Structure of PDB 6ety Chain A Binding Site BS04

Receptor Information
>6ety Chain A (length=696) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KHNMKAFLDELKAENIKKFLYNFTQIPHLAGTEQNFQLAKQIQSQWKEFG
LDSVELAHYDVLLSYPNKTHPNYISIINEDGNEIFNTSLFEPPPPGYENV
SDIVPPFSAFSPQGMPEGDLVYVNYARTEDFFKLERDMKINCSGKIVIAR
YGKVFRGNKVKNAQLAGAKGVILYSDPADYFAPGVKSYPDGWNLPGGGVQ
RGNILNLNGAGDPLTPGYPANEYAYRRGIAEAVGLPSIPVHPIGYYDAQK
LLEKMGGSAPPDSSWRGSLKVPYNVGPGFTGNFSTQKVKMHIHSTNEVTR
IYNVIGTLRGAVEPDRYVILGGHRDSWVFGGIDPQSGAAVVHEIVRSFGT
LKKEGWRPRRTILFASWDAEEFGLLGSTEWAEENSRLLQERGVAYINADS
SIEGNYTLRVDCTPLMYSLVHNLTKELKSPDEGFEGKSLYESWTKKSPSP
EFSGMPRISKLGSGNDFEVFFQRLGIASGRARYTKNWETNKFSGYPLYHS
VYETYELVEKFYDPMFKYHLTVAQVRGGMVFELANSIVLPFDCRDYAVVL
RKYADKIYSISMKHPQEMKTYSVSFDSLFSAVKNFTEIASKFSERLQDFD
KSNPIVLRMMNDQLMFLERAFIDPLGLPDRPFYRHVIYAPSSHNKYAGES
FPGIYDALFDIESKVDPSKAWGEVKRQIYVAAFTVQAAAETLSEVA
Ligand information
Ligand IDBXK
InChIInChI=1S/C12H19NO8/c1-6(2)5-7(10(16)17)13-12(20)21-8(11(18)19)3-4-9(14)15/h6-8H,3-5H2,1-2H3,(H,13,20)(H,14,15)(H,16,17)(H,18,19)/t7-,8+/m1/s1
InChIKeyWQDZXAWSGIQGKR-SFYZADRCSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6CC(C)CC(C(=O)O)NC(=O)OC(CCC(=O)O)C(=O)O
CACTVS 3.385CC(C)C[CH](NC(=O)O[CH](CCC(O)=O)C(O)=O)C(O)=O
OpenEye OEToolkits 2.0.6CC(C)C[C@H](C(=O)O)NC(=O)O[C@@H](CCC(=O)O)C(=O)O
CACTVS 3.385CC(C)C[C@@H](NC(=O)O[C@@H](CCC(O)=O)C(O)=O)C(O)=O
FormulaC12 H19 N O8
Name(2~{S})-2-[[(2~{R})-4-methyl-1-oxidanyl-1-oxidanylidene-pentan-2-yl]carbamoyloxy]pentanedioic acid
ChEMBLCHEMBL4473741
DrugBank
ZINC
PDB chain6ety Chain A Residue 820 [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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PDB6ety Structural and computational basis for potent inhibition of glutamate carboxypeptidase II by carbamate-based inhibitors.
Resolution1.68 Å
Binding residue
(original residue number in PDB)		R210 N257 E424 L428 S454 G518 Y552 H553 K699 Y700
Binding residue
(residue number reindexed from 1)		R156 N203 E370 L374 S400 G464 Y498 H499 K645 Y646
Annotation score2
Binding affinityPDBbind-CN: -logKd/Ki=8.05,IC50=8.9nM
BindingDB: IC50=8.9nM
Enzymatic activity
Enzyme Commision number 3.4.17.21: glutamate carboxypeptidase II.
Gene Ontology
Molecular Function
GO:0004180 carboxypeptidase activity
GO:0004181 metallocarboxypeptidase activity
GO:0008233 peptidase activity
GO:0008237 metallopeptidase activity
GO:0016805 dipeptidase activity
GO:0046872 metal ion binding
GO:1904492 Ac-Asp-Glu binding
GO:1904493 tetrahydrofolyl-poly(glutamate) polymer binding
Biological Process
GO:0006508 proteolysis
GO:0006760 folic acid-containing compound metabolic process
GO:0035609 C-terminal protein deglutamylation
Cellular Component
GO:0005737 cytoplasm
GO:0005886 plasma membrane
GO:0009986 cell surface
GO:0016020 membrane
GO:0070062 extracellular exosome

View graph for
Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6ety, PDBe:6ety, PDBj:6ety
PDBsum6ety
PubMed30552009
UniProtQ04609|FOLH1_HUMAN Glutamate carboxypeptidase 2 (Gene Name=FOLH1)

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