Structure of PDB 9cbt Chain A Binding Site BS02

Receptor Information
>9cbt Chain A (length=270) 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
SLVELLGWTEEMRDLVQRET
Ligand information
Ligand ID5IA
InChIInChI=1S/C51H85N9O16P2S/c1-5-9-10-11-12-13-14-15-16-17-21-27-40(53-28-23-22-26-37(48(64)54-29-30-60(6-2,7-3)8-4)58-51(65)70-31-36-24-19-18-20-25-36)75-45-43(62)39(74-50(45)79)33-72-78(68,69)76-77(66,67)71-32-38-42(61)44(63)49(73-38)59-35-57-41-46(52)55-34-56-47(41)59/h18-20,24-25,34-35,37-39,42-45,49-50,61-63H,5-17,21-23,26-33H2,1-4H3,(H6-,52,54,55,56,58,64,65,66,67,68,69,79)/p+1/b53-40-/t37-,38+,39+,42+,43+,44+,45+,49+,50+/m0/s1
InChIKeyNDEIYVWRFNKRPD-LQYQRRKDSA-O
SMILES
SoftwareSMILES
CACTVS 3.385CCCCCCCCCCCCCC(O[C@H]1[C@@H](S)O[C@H](CO[P](O)(=O)O[P](O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)n3cnc4c(N)ncnc34)[C@H]1O)=NCCCC[C@H](NC(=O)OCc5ccccc5)C(=O)NCC[N+](CC)(CC)CC
ACDLabs 12.01Nc1ncnc2c1ncn2C1OC(COP(=O)(O)OP(=O)(O)OCC2OC(S)C(O/C(=N\CCCCC(NC(=O)OCc3ccccc3)C(=O)NCC[N+](CC)(CC)CC)CCCCCCCCCCCCC)C2O)C(O)C1O
CACTVS 3.385CCCCCCCCCCCCCC(O[CH]1[CH](S)O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]2O[CH]([CH](O)[CH]2O)n3cnc4c(N)ncnc34)[CH]1O)=NCCCC[CH](NC(=O)OCc5ccccc5)C(=O)NCC[N+](CC)(CC)CC
OpenEye OEToolkits 2.0.7CCCCCCCCCCCCCC(=NCCCCC(C(=O)NCC[N+](CC)(CC)CC)NC(=O)OCc1ccccc1)OC2C(C(OC2S)COP(=O)(O)OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)O)O)O
OpenEye OEToolkits 2.0.7CCCCCCCCCCCCC/C(=N/CCCC[C@@H](C(=O)NCC[N+](CC)(CC)CC)NC(=O)OCc1ccccc1)/O[C@@H]2[C@@H]([C@H](O[C@@H]2S)COP(=O)(O)OP(=O)(O)OC[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4ncnc5N)O)O)O
FormulaC51 H86 N9 O16 P2 S
Name2-{[(2S)-6-[(Z)-(1-{[(2R,3R,4R,5R)-5-({[(R)-{[(R)-{[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}methyl)-4-hydroxy-2-sulfanyloxolan-3-yl]oxy}tetradecylidene)amino]-2-{[(benzyloxy)carbonyl]amino}hexanoyl]amino}-N,N,N-triethylethan-1-aminium (non-preferred name)
ChEMBL
DrugBank
ZINC
PDB chain9cbt 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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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 I154 D156 F157 R158 F180 L199 Q228 I230 D231 H248 V292 F293 F294 E296 P297 L298 G319 T320 S321 V324 E325 N344 R345 D365 V366
Binding residue
(residue number reindexed from 1)
G24 A25 G26 T29 I33 D35 F36 R37 F59 L78 Q107 I109 D110 H127 V171 F172 F173 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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