Structure of PDB 4ome Chain A Binding Site BS04

Receptor Information
>4ome 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
LKKEGWRPRRTILFASWDAEEFGLLGSTEWAEENSRLLQERGVAYINADS
SIEGNYTLRVDCTPLMYSLVHNLTKELKSPDEGFEGKSLYESWTKKSPSP
EFSGMPRISKLGSGNDFEVFFQRLGIASGRARYTKNWETFSGYPLYHSVY
ETYELVEKFYDPMFKYHLTVAQVRGGMVFELANSIVLPFDCRDYAVVLRK
YADKIYSISMKHPQEMKTYSVSFDSLFSAVKNFTEIASKFSERLQDFSNP
IVLRMMNDQLMFLERAFIDPLGLPDRPFYRHVIYAPSSHNKYAGESFPGI
YDALFDIESKVDPSKAWGEVKRQIYVAAFTVQAAAETLSEVA
Ligand information
Ligand IDDGQ
InChIInChI=1S/C15H31B10N3O8/c29-9(30)5-4-8(11(33)34)28-13(36)27-7(10(31)32)3-1-2-6-26-12(35)15-14-16(15)18(14)19(14)17(14,15)21(15)20(15,16)22(16,18)24(18,19)23(17,19,21)25(20,21,22)24/h7-8,14,16-25H,1-6H2,(H,26,35)(H,29,30)(H,31,32)(H,33,34)(H2,27,28,36)/t7-,8-/m0/s1
InChIKeyNYWNLUFFIRQESZ-YUMQZZPRSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6[BH]1234[BH]567[BH]189[BH]212[BH]33%10[BH]454[BH]656[BH]787[BH]911[CH]232[BH]4%105C7612C(=O)NCCCC[C@@H](C(=O)O)NC(=O)N[C@@H](CCC(=O)O)C(=O)O
CACTVS 3.385OC(=O)CC[CH](NC(=O)N[CH](CCCCNC(=O)[C]1234[BH]567[BH]89%10[BH]%11%12%13[BH]58%14[BH]%11%15%16[BH]%12%17%18[BH]9%13%19[BH]16%10[BH]2%17%19[CH]3%15%18[BH]47%14%16)C(O)=O)C(O)=O
OpenEye OEToolkits 1.7.6[BH]1234[BH]567[BH]189[BH]212[BH]33%10[BH]454[BH]656[BH]787[BH]911[CH]232[BH]4%105C7612C(=O)NCCCCC(C(=O)O)NC(=O)NC(CCC(=O)O)C(=O)O
CACTVS 3.385OC(=O)CC[C@H](NC(=O)N[C@@H](CCCCNC(=O)[C]1234[BH]567[BH]89%10[BH]%11%12%13[BH]58%14[BH]%11%15%16[BH]%12%17%18[BH]9%13%19[BH]16%10[BH]2%17%19[CH]3%15%18[BH]47%14%16)C(O)=O)C(O)=O
FormulaC15 H31 B10 N3 O8
Name(S)-2-(3-((S)-1-carboxy-5-(1,2-dicarba-closo-dodecarboranylamido) pentyl)ureido)pentanedioic acid;
DCCBL
ChEMBL
DrugBank
ZINC
PDB chain4ome Chain A Residue 819 [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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PDB4ome X-ray structure of human glutamate carboxypeptidase II in complex with DCCBL, a urea based inhibitor with distal carborane moiety
Resolution1.79 Å
Binding residue
(original residue number in PDB)		K207 R210 E424 L428 G518 N519 R536 W541 Y552 H553 K699 Y700
Binding residue
(residue number reindexed from 1)		K153 R156 E370 L374 G464 N465 R482 W487 Y496 H497 K641 Y642
Annotation score1
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:4ome, PDBe:4ome, PDBj:4ome
PDBsum4ome
PubMed
UniProtQ04609|FOLH1_HUMAN Glutamate carboxypeptidase 2 (Gene Name=FOLH1)

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