Structure of PDB 4jyw Chain A Binding Site BS04

Receptor Information
>4jyw 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 IDT57
InChIInChI=1S/C28H40FN4O14P/c29-18-9-7-17(8-10-18)25(38)30-15-3-1-2-6-22(34)32-20(27(41)42)11-13-23(35)31-19(26(39)40)5-4-16-47-48(45,46)33-21(28(43)44)12-14-24(36)37/h7-10,19-21H,1-6,11-16H2,(H,30,38)(H,31,35)(H,32,34)(H,36,37)(H,39,40)(H,41,42)(H,43,44)(H2,33,45,46)/t19-,20-,21-/m0/s1
InChIKeyIZLOSIXADNUSCM-ACRUOGEOSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6c1cc(ccc1C(=O)NCCCCCC(=O)NC(CCC(=O)NC(CCCOP(=O)(NC(CCC(=O)O)C(=O)O)O)C(=O)O)C(=O)O)F
OpenEye OEToolkits 1.7.6c1cc(ccc1C(=O)NCCCCCC(=O)N[C@@H](CCC(=O)N[C@@H](CCCOP(=O)(N[C@@H](CCC(=O)O)C(=O)O)O)C(=O)O)C(=O)O)F
CACTVS 3.370OC(=O)CC[CH](N[P](O)(=O)OCCC[CH](NC(=O)CC[CH](NC(=O)CCCCCNC(=O)c1ccc(F)cc1)C(O)=O)C(O)=O)C(O)=O
ACDLabs 12.01O=C(c1ccc(F)cc1)NCCCCCC(=O)NC(C(=O)O)CCC(=O)NC(C(=O)O)CCCOP(=O)(O)NC(C(=O)O)CCC(=O)O
CACTVS 3.370OC(=O)CC[C@H](N[P](O)(=O)OCCC[C@H](NC(=O)CC[C@H](NC(=O)CCCCCNC(=O)c1ccc(F)cc1)C(O)=O)C(O)=O)C(O)=O
FormulaC28 H40 F N4 O14 P
NameN-{6-[(4-fluorobenzoyl)amino]hexanoyl}-L-gamma-glutamyl-5-{[(S)-{[(1S)-1,3-dicarboxypropyl]amino}(hydroxy)phosphoryl]oxy}-L-norvaline
ChEMBLCHEMBL3427435
DrugBankDB14965
ZINCZINC000098209433
PDB chain4jyw 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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PDB4jyw A high affinity 18F-labeled phosphoramidate peptidomimetic inhibitor as a PSMA-targeted PET imaging agent for prostate cancer
Resolution1.73 Å
Binding residue
(original residue number in PDB)		R210 N257 D387 E424 E425 L428 R463 S501 R511 S513 G518 R536 K539 W541 Y552 H553 N698 K699 Y700 A701
Binding residue
(residue number reindexed from 1)		R156 N203 D333 E370 E371 L374 R409 S447 R457 S459 G464 R482 K485 W487 Y498 H499 N642 K643 Y644 A645
Annotation score1
Binding affinityBindingDB: IC50=400nM
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:4jyw, PDBe:4jyw, PDBj:4jyw
PDBsum4jyw
PubMed
UniProtQ04609|FOLH1_HUMAN Glutamate carboxypeptidase 2 (Gene Name=FOLH1)

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