Structure of PDB 4ngm Chain A Binding Site BS04

Receptor Information
>4ngm Chain A (length=696) 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
RKYADKIYSISMKHPQEMKTYSVSFDSLFSAVKNFTEIASKFSERLQDFD
KSNPIVLRMMNDQLMFLERAFIDPLGLPDRPFYRHVIYAPSSHNKYAGES
FPGIYDALFDIESKVDPSKAWGEVKRQIYVAAFTVQAAAETLSEVA
Ligand information
Ligand IDJB7
InChIInChI=1S/C21H28BrN3O8/c1-13(26)25(12-14-5-7-15(22)8-6-14)11-3-2-4-16(19(29)30)23-21(33)24-17(20(31)32)9-10-18(27)28/h5-8,16-17H,2-4,9-12H2,1H3,(H,27,28)(H,29,30)(H,31,32)(H2,23,24,33)/t16-,17-/m0/s1
InChIKeyARLQMQGVVFXZCW-IRXDYDNUSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CC(=O)N(CCCC[CH](NC(=O)N[CH](CCC(O)=O)C(O)=O)C(O)=O)Cc1ccc(Br)cc1
CACTVS 3.385CC(=O)N(CCCC[C@H](NC(=O)N[C@@H](CCC(O)=O)C(O)=O)C(O)=O)Cc1ccc(Br)cc1
ACDLabs 12.01Brc1ccc(cc1)CN(C(=O)C)CCCCC(C(=O)O)NC(=O)NC(C(=O)O)CCC(=O)O
OpenEye OEToolkits 1.7.6CC(=O)N(CCCCC(C(=O)O)NC(=O)NC(CCC(=O)O)C(=O)O)Cc1ccc(cc1)Br
OpenEye OEToolkits 1.7.6CC(=O)N(CCCC[C@@H](C(=O)O)NC(=O)N[C@@H](CCC(=O)O)C(=O)O)Cc1ccc(cc1)Br
FormulaC21 H28 Br N3 O8
NameN-({(1S)-5-[acetyl(4-bromobenzyl)amino]-1-carboxypentyl}carbamoyl)-L-glutamic acid;
(S)-2-(3-((S)-5-(N-(4-bromobenzyl)acetamido)-1-carboxypentyl)ureido)pentanedioic acid
ChEMBLCHEMBL3309678
DrugBank
ZINCZINC000098209039
PDB chain4ngm Chain A Residue 821 [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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PDB4ngm Rational design of urea-based glutamate carboxypeptidase II (GCPII) inhibitors as versatile tools for specific drug targeting and delivery.
Resolution1.84 Å
Binding residue
(original residue number in PDB)		G206 K207 R210 E424 L428 G518 N519 R536 F546 S547 G548 Y552 H553 K699 Y700 A701
Binding residue
(residue number reindexed from 1)		G152 K153 R156 E370 L374 G464 N465 R482 F492 S493 G494 Y498 H499 K645 Y646 A647
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=10.35,Ki=0.0449nM
BindingDB: Ki=0.044900nM
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:4ngm, PDBe:4ngm, PDBj:4ngm
PDBsum4ngm
PubMed24954515
UniProtQ04609|FOLH1_HUMAN Glutamate carboxypeptidase 2 (Gene Name=FOLH1)

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