Structure of PDB 4oc3 Chain A Binding Site BS04

Receptor Information
>4oc3 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 ID2QP
InChIInChI=1S/C21H24IN3O7/c22-14-8-6-13(7-9-14)18(26)23-10-2-1-5-16(19(27)28)24-21(31)25-17(20(29)30)12-15-4-3-11-32-15/h3-4,6-9,11,16-17H,1-2,5,10,12H2,(H,23,26)(H,27,28)(H,29,30)(H2,24,25,31)/t16-,17-/m0/s1
InChIKeyXDHPABCLBICMJM-IRXDYDNUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6c1cc(oc1)C[C@@H](C(=O)O)NC(=O)N[C@@H](CCCCNC(=O)c2ccc(cc2)I)C(=O)O
OpenEye OEToolkits 1.7.6c1cc(oc1)CC(C(=O)O)NC(=O)NC(CCCCNC(=O)c2ccc(cc2)I)C(=O)O
CACTVS 3.385OC(=O)[C@H](CCCCNC(=O)c1ccc(I)cc1)NC(=O)N[C@@H](Cc2occc2)C(O)=O
CACTVS 3.385OC(=O)[CH](CCCCNC(=O)c1ccc(I)cc1)NC(=O)N[CH](Cc2occc2)C(O)=O
ACDLabs 12.01Ic1ccc(cc1)C(=O)NCCCCC(C(=O)O)NC(=O)NC(C(=O)O)Cc2occc2
FormulaC21 H24 I N3 O7
NameN~2~-{[(1S)-1-carboxy-2-(furan-2-yl)ethyl]carbamoyl}-N~6~-(4-iodobenzoyl)-L-lysine
ChEMBLCHEMBL604257
DrugBank
ZINCZINC000049766737
PDB chain4oc3 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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PDB4oc3 Structural characterization of P1'-diversified urea-based inhibitors of glutamate carboxypeptidase II.
Resolution1.79 Å
Binding residue
(original residue number in PDB)		F209 R210 N257 E424 L428 R463 D465 G518 N519 R534 R536 Y552 H553 K699 Y700
Binding residue
(residue number reindexed from 1)		F155 R156 N203 E370 L374 R409 D411 G464 N465 R480 R482 Y498 H499 K643 Y644
Annotation score1
Binding affinityMOAD: Ki=5.3nM
PDBbind-CN: -logKd/Ki=8.28,Ki=5.3nM
BindingDB: Ki=5.3nM
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:4oc3, PDBe:4oc3, PDBj:4oc3
PDBsum4oc3
PubMed24731280
UniProtQ04609|FOLH1_HUMAN Glutamate carboxypeptidase 2 (Gene Name=FOLH1)

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