Structure of PDB 4oc4 Chain A Binding Site BS04

Receptor Information
>4oc4 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
LDSVELAHYDVLLSYPNKTHPNYISIINEDGNEIFNTSLFEPPPPGYNVS
DIVPPFSAFSPQGMPEGDLVYVNYARTEDFFKLERDMKINCSGKIVIARY
GKVFRGNKVKNAQLAGAKGVILYSDPADYFAPGVKSYPDGWNLPGGGVQR
GNILNLNGAGDPLTPGYPANEYAYRRGIAEAVGLPSIPVHPIGYYDAQKL
LEKMGGSAPPDSSWRGSLKVPYNVGPGFTGNFSTQKVKMHIHSTNEVTRI
YNVIGTLRGAVEPDRYVILGGHRDSWVFGGIDPQSGAAVVHEIVRSFGTL
KKEGWRPRRTILFASWDAEEFGLLGSTEWAEENSRLLQERGVAYINADSS
IEGNYTLRVDCTPLMYSLVHNLTKELKSPDEGFEGKSLYESWTKKSPSPE
FSGMPRISKLGSGNDFEVFFQRLGIASGRARYTKNNKFSGYPLYHSVYET
YELVEKFYDPMFKYHLTVAQVRGGMVFELANSIVLPFDCRDYAVVLRKYA
DKIYSISMKHPQEMKTYSVSFDSLFSAVKNFTEIASKFSERLQDFSNPIV
LRMMNDQLMFLERAFIDPLGLPDRPFYRHVIYAPSSHNKYAGESFPGIYD
ALFDIESKVDPSKAWGEVKRQIYVAAFTVQAAAETLSEVA
Ligand information
Ligand ID2QN
InChIInChI=1S/C22H25IN4O6/c23-16-6-4-15(5-7-16)19(28)25-10-2-1-3-17(20(29)30)26-22(33)27-18(21(31)32)13-14-8-11-24-12-9-14/h4-9,11-12,17-18H,1-3,10,13H2,(H,25,28)(H,29,30)(H,31,32)(H2,26,27,33)/t17-,18-/m0/s1
InChIKeyAHYKHJQLXJPPOS-ROUUACIJSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6c1cc(ccc1C(=O)NCCCCC(C(=O)O)NC(=O)NC(Cc2ccncc2)C(=O)O)I
ACDLabs 12.01Ic1ccc(cc1)C(=O)NCCCCC(C(=O)O)NC(=O)NC(C(=O)O)Cc2ccncc2
OpenEye OEToolkits 1.7.6c1cc(ccc1C(=O)NCCCC[C@@H](C(=O)O)NC(=O)N[C@@H](Cc2ccncc2)C(=O)O)I
CACTVS 3.385OC(=O)[CH](CCCCNC(=O)c1ccc(I)cc1)NC(=O)N[CH](Cc2ccncc2)C(O)=O
CACTVS 3.385OC(=O)[C@H](CCCCNC(=O)c1ccc(I)cc1)NC(=O)N[C@@H](Cc2ccncc2)C(O)=O
FormulaC22 H25 I N4 O6
NameN~2~-{[(1S)-1-carboxy-2-(pyridin-4-yl)ethyl]carbamoyl}-N~6~-(4-iodobenzoyl)-L-lysine
ChEMBLCHEMBL593331
DrugBank
ZINCZINC000049757101
PDB chain4oc4 Chain A Residue 818 [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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PDB4oc4 Structural characterization of P1'-diversified urea-based inhibitors of glutamate carboxypeptidase II.
Resolution1.66 Å
Binding residue
(original residue number in PDB)		F209 R210 E424 L428 R463 D465 G518 N519 R534 R536 F546 Y552 H553 K699 Y700
Binding residue
(residue number reindexed from 1)		F154 R155 E369 L373 R408 D410 G463 N464 R479 R481 F488 Y494 H495 K639 Y640
Annotation score1
Binding affinityMOAD: Ki=105nM
PDBbind-CN: -logKd/Ki=6.98,Ki=105nM
BindingDB: Ki=105nM
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:4oc4, PDBe:4oc4, PDBj:4oc4
PDBsum4oc4
PubMed24731280
UniProtQ04609|FOLH1_HUMAN Glutamate carboxypeptidase 2 (Gene Name=FOLH1)

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