Structure of PDB 4g8r Chain B Binding Site BS01

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 402 [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)		S6 Y7 H10
Binding residue
(residue number reindexed from 1)		S3 Y4 H7
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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