C47H63N11O19P2S/c1-25(2)55-43(65)31(18-27-19-49-29-13-7-6-12-28(27)29)56-42(64)30(57-46(66)71-20-26-10-4-3-5-11-26)14-8-9-16-53-47(54-17-15-34(59)60)76-39-37(62)33(75-45(39)80-47)22-73-79(69,70)77-78(67,68)72-21-32-36(61)38(63)44(74-32)58-24-52-35-40(48)50-23-51-41(35)58/h3-7,10-13,19,23-25,30-33,36-39,44-45,49,53-54,61-63H,8-9,14-18,20-22H2,1-2H3,(H,55,65)(H,56,64)(H,57,66)(H,59,60)(H,67,68)(H,69,70)(H2,48,50,51)/t30-,31-,32+,33+,36+,37+,38+,39+,44+,45+,47-/m0/s1
InChIKeyYXTVLLWQDXVSFE-WDVUSYHVSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6CC(C)NC(=O)C(Cc1c[nH]c2c1cccc2)NC(=O)C(CCCCNC3(OC4C(C(OC4S3)COP(=O)(O)OP(=O)(O)OCC5C(C(C(O5)n6cnc7c6ncnc7N)O)O)O)NCCC(=O)O)NC(=O)OCc8ccccc8
CACTVS 3.385CC(C)NC(=O)[C@H](Cc1c[nH]c2ccccc12)NC(=O)[C@H](CCCCN[C@]3(NCCC(O)=O)O[C@@H]4[C@H](O)[C@@H](CO[P](O)(=O)O[P](O)(=O)OC[C@H]5O[C@H]([C@H](O)[C@@H]5O)n6cnc7c(N)ncnc67)O[C@@H]4S3)NC(=O)OCc8ccccc8
OpenEye OEToolkits 2.0.6CC(C)NC(=O)[C@H](Cc1c[nH]c2c1cccc2)NC(=O)[C@H](CCCCN[C@@]3(O[C@@H]4[C@@H]([C@H](O[C@@H]4S3)COP(=O)(O)OP(=O)(O)OC[C@@H]5[C@H]([C@H]([C@@H](O5)n6cnc7c6ncnc7N)O)O)O)NCCC(=O)O)NC(=O)OCc8ccccc8
CACTVS 3.385CC(C)NC(=O)[CH](Cc1c[nH]c2ccccc12)NC(=O)[CH](CCCCN[C]3(NCCC(O)=O)O[CH]4[CH](O)[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]5O[CH]([CH](O)[CH]5O)n6cnc7c(N)ncnc67)O[CH]4S3)NC(=O)OCc8ccccc8
FormulaC47 H63 N11 O19 P2 S
Name3-[[(2~{S},3~{a}~{R},5~{R},6~{R},6~{a}~{R})-5-[[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxymethyl]-2-[[(5~{S})-6-[[(2~{S})-3-(1~{H}-indol-3-yl)-1-oxidanylidene-1-(propan-2-ylamino)propan-2-yl]amino]-6-oxidanylidene-5-(phenylmethoxycarbonylamino)hexyl]amino]-6-oxidanyl-3~{a},5,6,6~{a}-tetrahydrofuro[2,3-d][1,3]oxathiol-2-yl]amino]propanoic acid
ChEMBL
DrugBank
ZINC
PDB chain6eo0 Chain B Residue 303 [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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PDB6eo0 Mechanism-Based Inhibitors of the Human Sirtuin 5 Deacylase: Structure-Activity Relationship, Biostructural, and Kinetic Insight.
Resolution2.4 Å
Binding residue
(original residue number in PDB)
G54 A55 G56 F66 R67 R101 Q136 I138 H154 V217 F219 G220 E221 T222 G245 T246 S247 V250 Y251 N271 M272 C289
Binding residue
(residue number reindexed from 1)
G31 A32 G33 F43 R44 R78 Q113 I115 H131 V194 F196 G197 E198 T199 G222 T223 S224 V227 Y228 N248 M249 C266
Annotation score2
Enzymatic activity
Catalytic site (original residue number in PDB) P64 T65 F66 R67 N137 D139 H154
Catalytic site (residue number reindexed from 1) P41 T42 F43 R44 N114 D116 H131
Enzyme Commision number 2.3.1.-
Gene Ontology
Molecular Function
GO:0036054 protein-malonyllysine demalonylase activity
GO:0036055 protein-succinyllysine desuccinylase activity
GO:0070403 NAD+ binding

View graph for
Molecular Function
External links
PDB RCSB:6eo0, PDBe:6eo0, PDBj:6eo0
PDBsum6eo0
PubMed29044784
UniProtQ6DHI5|SIR5_DANRE NAD-dependent protein deacylase sirtuin-5, mitochondrial (Gene Name=sirt5)

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