Structure of PDB 4p45 Chain A Binding Site BS05

Receptor Information
>4p45 Chain A (length=690) 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
EFSGMPRISKLGSGNDFEVFFQRLGIASGRARYTKNWETGYPLYHSVYET
YELVEKFYDPMFKYHLTVAQVRGGMVFELANSIVLPFDCRDYAVVLRKYA
DKIYSISMKHPQEMKTYSVSFDSLFSAVKNFTEIASKFSERLQDFSNPIV
LRMMNDQLMFLERAFIDPLGLPDRPFYRHVIYAPSSHNKYAGESFPGIYD
ALFDIESKVDPSKAWGEVKRQIYVAAFTVQAAAETLSEVA
Ligand information
Ligand ID2F9
InChIInChI=1S/C20H27FN3O11P/c1-10(2)16(23-17(27)11-3-5-12(21)6-4-11)18(28)22-14(20(31)32)9-35-36(33,34)24-13(19(29)30)7-8-15(25)26/h3-6,10,13-14,16H,7-9H2,1-2H3,(H,22,28)(H,23,27)(H,25,26)(H,29,30)(H,31,32)(H2,24,33,34)/t13-,14-,16-/m0/s1
InChIKeyOEWFGJXRSPYZTR-DZKIICNBSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CC(C)[C@H](NC(=O)c1ccc(F)cc1)C(=O)N[C@@H](CO[P](O)(=O)N[C@@H](CCC(O)=O)C(O)=O)C(O)=O
OpenEye OEToolkits 1.9.2CC(C)C(C(=O)NC(COP(=O)(NC(CCC(=O)O)C(=O)O)O)C(=O)O)NC(=O)c1ccc(cc1)F
OpenEye OEToolkits 1.9.2CC(C)[C@@H](C(=O)N[C@@H](COP(=O)(N[C@@H](CCC(=O)O)C(=O)O)O)C(=O)O)NC(=O)c1ccc(cc1)F
CACTVS 3.385CC(C)[CH](NC(=O)c1ccc(F)cc1)C(=O)N[CH](CO[P](O)(=O)N[CH](CCC(O)=O)C(O)=O)C(O)=O
ACDLabs 12.01O=C(c1ccc(F)cc1)NC(C(=O)NC(C(=O)O)COP(=O)(O)NC(C(=O)O)CCC(=O)O)C(C)C
FormulaC20 H27 F N3 O11 P
NameN-(4-fluorobenzoyl)-L-valyl-O-[(S)-{[(1S)-1,3-dicarboxypropyl]amino}(hydroxy)phosphoryl]-L-serine
ChEMBL
DrugBank
ZINCZINC000214699457
PDB chain4p45 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

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PDB4p45 Design of composite inhibitors targeting glutamate carboxypeptidase II: the importance of effector functionalities.
Resolution1.87 Å
Binding residue
(original residue number in PDB)		R210 D387 E424 E425 L428 G518 N519 R534 G548 Y552 H553 N698 K699 Y700 A701
Binding residue
(residue number reindexed from 1)		R156 D333 E370 E371 L374 G464 N465 R480 G490 Y494 H495 N638 K639 Y640 A641
Annotation score1
Binding affinityMOAD: ic50=16nM
PDBbind-CN: -logKd/Ki=7.80,IC50=16nM
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:4p45, PDBe:4p45, PDBj:4p45
PDBsum4p45
PubMed26460595
UniProtQ04609|FOLH1_HUMAN Glutamate carboxypeptidase 2 (Gene Name=FOLH1)

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