Structure of PDB 3d7h Chain A Binding Site BS04

Receptor Information
>3d7h 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 IDYC2
InChIInChI=1S/C19H24IN3O8/c20-12-6-4-11(5-7-12)16(26)21-10-2-1-3-13(17(27)28)22-19(31)23-14(18(29)30)8-9-15(24)25/h4-7,13-14H,1-3,8-10H2,(H,21,26)(H,24,25)(H,27,28)(H,29,30)(H2,22,23,31)/t13-,14-/m0/s1
InChIKeyROXRILBFJQYPNZ-KBPBESRZSA-N
SMILES
SoftwareSMILES
CACTVS 3.341OC(=O)CC[CH](NC(=O)N[CH](CCCCNC(=O)c1ccc(I)cc1)C(O)=O)C(O)=O
ACDLabs 10.04O=C(c1ccc(I)cc1)NCCCCC(C(=O)O)NC(=O)NC(C(=O)O)CCC(=O)O
OpenEye OEToolkits 1.5.0c1cc(ccc1C(=O)NCCCC[C@@H](C(=O)O)NC(=O)N[C@@H](CCC(=O)O)C(=O)O)I
CACTVS 3.341OC(=O)CC[C@H](NC(=O)N[C@@H](CCCCNC(=O)c1ccc(I)cc1)C(O)=O)C(O)=O
OpenEye OEToolkits 1.5.0c1cc(ccc1C(=O)NCCCCC(C(=O)O)NC(=O)NC(CCC(=O)O)C(=O)O)I
FormulaC19 H24 I N3 O8
NameN-{[(1S)-1-carboxy-5-{[(4-iodophenyl)carbonyl]amino}pentyl]carbamoyl}-L-glutamic acid;
(S)-2-(3-((S)-1-carboxy-(4-iodobenzamido)pentyl)ureido)pentanedioic acid
ChEMBLCHEMBL510924
DrugBank
ZINCZINC000039112304
PDB chain3d7h Chain A Residue 1 [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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PDB3d7h Interactions between Human Glutamate Carboxypeptidase II and Urea-Based Inhibitors: Structural Characterization
Resolution1.55 Å
Binding residue
(original residue number in PDB)		R210 E424 R463 D465 G518 N519 R534 R536 F546 Y552 H553 K699 Y700
Binding residue
(residue number reindexed from 1)		R156 E370 R409 D411 G464 N465 R480 R482 F492 Y498 H499 K643 Y644
Annotation score1
Binding affinityMOAD: ic50=0.06nM
PDBbind-CN: -logKd/Ki=10.22,IC50=0.06nM
BindingDB: Ki=0.01nM,IC50=0.021000nM
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:3d7h, PDBe:3d7h, PDBj:3d7h
PDBsum3d7h
PubMed19053759
UniProtQ04609|FOLH1_HUMAN Glutamate carboxypeptidase 2 (Gene Name=FOLH1)

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