Structure of PDB 6eqs Chain A Binding Site BS02

Receptor Information
>6eqs Chain A (length=269) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ARPSSSMADFRKFFAKAKHIVIISGAGVSAESGVPTFRGAGGYWRKWQAQ
DLATPLAFAHNPSRVWEFYHYRREVMGSKEPNAGHRAIAECETRLGKQGR
RVVVITQNIDELHRKAGTKNLLEIHGSLFKTRCTSCGVVAENYKSPICPA
LSGKGAPEPGTQDASIPVEKLPRCEEAGCGGLLRPHVVWFGENLDPAILE
EVDRELAHCDLCLVVGTSSVVYPAAMFAPQVAARGVPVAEFNTETTPATN
RFRFHFQGPCGTTLPEALA
Ligand information
Ligand IDBV8
InChIInChI=1S/C47H63N11O19P2S/c1-25(2)55-43(66)31(18-27-19-51-29-13-7-6-12-28(27)29)56-42(65)30(57-47(67)72-20-26-10-4-3-5-11-26)14-8-9-16-49-46(50-17-15-34(59)60)80-45-39(64)37(62)33(76-45)22-74-79(70,71)77-78(68,69)73-21-32-36(61)38(63)44(75-32)58-24-54-35-40(48)52-23-53-41(35)58/h3-7,10-13,19,23-25,30-33,36-39,44-45,51,61-64H,8-9,14-18,20-22H2,1-2H3,(H,49,50)(H,55,66)(H,56,65)(H,57,67)(H,59,60)(H,68,69)(H,70,71)(H2,48,52,53)/t30-,31-,32+,33+,36+,37+,38+,39+,44+,45+/m0/s1
InChIKeyGGZPCSBRGOFORP-PVLZSEPSSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CC(C)NC(=O)[C@H](Cc1c[nH]c2ccccc12)NC(=O)[C@H](CCCCN=C(NCCC(O)=O)S[C@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)OC[C@H]4O[C@H]([C@H](O)[C@@H]4O)n5cnc6c(N)ncnc56)[C@@H](O)[C@H]3O)NC(=O)OCc7ccccc7
CACTVS 3.385CC(C)NC(=O)[CH](Cc1c[nH]c2ccccc12)NC(=O)[CH](CCCCN=C(NCCC(O)=O)S[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]4O[CH]([CH](O)[CH]4O)n5cnc6c(N)ncnc56)[CH](O)[CH]3O)NC(=O)OCc7ccccc7
OpenEye OEToolkits 2.0.6CC(C)NC(=O)C(Cc1c[nH]c2c1cccc2)NC(=O)C(CCCCN=C(NCCC(=O)O)SC3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)n5cnc6c5ncnc6N)O)O)O)O)NC(=O)OCc7ccccc7
OpenEye OEToolkits 2.0.6CC(C)NC(=O)[C@H](Cc1c[nH]c2c1cccc2)NC(=O)[C@H](CCCC/N=C(/NCCC(=O)O)\S[C@@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)OP(=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)n5cnc6c5ncnc6N)O)O)O)O)NC(=O)OCc7ccccc7
FormulaC47 H63 N11 O19 P2 S
Name3-[[(~{Z})-~{C}-[(2~{R},3~{R},4~{S},5~{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]-3,4-bis(oxidanyl)oxolan-2-yl]sulfanyl-~{N}-[(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]carbonimidoyl]amino]propanoic acid
ChEMBL
DrugBank
ZINC
PDB chain6eqs Chain A Residue 402 [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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PDB6eqs Mechanism-Based Inhibitors of the Human Sirtuin 5 Deacylase: Structure-Activity Relationship, Biostructural, and Kinetic Insight.
Resolution1.32 Å
Binding residue
(original residue number in PDB)
G58 A59 G60 E64 F70 R71 Y102 R105 Q140 I142 H158 V221 F223 G224 E225 N226 G249 T250 S251 V254 Y255 N275 T276 E277 C293
Binding residue
(residue number reindexed from 1)
G25 A26 G27 E31 F37 R38 Y69 R72 Q107 I109 H125 V188 F190 G191 E192 N193 G216 T217 S218 V221 Y222 N242 T243 E244 C260
Annotation score2
Binding affinityPDBbind-CN: -logKd/Ki=6.43,IC50=0.37uM
Enzymatic activity
Catalytic site (original residue number in PDB) P68 T69 F70 R71 N141 D143 H158
Catalytic site (residue number reindexed from 1) P35 T36 F37 R38 N108 D110 H125
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:6eqs, PDBe:6eqs, PDBj:6eqs
PDBsum6eqs
PubMed29044784
UniProtQ9NXA8|SIR5_HUMAN NAD-dependent protein deacylase sirtuin-5, mitochondrial (Gene Name=SIRT5)

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