Structure of PDB 6v7d Chain F Binding Site BS03

Receptor Information
>6v7d Chain F (length=319) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SAKSRTIGIIGAPFSKGQPRGGVEEGPTVLRKAGLLEKLKEQECDVKDYG
DLPFADIPNDSPFQIVKNPRSVGKASEQLAGKVAEVKKNGRISLVLGGDH
SLAIGSISGHARVHPDLGVIWVDAHTDINTPLTTTSGNLHGQPVSFLLKE
LKGKIPDVPGFSWVTPCISAKDIVYIGLRDVDPGEHYILKTLGIKYFSMT
EVDRLGIGKVMEETLSYLLGRKKRPIHLSFDVDGLDPSFTPATGTPVVGG
LTYREGLYITEEIYKTGLLSGLDIMEVNPSLGKTPEEVTRTVNTAVAITL
ACFGLAREGNHKPIDYLNP
Ligand information
Ligand IDQR4
InChIInChI=1S/C11H22BN2O5/c13-11(10(15)16)7(2-1-4-12(17,18)19)6-9-8(11)3-5-14-9/h7-9,14,17-19H,1-6,13H2,(H,15,16)/q-1/p+2/t7-,8+,9+,11+/m0/s1
InChIKeyZNCURAYGFUECIT-YSSBGUOXSA-P
SMILES
SoftwareSMILES
CACTVS 3.385[NH3+][C@@]1([C@@H](CCC[B-](O)(O)O)C[C@H]2[NH2+]CC[C@@H]12)C(O)=O
OpenEye OEToolkits 2.0.7[B-](CCCC1CC2C(C1(C(=O)O)[NH3+])CC[NH2+]2)(O)(O)O
OpenEye OEToolkits 2.0.7[B-](CCC[C@H]1C[C@@H]2[C@H]([C@]1(C(=O)O)[NH3+])CC[NH2+]2)(O)(O)O
CACTVS 3.385[NH3+][C]1([CH](CCC[B-](O)(O)O)C[CH]2[NH2+]CC[CH]12)C(O)=O
ACDLabs 12.01O=C(C1(C2C(CC1CCC[B-](O)(O)O)[NH2+]CC2)[NH3+])O
FormulaC11 H24 B N2 O5
Name{3-[(3aR,4R,5S,6aR)-4-azaniumyl-4-carboxyoctahydrocyclopenta[b]pyrrol-1-ium-5-yl]propyl}(trihydroxy)borate(1-)
ChEMBL
DrugBank
ZINC
PDB chain6v7d Chain F 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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PDB6v7d Discovery and Optimization of Rationally Designed Bicyclic Inhibitors of Human Arginase to Enhance Cancer Immunotherapy.
Resolution1.82 Å
Binding residue
(original residue number in PDB)		D124 H126 D128 N130 S137 H141 G142 D183 D232 D234 T246
Binding residue
(residue number reindexed from 1)		D123 H125 D127 N129 S136 H140 G141 D182 D231 D233 T245
Annotation score1
Binding affinityMOAD: ic50=22nM
Enzymatic activity
Catalytic site (original residue number in PDB) H101 D124 H126 D128 H141 D232 D234 E277
Catalytic site (residue number reindexed from 1) H100 D123 H125 D127 H140 D231 D233 E276
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
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Cellular Component
External links
PDB RCSB:6v7d, PDBe:6v7d, PDBj:6v7d
PDBsum6v7d
PubMed32292567
UniProtP05089|ARGI1_HUMAN Arginase-1 (Gene Name=ARG1)

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