Structure of PDB 6fe5 Chain A Binding Site BS04

Receptor Information
>6fe5 Chain A (length=693) 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
LKKEGWRPRRTILFASWDAMEFGLLGSTEWAEENSRLLQERGVAYINADS
SIEGNYTLRVDCTPLMYSLVHNLTKELKSPDEGFEGKSLYESWTKKSPSP
EFSGMPRISKLGSGNDFEVFFQRLGIASGRARYTKNNKFSGYPLYHSVYE
TYELVEKFYDPMFKYHLTVAQVRGGMVFELANSIVLPFDCRDYAVVLRKY
ADKIYSISMKHPQEMKTYSVSFDSLFSAVKNFTEIASKFSERLQDFDKSN
PIVLRMMNDQLMFLERAFIDPLGLPDRPFYRHVIYAPSSHNKYAGESFPG
IYDALFDIESKVDPSKAWGEVKRQIYVAAFTVQAAAETLSEVA
Ligand information
Ligand IDD6E
InChIInChI=1S/C12H20N2O7/c1-6(2)5-8(11(19)20)14-12(21)13-7(10(17)18)3-4-9(15)16/h6-8H,3-5H2,1-2H3,(H,15,16)(H,17,18)(H,19,20)(H2,13,14,21)/t7-,8-/m0/s1
InChIKeyBSGWCSGMXAVYRT-YUMQZZPRSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6CC(C)CC(C(=O)O)NC(=O)NC(CCC(=O)O)C(=O)O
OpenEye OEToolkits 2.0.6CC(C)C[C@@H](C(=O)O)NC(=O)N[C@@H](CCC(=O)O)C(=O)O
CACTVS 3.385CC(C)C[CH](NC(=O)N[CH](CCC(O)=O)C(O)=O)C(O)=O
CACTVS 3.385CC(C)C[C@H](NC(=O)N[C@@H](CCC(O)=O)C(O)=O)C(O)=O
FormulaC12 H20 N2 O7
Name(2~{S})-2-[[(2~{S})-4-methyl-1-oxidanyl-1-oxidanylidene-pentan-2-yl]carbamoylamino]pentanedioic acid
ChEMBLCHEMBL596351
DrugBank
ZINCZINC000003962955
PDB chain6fe5 Chain A Residue 821 [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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PDB6fe5 Structural and computational basis for potent inhibition of glutamate carboxypeptidase II by carbamate-based inhibitors.
Resolution1.52 Å
Binding residue
(original residue number in PDB)		R210 M424 L428 G518 N519 R534 R536 Y552 H553 K699 Y700
Binding residue
(residue number reindexed from 1)		R156 M370 L374 G464 N465 R480 R482 Y495 H496 K642 Y643
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=9.30,IC50=0.50nM
BindingDB: Ki=0.580000nM,IC50=0.500000nM
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
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6fe5, PDBe:6fe5, PDBj:6fe5
PDBsum6fe5
PubMed30552009
UniProtQ04609|FOLH1_HUMAN Glutamate carboxypeptidase 2 (Gene Name=FOLH1)

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