Structure of PDB 6s8l Chain B Binding Site BS01

Receptor Information
>6s8l Chain B (length=420) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
REIVHIQAGQCGNQIGAKFWEVISDEHGIDPSGNYVGDSDLQLERISVYY
NEASSHKYVPRAILVDLEPGTMDSVRSGAFGHLFRPDNFIFGQSGAGNNW
AKGHYTEGAELVDSVLDVVRKECENCDCLQGFQLTHSLGGGTGSGMGTLL
ISKVREEYPDRIMNTFSVVPSPKVSTVVEPYNATLSIHQLVENTDETYCI
DNEALYDICFRTLKLATPTYGDLNHLVSATMSGVTTSLRFPLNADLRKLA
VNMVPFPRLHFFMPGFAPLTARALTVPELTQQMFDAKNMMAACDPRHGRY
LTVATVFRGRMSMKEVDEQMLAIQSKNSSYFVEWIPNNVKVAVCDIPPRG
LKMSSTFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTE
AESNMNDLVSEYQQYQDATA
Ligand information
Ligand IDPN6
InChIInChI=1S/C19H20N4O2/c1-19(2,3)16-13(20-11-21-16)10-15-18(25)22-14(17(24)23-15)9-12-7-5-4-6-8-12/h4-11H,1-3H3,(H,20,21)(H,22,25)(H,23,24)/b14-9-,15-10-
InChIKeyUNRCMCRRFYFGFX-TYPNBTCFSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CC(C)(C)c1[nH]cnc1C=C2NC(=O)C(NC2=O)=Cc3ccccc3
ACDLabs 12.01[C@H](c1ncnc1C(C)(C)C)=C2NC(=O)C(NC2=O)=[C@H]c3ccccc3
OpenEye OEToolkits 1.9.2CC(C)(C)c1c(nc[nH]1)/C=C\2/C(=O)N/C(=C\c3ccccc3)/C(=O)N2
OpenEye OEToolkits 1.9.2CC(C)(C)c1c(nc[nH]1)C=C2C(=O)NC(=Cc3ccccc3)C(=O)N2
CACTVS 3.385CC(C)(C)c1[nH]cnc1/C=C/2NC(=O)C(/NC/2=O)=C/c3ccccc3
FormulaC19 H20 N4 O2
Name(3Z,6Z)-3-benzylidene-6-[(5-tert-butyl-1H-imidazol-4-yl)methylidene]piperazine-2,5-dione;
Plinabulin
ChEMBLCHEMBL1096380
DrugBankDB05992
ZINCZINC000003819466
PDB chain6s8l Chain B Residue 501 [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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PDB6s8l Structure, Thermodynamics, and Kinetics of Plinabulin Binding to Two Tubulin Isotypes
Resolution1.801 Å
Binding residue
(original residue number in PDB)		E200 Y202 V238 T239 S241 L242 L248 L252 L255 A316 I378
Binding residue
(residue number reindexed from 1)		E196 Y198 V234 T235 S237 L238 L242 L246 L249 A304 I358
Annotation score1
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003924 GTPase activity
GO:0005200 structural constituent of cytoskeleton
GO:0005515 protein binding
GO:0005525 GTP binding
GO:0042277 peptide binding
GO:0046872 metal ion binding
GO:1990890 netrin receptor binding
Biological Process
GO:0000226 microtubule cytoskeleton organization
GO:0000278 mitotic cell cycle
GO:0007017 microtubule-based process
GO:0007411 axon guidance
GO:0030182 neuron differentiation
GO:0038007 netrin-activated signaling pathway
GO:1990791 dorsal root ganglion development
Cellular Component
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005856 cytoskeleton
GO:0005874 microtubule
GO:0015630 microtubule cytoskeleton
GO:0030027 lamellipodium
GO:0030175 filopodium
GO:0030424 axon
GO:0030425 dendrite
GO:0030426 growth cone
GO:0042995 cell projection
GO:0043025 neuronal cell body
GO:0045171 intercellular bridge
GO:0070062 extracellular exosome
GO:0071944 cell periphery
GO:0072686 mitotic spindle

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:6s8l, PDBe:6s8l, PDBj:6s8l
PDBsum6s8l
PubMed
UniProtQ13509|TBB3_HUMAN Tubulin beta-3 chain (Gene Name=TUBB3)

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