Structure of PDB 6i16 Chain A Binding Site BS01

Receptor Information
>6i16 Chain A (length=484) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VQIQFGLINCGNKYLTAEAFGFKVNASASSLKKKQIWTLEQPPDEAGSAA
VCLRSHLGRYLAADKDGNVTCEREVPGPDCRFLIVAHDDGRWSLQSEAHR
RYFGGTEDRLSCFAQTVSPAEKWSVHIAMHPQVNIYSVTRKRYAHLSARP
ADEIAVDRDVPWGVDSLITLAFQDQRYSVQTADHRFLRHDGRLVARPEPA
TGYTLEFRSGKVAFRDCEGRYLAPSGPSGTLKAGKATKVGKDELFALEQS
CAQVVLQAANERNVSTRQGMDLSANQDEETDQETFQLEIDRDTKKCAFRT
HTGKYWTLTATGGVQSTASSKNASCYFDIEWRDRRITLRASNGKFVTSKK
NGQLAASVETAGDSELFLMKLINRPIIVFRGEHGFIGCRKVTGTLDANRS
SYDVFQLEFNDGAYNIKDSTGKYWTVGSDSAVTSSGDTPVDFFFEFCDYN
KVAIKVGGRYLKGDHAGVLKASAETVDPASLWEY
Ligand information
Ligand IDH0B
InChIInChI=1S/C20H15Cl2N5O2/c1-26-10-13(8-24-26)25-19(28)15-11-27(9-12-4-5-16(21)17(22)7-12)20(29)14-3-2-6-23-18(14)15/h2-8,10-11H,9H2,1H3,(H,25,28)
InChIKeySVPAXEMWEZLCLS-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6Cn1cc(cn1)NC(=O)C2=CN(C(=O)c3c2nccc3)Cc4ccc(c(c4)Cl)Cl
CACTVS 3.385Cn1cc(NC(=O)C2=CN(Cc3ccc(Cl)c(Cl)c3)C(=O)c4cccnc24)cn1
FormulaC20 H15 Cl2 N5 O2
Name6-[(3,4-dichlorophenyl)methyl]-~{N}-(1-methylpyrazol-4-yl)-5-oxidanylidene-1,6-naphthyridine-8-carboxamide
ChEMBLCHEMBL4448440
DrugBank
ZINC
PDB chain6i16 Chain A Residue 502 [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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PDB6i16 Structure-based design, synthesis and biological evaluation of a novel series of isoquinolone and pyrazolo[4,3-c]pyridine inhibitors of fascin 1 as potential anti-metastatic agents.
Resolution2.0 Å
Binding residue
(original residue number in PDB)		F14 L48 Q50 S57 A58 I93 W101 V134 E215 F216
Binding residue
(residue number reindexed from 1)		F5 L39 Q41 S48 A49 I84 W92 V125 E206 F207
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=4.00,Kd>100uM
BindingDB: Kd=>100000nM
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003723 RNA binding
GO:0003779 actin binding
GO:0005515 protein binding
GO:0030674 protein-macromolecule adaptor activity
GO:0045296 cadherin binding
GO:0051015 actin filament binding
Biological Process
GO:0007015 actin filament organization
GO:0007043 cell-cell junction assembly
GO:0007163 establishment or maintenance of cell polarity
GO:0010592 positive regulation of lamellipodium assembly
GO:0016477 cell migration
GO:0030035 microspike assembly
GO:0030036 actin cytoskeleton organization
GO:0030046 parallel actin filament bundle assembly
GO:0032534 regulation of microvillus assembly
GO:0032956 regulation of actin cytoskeleton organization
GO:0035089 establishment of apical/basal cell polarity
GO:0048870 cell motility
GO:0051017 actin filament bundle assembly
GO:0051491 positive regulation of filopodium assembly
GO:0071803 positive regulation of podosome assembly
GO:0090091 positive regulation of extracellular matrix disassembly
Cellular Component
GO:0001725 stress fiber
GO:0001726 ruffle
GO:0002102 podosome
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005856 cytoskeleton
GO:0005902 microvillus
GO:0005911 cell-cell junction
GO:0005938 cell cortex
GO:0015629 actin cytoskeleton
GO:0030027 lamellipodium
GO:0030175 filopodium
GO:0030426 growth cone
GO:0031253 cell projection membrane
GO:0042995 cell projection
GO:0044393 microspike
GO:0070062 extracellular exosome
GO:0070161 anchoring junction

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6i16, PDBe:6i16, PDBj:6i16
PDBsum6i16
PubMed30773430
UniProtQ16658|FSCN1_HUMAN Fascin (Gene Name=FSCN1)

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