Structure of PDB 4p4b Chain A Binding Site BS04

Receptor Information
>4p4b Chain A (length=694) 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
EFSGMPRISKLGSGNDFEVFFQRLGIASGRARYTKNWETNKFSGYPLYHS
VYETYELVEKFYDPMFKYHLTVAQVRGGMVFELANSIVLPFDCRDYAVVL
RKYADKIYSISMKHPQEMKTYSVSFDSLFSAVKNFTEIASKFSERLQDFS
NPIVLRMMNDQLMFLERAFIDPLGLPDRPFYRHVIYAPSSHNKYAGESFP
GIYDALFDIESKVDPSKAWGEVKRQIYVAAFTVQAAAETLSEVA
Ligand information
Ligand ID2G2
InChIInChI=1S/C13H22N3O12P/c14-6(11(20)21)1-3-9(17)15-8(13(24)25)5-28-29(26,27)16-7(12(22)23)2-4-10(18)19/h6-8H,1-5,14H2,(H,15,17)(H,18,19)(H,20,21)(H,22,23)(H,24,25)(H2,16,26,27)/t6-,7-,8-/m0/s1
InChIKeyKSAFNYJPIDGLBS-FXQIFTODSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.9.2C(CC(=O)N[C@@H](COP(=O)(N[C@@H](CCC(=O)O)C(=O)O)O)C(=O)O)[C@@H](C(=O)O)N
OpenEye OEToolkits 1.9.2C(CC(=O)NC(COP(=O)(NC(CCC(=O)O)C(=O)O)O)C(=O)O)C(C(=O)O)N
CACTVS 3.385N[C@@H](CCC(=O)N[C@@H](CO[P](O)(=O)N[C@@H](CCC(O)=O)C(O)=O)C(O)=O)C(O)=O
CACTVS 3.385N[CH](CCC(=O)N[CH](CO[P](O)(=O)N[CH](CCC(O)=O)C(O)=O)C(O)=O)C(O)=O
ACDLabs 12.01O=P(OCC(NC(=O)CCC(C(=O)O)N)C(=O)O)(O)NC(C(=O)O)CCC(=O)O
FormulaC13 H22 N3 O12 P
NameL-gamma-glutamyl-O-[(S)-{[(1S)-1,3-dicarboxypropyl]amino}(hydroxy)phosphoryl]-L-serine
ChEMBLCHEMBL1921897
DrugBank
ZINCZINC000073168864
PDB chain4p4b Chain A Residue 820 [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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PDB4p4b Design of composite inhibitors targeting glutamate carboxypeptidase II: the importance of effector functionalities.
Resolution1.93 Å
Binding residue
(original residue number in PDB)		R210 Y234 N257 D387 E424 E425 L428 G518 N519 R534 R536 S547 Y552 H553 K699 Y700
Binding residue
(residue number reindexed from 1)		R156 Y180 N203 D333 E370 E371 L374 G464 N465 R480 R482 S493 Y498 H499 K643 Y644
Annotation score2
Binding affinityMOAD: ic50=14nM
PDBbind-CN: -logKd/Ki=7.85,IC50=14nM
BindingDB: IC50=14nM
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:4p4b, PDBe:4p4b, PDBj:4p4b
PDBsum4p4b
PubMed26460595
UniProtQ04609|FOLH1_HUMAN Glutamate carboxypeptidase 2 (Gene Name=FOLH1)

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