Structure of PDB 3dxm Chain A Binding Site BS01

Receptor Information
>3dxm Chain A (length=399) Species: 9913 (Bos taurus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GRLPACVVDCGTGYTKLGYAGNTEPQFIIPSCIAIKEVMKGVDDLDFFIG
DEAIEKPTYATKWPIRHGIVEDWDLMERFMEQVIFKYLRAEPEDHYFLLT
EPPLNTPENREYTAEIMFESFNVPGLYIAVQAVLALAASWTSRQVGERTL
TGTVIDSGDGVTHVIPVAEGYVIGSCIKHIPIAGRDITYFIQQLLRDREV
GIPPEQSLETAKAVKERYSYVCPDLVKEFNKYDTDGSKWIKQYTGINAIS
KKEFSIDVGYERFLGPEIFFHPEFANPDFTQPISEVVDEVIQNCPIDVRR
PLYKNIVLSGGSTMFRDFGRRLQRDLKRTVDARLKLSEELSKPKPIDVQV
ITHHMQRYAVWFGGSMLASTPEFYQVCHTKKDYEEIGPSICRHNPVFGV
Ligand information
Ligand IDN24
InChIInChI=1S/C15H11BrClNO2S/c16-10-3-1-2-9(6-10)15-18(14(20)8-21-15)12-7-11(17)4-5-13(12)19/h1-7,15,19H,8H2/t15-/m0/s1
InChIKeyKEGQNJITMFBVAC-HNNXBMFYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341Oc1ccc(Cl)cc1N2[CH](SCC2=O)c3cccc(Br)c3
CACTVS 3.341Oc1ccc(Cl)cc1N2[C@@H](SCC2=O)c3cccc(Br)c3
OpenEye OEToolkits 1.5.0c1cc(cc(c1)Br)[C@H]2N(C(=O)CS2)c3cc(ccc3O)Cl
OpenEye OEToolkits 1.5.0c1cc(cc(c1)Br)C2N(C(=O)CS2)c3cc(ccc3O)Cl
ACDLabs 10.04Clc3cc(N2C(=O)CSC2c1cc(Br)ccc1)c(O)cc3
FormulaC15 H11 Br Cl N O2 S
Name(2S)-2-(3-bromophenyl)-3-(5-chloro-2-hydroxyphenyl)-1,3-thiazolidin-4-one
ChEMBL
DrugBankDB08236
ZINCZINC000002949834
PDB chain3dxm Chain A Residue 419 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB3dxm Characterization of two classes of small molecule inhibitors of Arp2/3 complex
Resolution2.85 Å
Binding residue
(original residue number in PDB)		C12 E84 M89 M93 T113 N118 T126
Binding residue
(residue number reindexed from 1)		C10 E71 M76 M80 T100 N105 T113
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=6.00,Kd=1.0uM
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:0030030 cell projection organization
GO:0034314 Arp2/3 complex-mediated actin nucleation
GO:0045944 positive regulation of transcription by RNA polymerase II
GO:0060271 cilium assembly
Cellular Component
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005856 cytoskeleton
GO:0005885 Arp2/3 protein complex
GO:0035861 site of double-strand break
GO:0042995 cell projection

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:3dxm, PDBe:3dxm, PDBj:3dxm
PDBsum3dxm
PubMed19648907
UniProtP61157|ARP3_BOVIN Actin-related protein 3 (Gene Name=ACTR3)

[Back to BioLiP]