Structure of PDB 4g8r Chain B Binding Site BS02

Receptor Information
>4g8r Chain B (length=368) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
APSYVAHLASDFGVRVFQQVAQASKDRNVVFSPYGVASVLAMLQLTTGGE
TQQQIQAAMGFKIDDKGMAPALRHLYKELMGPWNKDEISTTDAIFVQRDL
KLVQGFMPHFFRLFRSTVKQVDFSEVERARFIINDWVKTHTKGMISHLLG
TGAVDQLTRLVLVNALYFNGQWKTPFPDSSTHRRLFHKSDGSTVSVPMMA
QTNKFNYTEFTTPDGHYYDILELPYHGDTLSMFIAAPYEKEVPLSALTNI
LSAQLISHWKGNMTRLPRLLVLPKFSLETEVDLRKPLENLGMTDMFRQFQ
ADFTSLSDQEPLHVALALQKVKIEVNESAVIVSARMAPEEIIIDRPFLFV
VRHNPTGTVLFMGQVMEP
Ligand information
Ligand ID96P
InChIInChI=1S/C25H20F3NO12/c26-25(27,28)13-2-1-3-14(8-13)41-24(38)29-9-15(40-23(37)12-6-18(32)21(35)19(33)7-12)10-39-22(36)11-4-16(30)20(34)17(31)5-11/h1-8,15,30-35H,9-10H2,(H,29,38)/t15-/m0/s1
InChIKeyOXWKLJPAKUDPJY-HNNXBMFYSA-N
SMILES
SoftwareSMILES
CACTVS 3.370Oc1cc(cc(O)c1O)C(=O)OC[CH](CNC(=O)Oc2cccc(c2)C(F)(F)F)OC(=O)c3cc(O)c(O)c(O)c3
CACTVS 3.370Oc1cc(cc(O)c1O)C(=O)OC[C@H](CNC(=O)Oc2cccc(c2)C(F)(F)F)OC(=O)c3cc(O)c(O)c(O)c3
OpenEye OEToolkits 1.7.6c1cc(cc(c1)OC(=O)NC[C@@H](COC(=O)c2cc(c(c(c2)O)O)O)OC(=O)c3cc(c(c(c3)O)O)O)C(F)(F)F
OpenEye OEToolkits 1.7.6c1cc(cc(c1)OC(=O)NCC(COC(=O)c2cc(c(c(c2)O)O)O)OC(=O)c3cc(c(c(c3)O)O)O)C(F)(F)F
ACDLabs 12.01FC(F)(F)c3cc(OC(=O)NCC(OC(=O)c1cc(O)c(O)c(O)c1)COC(=O)c2cc(O)c(O)c(O)c2)ccc3
FormulaC25 H20 F3 N O12
Name(2S)-3-({[3-(trifluoromethyl)phenoxy]carbonyl}amino)propane-1,2-diyl bis(3,4,5-trihydroxybenzoate)
ChEMBL
DrugBank
ZINCZINC000098208613
PDB chain4g8r Chain B Residue 403 [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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PDB4g8r Mechanistic characterization and crystal structure of a small molecule inactivator bound to plasminogen activator inhibitor-1.
Resolution2.19 Å
Binding residue
(original residue number in PDB)		S41 M45 L75 R76 Y79 F117 R118
Binding residue
(residue number reindexed from 1)		S38 M42 L72 R73 Y76 F114 R115
Annotation score1
Binding affinityMOAD: Kd=22nM
PDBbind-CN: -logKd/Ki=7.66,Kd=22nM
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0002020 protease binding
GO:0004867 serine-type endopeptidase inhibitor activity
GO:0005102 signaling receptor binding
GO:0005515 protein binding
Biological Process
GO:0001525 angiogenesis
GO:0010466 negative regulation of peptidase activity
GO:0010469 regulation of signaling receptor activity
GO:0010757 negative regulation of plasminogen activation
GO:0010951 negative regulation of endopeptidase activity
GO:0014912 negative regulation of smooth muscle cell migration
GO:0030194 positive regulation of blood coagulation
GO:0030195 negative regulation of blood coagulation
GO:0030336 negative regulation of cell migration
GO:0032757 positive regulation of interleukin-8 production
GO:0033629 negative regulation of cell adhesion mediated by integrin
GO:0035491 positive regulation of leukotriene production involved in inflammatory response
GO:0042730 fibrinolysis
GO:0045766 positive regulation of angiogenesis
GO:0048260 positive regulation of receptor-mediated endocytosis
GO:0050729 positive regulation of inflammatory response
GO:0050829 defense response to Gram-negative bacterium
GO:0051918 negative regulation of fibrinolysis
GO:0061044 negative regulation of vascular wound healing
GO:0061045 negative regulation of wound healing
GO:0071222 cellular response to lipopolysaccharide
GO:0090026 positive regulation of monocyte chemotaxis
GO:0090399 replicative senescence
GO:0097187 dentinogenesis
GO:1901331 positive regulation of odontoblast differentiation
GO:1902042 negative regulation of extrinsic apoptotic signaling pathway via death domain receptors
GO:2000098 negative regulation of smooth muscle cell-matrix adhesion
GO:2000352 negative regulation of endothelial cell apoptotic process
Cellular Component
GO:0005576 extracellular region
GO:0005615 extracellular space
GO:0005886 plasma membrane
GO:0031093 platelet alpha granule lumen
GO:0062023 collagen-containing extracellular matrix
GO:0070062 extracellular exosome
GO:0097180 serine protease inhibitor complex
GO:1904090 peptidase inhibitor complex

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Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4g8r, PDBe:4g8r, PDBj:4g8r
PDBsum4g8r
PubMed24297881
UniProtP05121|PAI1_HUMAN Plasminogen activator inhibitor 1 (Gene Name=SERPINE1)

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