Structure of PDB 9cbt Chain B Binding Site BS03

Receptor Information
>9cbt Chain B (length=274) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KLSLQDVAELIRARACQRVVVMVGAGISTPSGIPDFRSPGSGLYSNLQQY
DLPYPEAIFELPFFFHNPKPFFTLAKELYPGNYKPNVTHYFLRLLHDKGL
LLRLYTQNIDGLERVSGIPASKLVEAHGTFASATCTVCQRPFPGEDIRAD
VMADRVPRCPVCTGVVKPDIVFFGEPLPQRFLLHVVDFPMADLLLILGTS
LEVEPFASLTEAVRSSVPRLLINRDLVGPLAWHPRSRDVAQLGDVVHGVE
SLVELLGWTEEMRDLVQRETGKLD
Ligand information
Ligand ID5I7
InChIInChI=1S/C51H85N9O16P2S/c1-5-9-10-11-12-13-14-15-16-17-22-27-51(57-28-23-21-26-37(47(64)53-29-30-60(6-2,7-3)8-4)58-50(65)70-31-36-24-19-18-20-25-36)75-44-42(62)39(74-49(44)79-51)33-72-78(68,69)76-77(66,67)71-32-38-41(61)43(63)48(73-38)59-35-56-40-45(52)54-34-55-46(40)59/h18-20,24-25,34-35,37-39,41-44,48-49,57,61-63H,5-17,21-23,26-33H2,1-4H3,(H5-,52,53,54,55,58,64,65,66,67,68,69)/p+1/t37-,38+,39+,41+,42+,43+,44+,48+,49+,51+/m0/s1
InChIKeyDVXJRXQMZVZLQP-OACJPHNQSA-O
SMILES
SoftwareSMILES
ACDLabs 12.01CC[N+](CC)(CC)CCNC(=O)C(NC(=O)OCc1ccccc1)CCCCNC1(OC2C(O)C(COP(=O)(O)OP(=O)(O)OCC3OC(n4cnc5c(N)ncnc54)C(O)C3O)OC2S1)CCCCCCCCCCCCC
CACTVS 3.385CCCCCCCCCCCCC[C@@]1(NCCCC[C@H](NC(=O)OCc2ccccc2)C(=O)NCC[N+](CC)(CC)CC)O[C@@H]3[C@H](O)[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)O[C@@H]3S1
OpenEye OEToolkits 2.0.7CCCCCCCCCCCCCC1(OC2C(C(OC2S1)COP(=O)(O)OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)O)O)O)NCCCCC(C(=O)NCC[N+](CC)(CC)CC)NC(=O)OCc6ccccc6
OpenEye OEToolkits 2.0.7CCCCCCCCCCCCC[C@]1(O[C@@H]2[C@@H]([C@H](O[C@@H]2S1)COP(=O)(O)OP(=O)(O)OC[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4ncnc5N)O)O)O)NCCCC[C@@H](C(=O)NCC[N+](CC)(CC)CC)NC(=O)OCc6ccccc6
CACTVS 3.385CCCCCCCCCCCCC[C]1(NCCCC[CH](NC(=O)OCc2ccccc2)C(=O)NCC[N+](CC)(CC)CC)O[CH]3[CH](O)[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]4O[CH]([CH](O)[CH]4O)n5cnc6c(N)ncnc56)O[CH]3S1
FormulaC51 H86 N9 O16 P2 S
Name(phenylmethyl) ~{N}-[(2~{S})-6-[[(2~{R},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]-6-oxidanyl-2-tridecyl-3~{a},5,6,6~{a}-tetrahydrofuro[2,3-d][1,3]oxathiol-2-yl]amino]-1-oxidanylidene-1-[2-(triethyl-$l^{4}-azanyl)ethylamino]hexan-2-yl]carbamate
ChEMBL
DrugBank
ZINC
PDB chain9cbt Chain B Residue 403 [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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PDB9cbt Crystal structure of human sirtuin 3 fragment (residues 118-399) bound to intermediates from reaction with NAD and inhibitor NH6-10
Resolution1.95 Å
Binding residue
(original residue number in PDB)
G145 A146 G147 T150 D156 F157 R158 F180 L199 Y204 Q228 I230 H248 V292 F294 G295 E296 P297 L298 G319 T320 S321 V324 E325 N344 R345 D365 V366
Binding residue
(residue number reindexed from 1)
G24 A25 G26 T29 D35 F36 R37 F59 L78 Y83 Q107 I109 H127 V171 F173 G174 E175 P176 L177 G198 T199 S200 V203 E204 N223 R224 D244 V245
Annotation score2
External links
PDB RCSB:9cbt, PDBe:9cbt, PDBj:9cbt
PDBsum9cbt
PubMed
UniProtQ9NTG7|SIR3_HUMAN NAD-dependent protein deacetylase sirtuin-3, mitochondrial (Gene Name=SIRT3)

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