Structure of PDB 5of0 Chain A Binding Site BS05

Receptor Information
>5of0 Chain A (length=692) 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
EFSGMPRISKLGSGNDFEVFFQRLGIASGRARYTKNWFSGYPLYHSVYET
YELVEKFYDPMFKYHLTVAQVRGGMVFELANSIVLPFDCRDYAVVLRKYA
DKIYSISMKHPQEMKTYSVSFDSLFSAVKNFTEIASKFSERLQDFDKSNP
IVLRMMNDQLMFLERAFIDPLGLPDRPFYRHVIYAPSSHNKYAGESFPGI
YDALFDIESKVDPSKAWGEVKRQIYVAAFTVQAAAETLSEVA
Ligand information
Ligand ID9TB
InChIInChI=1S/C19H24FN3O8/c20-12-6-4-11(5-7-12)10-21-15(24)3-1-2-13(17(27)28)22-19(31)23-14(18(29)30)8-9-16(25)26/h4-7,13-14H,1-3,8-10H2,(H,21,24)(H,25,26)(H,27,28)(H,29,30)(H2,22,23,31)/t13-,14-/m0/s1
InChIKeyZCBCSGACSCSXNO-KBPBESRZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6c1cc(ccc1CNC(=O)CCCC(C(=O)O)NC(=O)NC(CCC(=O)O)C(=O)O)F
OpenEye OEToolkits 2.0.6c1cc(ccc1CNC(=O)CCC[C@@H](C(=O)O)NC(=O)N[C@@H](CCC(=O)O)C(=O)O)F
CACTVS 3.385OC(=O)CC[C@H](NC(=O)N[C@@H](CCCC(=O)NCc1ccc(F)cc1)C(O)=O)C(O)=O
CACTVS 3.385OC(=O)CC[CH](NC(=O)N[CH](CCCC(=O)NCc1ccc(F)cc1)C(O)=O)C(O)=O
FormulaC19 H24 F N3 O8
Name(2~{S})-2-[[(2~{S})-6-[(4-fluorophenyl)methylamino]-1-oxidanyl-1,6-bis(oxidanylidene)hexan-2-yl]carbamoylamino]pentanedioic acid;
CFBzOG
ChEMBLCHEMBL4279502
DrugBank
ZINC
PDB chain5of0 Chain A Residue 822 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB5of0 2-Aminoadipic Acid-C(O)-Glutamate Based Prostate-Specific Membrane Antigen Ligands for Potential Use as Theranostics.
Resolution1.48 Å
Binding residue
(original residue number in PDB)		R210 M424 L428 R463 D465 G518 N519 R534 R536 F546 Y552 H553 K699 Y700
Binding residue
(residue number reindexed from 1)		R156 M370 L374 R409 D411 G464 N465 R480 R482 F488 Y494 H495 K641 Y642
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=8.63,IC50=2.32nM
BindingDB: IC50=2.3nM
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
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5of0, PDBe:5of0, PDBj:5of0
PDBsum5of0
PubMed30429952
UniProtQ04609|FOLH1_HUMAN Glutamate carboxypeptidase 2 (Gene Name=FOLH1)

[Back to BioLiP]