Structure of PDB 4rn1 Chain B Binding Site BS03

Receptor Information
>4rn1 Chain B (length=359) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SLVPVYIYSPEYVSMCDSLAKIPKRADMVHSLIEAYALHKQMRIVKPKVA
SMEEMATFHTDAYLQHLQKVSQDHPDSIEYGLGCPATEGIFDYAAAIGGA
TITAAQCLIDGMCKVAINWSGGWHHAKKDEASGFCYLNDAVLGILRLRRK
FERILYVDLDLHHGDGVEDAFSFTSKVMTVSLHKFSPGFFPGTGDVSDVG
LGKGRYYSVNVPIQDGIQDEKYYQICESVLKEVYQAFNPKAVVLQLGADT
IAGDPMCSFNMTPVGIGKCLKYILQWQLATLILGGGGYNLANTARCWTYL
TGVILGKTLSSEIPDHEFFTAYGPDYVLEITPSCRPDRNEPHRIQQILNY
IKGNLKHVV
Ligand information
Ligand IDL8G
InChIInChI=1S/C23H31N5O3S2/c1-14(2)19-20(30)26-15(7-4-5-10-32)11-18(29)24-12-16-8-6-9-17(25-16)21-28-23(3,13-33-21)22(31)27-19/h4,6-9,14-15,19,32H,5,10-13H2,1-3H3,(H,24,29)(H,26,30)(H,27,31)/b7-4+/t15-,19+,23+/m1/s1
InChIKeyPFXMQZVRILDSDW-XUFAZQDHSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6CC(C)C1C(=O)NC(CC(=O)NCc2cccc(n2)C3=NC(CS3)(C(=O)N1)C)C=CCCS
CACTVS 3.385CC(C)[CH]1NC(=O)[C]2(C)CSC(=N2)c3cccc(CNC(=O)C[CH](NC1=O)C=CCCS)n3
CACTVS 3.385CC(C)[C@@H]1NC(=O)[C@]2(C)CSC(=N2)c3cccc(CNC(=O)C[C@H](NC1=O)\C=C\CCS)n3
OpenEye OEToolkits 1.7.6CC(C)[C@H]1C(=O)N[C@@H](CC(=O)NCc2cccc(n2)C3=N[C@@](CS3)(C(=O)N1)C)/C=C/CCS
ACDLabs 12.01O=C1NC(C(=O)NC(/C=C/CCS)CC(=O)NCc3nc(C2=NC1(C)CS2)ccc3)C(C)C
FormulaC23 H31 N5 O3 S2
Name(5R,8S,11S)-5-methyl-8-(propan-2-yl)-11-[(1E)-4-sulfanylbut-1-en-1-yl]-3-thia-7,10,14,20,21-pentaazatricyclo[14.3.1.1~2,5~]henicosa-1(20),2(21),16,18-tetraene-6,9,13-trione
ChEMBLCHEMBL3593413
DrugBank
ZINCZINC000230838923
PDB chain4rn1 Chain B Residue 404 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4rn1 Variable Active Site Loop Conformations Accommodate the Binding of Macrocyclic Largazole Analogues to HDAC8.
Resolution2.18 Å
Binding residue
(original residue number in PDB)		K33 H143 F152 H180 F208 Y306
Binding residue
(residue number reindexed from 1)		K21 H125 F134 H162 F190 Y288
Annotation score1
Enzymatic activity
Enzyme Commision number 3.5.1.-
3.5.1.98: histone deacetylase.
Gene Ontology
Molecular Function
GO:0004407 histone deacetylase activity
GO:0005515 protein binding
GO:0016787 hydrolase activity
GO:0030544 Hsp70 protein binding
GO:0033558 protein lysine deacetylase activity
GO:0046872 metal ion binding
GO:0051879 Hsp90 protein binding
GO:0140297 DNA-binding transcription factor binding
GO:0160008 protein decrotonylase activity
GO:0160009 histone decrotonylase activity
Biological Process
GO:0000122 negative regulation of transcription by RNA polymerase II
GO:0006325 chromatin organization
GO:0007064 mitotic sister chromatid cohesion
GO:0031397 negative regulation of protein ubiquitination
GO:0031647 regulation of protein stability
GO:0032204 regulation of telomere maintenance
GO:0040029 epigenetic regulation of gene expression
Cellular Component
GO:0000118 histone deacetylase complex
GO:0000228 nuclear chromosome
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005694 chromosome
GO:0005737 cytoplasm

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4rn1, PDBe:4rn1, PDBj:4rn1
PDBsum4rn1
PubMed25793284
UniProtQ9BY41|HDAC8_HUMAN Histone deacetylase 8 (Gene Name=HDAC8)

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