Structure of PDB 7cl1 Chain A Binding Site BS02

Receptor Information
>7cl1 Chain A (length=296) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NYAAGLSPYADKGKCGLPEIFDPPEELERKVWELARLVWQSSSVVFHTGA
GISTASGIPDFRGPHGVWTMEERGLAPKFDTTFESARPTQTHMALVQLER
VGLLRFLVSQNVDGLHVRSGFPRDKLAELHGNMFVEECAKCKTQYVRDTV
VGTMGLKATGRLCTVAKARGLRACRGELRDTILDWEDSLPDRDLALADEA
SRNADLSITLGTSLQIRPSGNLPLATKRRGGRLVIVNLQPTKHDRHADLR
IHGYVDEVMTRLMKHLGLEIPAWDGPRVLERALPPLPRPPTPKLEP
Ligand information
Ligand IDAR6
InChIInChI=1S/C15H23N5O14P2/c16-12-7-13(18-3-17-12)20(4-19-7)14-10(23)8(21)5(32-14)1-30-35(26,27)34-36(28,29)31-2-6-9(22)11(24)15(25)33-6/h3-6,8-11,14-15,21-25H,1-2H2,(H,26,27)(H,28,29)(H2,16,17,18)/t5-,6-,8-,9-,10-,11-,14-,15+/m1/s1
InChIKeySRNWOUGRCWSEMX-ZQSHOCFMSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)O)O)O)O)O)N
OpenEye OEToolkits 1.7.6c1nc(c2c(n1)n(cn2)[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)O)O)O)O)O)N
ACDLabs 12.01O=P(OCC3OC(n1c2ncnc(N)c2nc1)C(O)C3O)(O)OP(=O)(O)OCC4OC(O)C(O)C4O
CACTVS 3.370Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)OC[C@H]4O[C@H](O)[C@H](O)[C@@H]4O)[C@@H](O)[C@H]3O
CACTVS 3.370Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]4O[CH](O)[CH](O)[CH]4O)[CH](O)[CH]3O
FormulaC15 H23 N5 O14 P2
Name[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE;
Adenosine-5-Diphosphoribose
ChEMBL
DrugBankDB02059
ZINCZINC000014880207
PDB chain7cl1 Chain A Residue 401 [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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PDB7cl1 Reply to: Binding site for MDL-801 on SIRT6.
Resolution3.2 Å
Binding residue
(original residue number in PDB)		G50 A51 G52 T55 D61 F62 R63 W69 Q111 H131 G212 T213 S214 I217 N238 L239 Q240 G254 Y255 V256
Binding residue
(residue number reindexed from 1)		G49 A50 G51 T54 D60 F61 R62 W68 Q110 H130 G211 T212 S213 I216 N237 L238 Q239 G253 Y254 V255
Annotation score3
Enzymatic activity
Catalytic site (original residue number in PDB) P60 D61 F62 R63 N112 D114 H131
Catalytic site (residue number reindexed from 1) P59 D60 F61 R62 N111 D113 H130
Enzyme Commision number 2.3.1.-
2.3.1.286: protein acetyllysine N-acetyltransferase.
2.4.2.-
Gene Ontology
Molecular Function
GO:0003677 DNA binding
GO:0003682 chromatin binding
GO:0003684 damaged DNA binding
GO:0003714 transcription corepressor activity
GO:0003723 RNA binding
GO:0003950 NAD+-protein poly-ADP-ribosyltransferase activity
GO:0005515 protein binding
GO:0008270 zinc ion binding
GO:0016746 acyltransferase activity
GO:0016757 glycosyltransferase activity
GO:0016779 nucleotidyltransferase activity
GO:0017136 NAD-dependent histone deacetylase activity
GO:0031490 chromatin DNA binding
GO:0031491 nucleosome binding
GO:0032129 histone H3K9 deacetylase activity
GO:0034979 NAD-dependent protein lysine deacetylase activity
GO:0042803 protein homodimerization activity
GO:0046872 metal ion binding
GO:0046969 NAD-dependent histone H3K9 deacetylase activity
GO:0070403 NAD+ binding
GO:0097372 NAD-dependent histone H3K18 deacetylase activity
GO:0106222 lncRNA binding
GO:0106274 NAD+-protein-arginine ADP-ribosyltransferase activity
GO:0140612 DNA damage sensor activity
GO:0140765 NAD-dependent histone H3K56 deacetylase activity
GO:0140773 NAD-dependent protein demyristoylase activity
GO:0140774 NAD-dependent protein depalmitoylase activity
GO:0140804 NAD+-protein-lysine ADP-ribosyltransferase activity
GO:1904841 TORC2 complex binding
GO:1990404 NAD+-protein ADP-ribosyltransferase activity
Biological Process
GO:0000122 negative regulation of transcription by RNA polymerase II
GO:0006281 DNA repair
GO:0006284 base-excision repair
GO:0006302 double-strand break repair
GO:0006325 chromatin organization
GO:0006338 chromatin remodeling
GO:0006476 protein deacetylation
GO:0006606 protein import into nucleus
GO:0008285 negative regulation of cell population proliferation
GO:0008340 determination of adult lifespan
GO:0009411 response to UV
GO:0010526 retrotransposon silencing
GO:0010569 regulation of double-strand break repair via homologous recombination
GO:0019216 regulation of lipid metabolic process
GO:0031508 pericentric heterochromatin formation
GO:0031509 subtelomeric heterochromatin formation
GO:0031648 protein destabilization
GO:0032024 positive regulation of insulin secretion
GO:0032206 positive regulation of telomere maintenance
GO:0032436 positive regulation of proteasomal ubiquitin-dependent protein catabolic process
GO:0032922 circadian regulation of gene expression
GO:0034244 negative regulation of transcription elongation by RNA polymerase II
GO:0042181 ketone biosynthetic process
GO:0042308 negative regulation of protein import into nucleus
GO:0042593 glucose homeostasis
GO:0042752 regulation of circadian rhythm
GO:0043687 post-translational protein modification
GO:0045600 positive regulation of fat cell differentiation
GO:0045721 negative regulation of gluconeogenesis
GO:0045814 negative regulation of gene expression, epigenetic
GO:0045820 negative regulation of glycolytic process
GO:0045892 negative regulation of DNA-templated transcription
GO:0046325 negative regulation of D-glucose import
GO:0046827 positive regulation of protein export from nucleus
GO:0048146 positive regulation of fibroblast proliferation
GO:0050708 regulation of protein secretion
GO:0050994 regulation of lipid catabolic process
GO:0051697 protein delipidation
GO:0055007 cardiac muscle cell differentiation
GO:0120162 positive regulation of cold-induced thermogenesis
GO:0120186 negative regulation of protein localization to chromatin
GO:0120187 positive regulation of protein localization to chromatin
GO:0140861 DNA repair-dependent chromatin remodeling
GO:1902459 positive regulation of stem cell population maintenance
GO:1902732 positive regulation of chondrocyte proliferation
GO:1903076 regulation of protein localization to plasma membrane
GO:1905555 positive regulation of blood vessel branching
GO:1905564 positive regulation of vascular endothelial cell proliferation
GO:1990166 protein localization to site of double-strand break
GO:2000648 positive regulation of stem cell proliferation
GO:2000738 positive regulation of stem cell differentiation
GO:2000773 negative regulation of cellular senescence
GO:2000781 positive regulation of double-strand break repair
Cellular Component
GO:0000781 chromosome, telomeric region
GO:0000785 chromatin
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005694 chromosome
GO:0005721 pericentric heterochromatin
GO:0005730 nucleolus
GO:0005783 endoplasmic reticulum
GO:0035861 site of double-strand break
GO:0043231 intracellular membrane-bounded organelle
GO:0090734 site of DNA damage
GO:0099115 chromosome, subtelomeric region

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:7cl1, PDBe:7cl1, PDBj:7cl1
PDBsum7cl1
PubMed33649600
UniProtQ8N6T7|SIR6_HUMAN NAD-dependent protein deacylase sirtuin-6 (Gene Name=SIRT6)

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