Structure of PDB 3dxk Chain B Binding Site BS01

Receptor Information
>3dxk Chain B (length=211) Species: 9913 (Bos taurus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QAVLTLYAQGLLGVVVDSGDGVTHICPVYEGFSLPHLTRRLDIAGRDITR
YLIKLLLLRGYAFNHSADFETVRMIKEKLCYVGYNIEQEQKLALETTVLV
ESYTLPDGRIIKVGGERFEAPEALFQPHLINVEGVGVAELLFNTIQAADI
DTRSEFYKHIVLSGGSTMYPGLPSRLERELKQLYLERVLKGDVEKLSKFK
IRIEDPPRRKH
Ligand information
Ligand IDN23
InChIInChI=1S/C16H16N2OS/c1-11-12(13-5-2-3-6-14(13)18-11)8-9-17-16(19)15-7-4-10-20-15/h2-7,10,18H,8-9H2,1H3,(H,17,19)
InChIKeyACAKNPKRLPMONU-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0Cc1c(c2ccccc2[nH]1)CCNC(=O)c3cccs3
ACDLabs 10.04O=C(NCCc2c1ccccc1nc2C)c3sccc3
CACTVS 3.341Cc1[nH]c2ccccc2c1CCNC(=O)c3sccc3
FormulaC16 H16 N2 O S
NameN-[2-(2-methyl-1H-indol-3-yl)ethyl]thiophene-2-carboxamide
ChEMBLCHEMBL1234574
DrugBankDB08235
ZINCZINC000000140471
PDB chain3dxk Chain B Residue 395 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3dxk Characterization of two classes of small molecule inhibitors of Arp2/3 complex
Resolution2.7 Å
Binding residue
(original residue number in PDB)		Y202 A203 F204 D209 L246 P247 D248 R250
Binding residue
(residue number reindexed from 1)		Y61 A62 F63 D68 L105 P106 D107 R109
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=6.33,Kd=470nM
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003779 actin binding
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0051015 actin filament binding
Biological Process
GO:0010592 positive regulation of lamellipodium assembly
GO:0034314 Arp2/3 complex-mediated actin nucleation
GO:0045944 positive regulation of transcription by RNA polymerase II
GO:1905168 positive regulation of double-strand break repair via homologous recombination
GO:2001032 regulation of double-strand break repair via nonhomologous end joining
Cellular Component
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005856 cytoskeleton
GO:0005885 Arp2/3 protein complex
GO:0005938 cell cortex
GO:0035861 site of double-strand break
GO:0042995 cell projection

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:3dxk, PDBe:3dxk, PDBj:3dxk
PDBsum3dxk
PubMed19648907
UniProtA7MB62|ARP2_BOVIN Actin-related protein 2 (Gene Name=ACTR2)

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