Structure of PDB 5ely Chain A Binding Site BS04

Receptor Information
>5ely Chain A (length=682) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KHNMKAFLDELKAENIKKFLYNFTQIPHLAGTEQNFQLAKQIQSQWKEFG
LDSVELAHYDVLLSYPNKTHPNYISIINEIFNTSLFEPPPPGYENVSDIV
PPFSAFSPQGMPEGDLVYVNYARTEDFFKLERDMKINCSGKIVIARYGKV
FRGNKVKNAQLAGAKGVILYSDPADYFAPGVKSYPDGWNLPGGGVQRGNI
LNLNGAGDPLTPGYPANEYAYRRGIAEAVGLPSIPVHPIGYYDAQKLLEK
MGGSAPPDSSWRGSLKVPYNVGPGFTGNFSTQKVKMHIHSTNEVTRIYNV
IGTLRGAVEPDRYVILGGHRDSWVFGGIDPQSGAAVVHEIVRSFGTLKKE
GWRPRRTILFASWDAEEFGLLGSTEWAEENSRLLQERGVAYINADSSIEG
NYTLRVDCTPLMYSLVHNLTKELKSPDEGFEGKSLYESWTKKSPSPEFSG
MPRISKLGSGNDFEVFFQRLGIASGRARYTKNWETGYPLYHSVYETYELV
EKFYDPMFKYHLTVAQVRGGMVFELANSIVLPFDCRDYAVVLRKYADKIY
SISMKHPQEMKTYSVSFDSLFSAVKNFTEIASKFSERLQDFSNPIVLRMM
NDQLMFLERAFIDPLGLPDRPFYRHVIYAPSSHNESFPGIYDALFDIESK
VDPSKAWGEVKRQIYVAAFTVQAAAETLSEVA
Ligand information
Ligand ID5PU
InChIInChI=1S/C13H15NO6/c15-11(14-20)6-5-10(13(18)19)7-8-1-3-9(4-2-8)12(16)17/h1-4,10,20H,5-7H2,(H,14,15)(H,16,17)(H,18,19)/t10-/m1/s1
InChIKeyVUDGMYIWOPKVSL-SNVBAGLBSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.4c1cc(ccc1CC(CCC(=O)NO)C(=O)O)C(=O)O
CACTVS 3.385ONC(=O)CC[CH](Cc1ccc(cc1)C(O)=O)C(O)=O
CACTVS 3.385ONC(=O)CC[C@H](Cc1ccc(cc1)C(O)=O)C(O)=O
OpenEye OEToolkits 2.0.4c1cc(ccc1C[C@@H](CCC(=O)NO)C(=O)O)C(=O)O
FormulaC13 H15 N O6
Name4-[(2~{R})-2-carboxy-5-(oxidanylamino)-5-oxidanylidene-pentyl]benzoic acid;
JHU242
ChEMBLCHEMBL3818203
DrugBank
ZINCZINC000003818088
PDB chain5ely Chain A Residue 817 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5ely Unprecedented Binding Mode of Hydroxamate-Based Inhibitors of Glutamate Carboxypeptidase II: Structural Characterization and Biological Activity.
Resolution1.81 Å
Binding residue
(original residue number in PDB)		Y234 H377 D387 E424 E425 D453 R534 G548 Y552 H553
Binding residue
(residue number reindexed from 1)		Y176 H319 D329 E366 E367 D395 R476 G486 Y490 H491
Annotation score1
Binding affinityMOAD: ic50=44nM
PDBbind-CN: -logKd/Ki=7.36,IC50=44nM
BindingDB: IC50=44nM
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

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5ely, PDBe:5ely, PDBj:5ely
PDBsum5ely
PubMed27074627
UniProtQ04609|FOLH1_HUMAN Glutamate carboxypeptidase 2 (Gene Name=FOLH1)

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