Structure of PDB 2jbj Chain A Binding Site BS04

Receptor Information
>2jbj Chain A (length=687) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NMKAFLDELKAENIKKFLYNFTQIPHLAGTEQNFQLAKQIQSQWKEFGLD
SVELAHYDVLLSYPNKTHPNYISIINEDGNEIFNTSLFEPPPPGYENVSD
IVPPFSAFSPQGMPEGDLVYVNYARTEDFFKLERDMKINCSGKIVIARYG
KVFRGNKVKNAQLAGAKGVILYSDPADYFAPGVKSYPDGWNLPGGGVQRG
NILNLNGAGDPLTPGYPANEYAYRRGIAEAVGLPSIPVHPIGYYDAQKLL
EKMGGSAPPDSSWRGSLKVPYNVGPGFTFSTQKVKMHIHSTNEVTRIYNV
IGTLRGAVEPDRYVILGGHRDSWVFGGIDPQSGAAVVHEIVRSFGTLKKE
GWRPRRTILFASWDAEEFGLLGSTEWAEENSRLLQERGVAYINADSSIEG
NYTLRVDCTPLMYSLVHNLTKELKSPDEGFEGKSLYESWTKKSPSPEFSG
MPRISKLGSGNDFEVFFQRLGIASGRARYTKNFSGYPLYHSVYETYELVE
KFYDPMFKYHLTVAQVRGGMVFELANSIVLPFDCRDYAVVLRKYADKIYS
ISMKHPQEMKTYSVSFDSLFSAVKNFTEIASKFSERLQDFDKSNPIVLRM
MNDQLMFLERAFIDPLGLPDRPFYRHVIYAPSSHNKYAGESFPGIYDALF
DIESKVDPSKAWGEVKRQIYVAAFTVQAAAETLSEVA
Ligand information
Ligand IDG88
InChIInChI=1S/C6H11O7P/c7-5(8)2-1-4(6(9)10)3-14(11,12)13/h4H,1-3H2,(H,7,8)(H,9,10)(H2,11,12,13)/t4-/m1/s1
InChIKeyISEYJGQFXSTPMQ-SCSAIBSYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C(CC(=O)O)C(CP(=O)(O)O)C(=O)O
CACTVS 3.341OC(=O)CC[CH](C[P](O)(O)=O)C(O)=O
ACDLabs 10.04O=P(O)(O)CC(C(=O)O)CCC(=O)O
OpenEye OEToolkits 1.5.0C(CC(=O)O)[C@H](CP(=O)(O)O)C(=O)O
CACTVS 3.341OC(=O)CC[C@H](C[P](O)(O)=O)C(O)=O
FormulaC6 H11 O7 P
Name(2S)-2-(PHOSPHONOMETHYL)PENTANEDIOIC ACID
ChEMBLCHEMBL189217
DrugBank
ZINCZINC000013470225
PDB chain2jbj Chain A Residue 1768 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2jbj Human Glutamate Carboxypeptidase II Inhibition: Structures of Gcpii in Complex with Two Potent Inhibitors, Quisqualate and 2-Pmpa.
Resolution2.19 Å
Binding residue
(original residue number in PDB)		R210 N257 D387 E424 E425 D453 G518 Y552 H553 K699 Y700
Binding residue
(residue number reindexed from 1)		R154 N201 D329 E366 E367 D395 G460 Y489 H490 K636 Y637
Annotation score2
Binding affinityMOAD: Ki=0.2nM
PDBbind-CN: -logKd/Ki=9.70,Ki=0.2nM
BindingDB: Ki=0.280000nM,IC50=300nM,Kd=0.5nM,EC50=0.620000nM
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:2jbj, PDBe:2jbj, PDBj:2jbj
PDBsum2jbj
PubMed17372356
UniProtQ04609|FOLH1_HUMAN Glutamate carboxypeptidase 2 (Gene Name=FOLH1)

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