Structure of PDB 8e5m Chain D Binding Site BS03

Receptor Information
>8e5m Chain D (length=317) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AKSRTIGIIGAPFSKGQPRGGVEEGPTVLRKAGLLEKLKEQECDVKDYGD
LPFADIPNDSPFQIVKNPRSVGKASEQLAGKVAEVKKNGRISLVLGGDHS
LAIGSISGHARVHPDLGVIWVDAHTDINTPLTTTSGNLHGQPVSFLLKEL
KGKIPDVPGFSWVTPCISAKDIVYIGLRDVDPGEHYILKTLGIKYFSMTE
VDRLGIGKVMEETLSYLLGRKKRPIHLSFDVDGLDPSFTPATGTPVVGGL
TYREGLYITEEIYKTGLLSGLDIMEVNPSLGKTPEEVTRTVNTAVAITLA
CFGLAREGNHKPIDYLN
Ligand information
Ligand IDUKR
InChIInChI=1S/C31H40F2N2O4S/c32-26-6-8-28(9-7-26)40(38,39)17-12-23-10-15-34(16-11-23)19-25-20-35(22-31(30(36)37)13-1-2-14-31)21-29(25)24-4-3-5-27(33)18-24/h3-9,18,23,25,29H,1-2,10-17,19-22H2,(H,36,37)/t25-,29+/m0/s1
InChIKeyJLKKIAYYHXNZIY-ABYGYWHVSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01Fc1ccc(cc1)S(=O)(=O)CCC1CCN(CC1)CC1CN(CC2(CCCC2)C(=O)O)CC1c1cccc(F)c1
CACTVS 3.385OC(=O)C1(CCCC1)CN2C[CH](CN3CCC(CC3)CC[S](=O)(=O)c4ccc(F)cc4)[CH](C2)c5cccc(F)c5
OpenEye OEToolkits 2.0.7c1cc(cc(c1)F)C2CN(CC2CN3CCC(CC3)CCS(=O)(=O)c4ccc(cc4)F)CC5(CCCC5)C(=O)O
OpenEye OEToolkits 2.0.7c1cc(cc(c1)F)[C@H]2CN(C[C@@H]2CN3CCC(CC3)CCS(=O)(=O)c4ccc(cc4)F)CC5(CCCC5)C(=O)O
CACTVS 3.385OC(=O)C1(CCCC1)CN2C[C@H](CN3CCC(CC3)CC[S](=O)(=O)c4ccc(F)cc4)[C@H](C2)c5cccc(F)c5
FormulaC31 H40 F2 N2 O4 S
Name1-{[(3S,4S)-3-({4-[2-(4-fluorobenzene-1-sulfonyl)ethyl]piperidin-1-yl}methyl)-4-(3-fluorophenyl)pyrrolidin-1-yl]methyl}cyclopentane-1-carboxylic acid
ChEMBLCHEMBL5280882
DrugBank
ZINC
PDB chain8e5m Chain D Residue 1003 [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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PDB8e5m Discovery of non-boronic acid Arginase 1 inhibitors through virtual screening and biophysical methods.
Resolution1.84 Å
Binding residue
(original residue number in PDB)		D128 T136 S137 H141 G142 D181 D183 V248 V249
Binding residue
(residue number reindexed from 1)		D126 T134 S135 H139 G140 D179 D181 V246 V247
Annotation score1
Enzymatic activity
Enzyme Commision number 3.5.3.1: arginase.
Gene Ontology
Molecular Function
GO:0004053 arginase activity
GO:0005515 protein binding
GO:0016787 hydrolase activity
GO:0016813 hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amidines
GO:0030145 manganese ion binding
GO:0046872 metal ion binding
Biological Process
GO:0000050 urea cycle
GO:0002250 adaptive immune response
GO:0006525 arginine metabolic process
GO:0006527 arginine catabolic process
GO:0009624 response to nematode
GO:0019547 arginine catabolic process to ornithine
GO:0042130 negative regulation of T cell proliferation
GO:0042832 defense response to protozoan
GO:0045087 innate immune response
GO:0046007 negative regulation of activated T cell proliferation
GO:0060336 negative regulation of type II interferon-mediated signaling pathway
GO:0070965 positive regulation of neutrophil mediated killing of fungus
GO:2000552 negative regulation of T-helper 2 cell cytokine production
Cellular Component
GO:0005576 extracellular region
GO:0005615 extracellular space
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0035578 azurophil granule lumen
GO:0035580 specific granule lumen

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8e5m, PDBe:8e5m, PDBj:8e5m
PDBsum8e5m
PubMed36822300
UniProtP05089|ARGI1_HUMAN Arginase-1 (Gene Name=ARG1)

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