Structure of PDB 3d7d Chain A Binding Site BS04

Receptor Information
>3d7d 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 IDFBD
InChIInChI=1S/C16H19FN2O7S/c17-10-3-1-9(2-4-10)7-27-8-12(15(24)25)19-16(26)18-11(14(22)23)5-6-13(20)21/h1-4,11-12H,5-8H2,(H,20,21)(H,22,23)(H,24,25)(H2,18,19,26)/t11-,12-/m0/s1
InChIKeyIDTMSHGCAZPVLC-RYUDHWBXSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1cc(ccc1CSC[C@@H](C(=O)O)NC(=O)N[C@@H](CCC(=O)O)C(=O)O)F
OpenEye OEToolkits 1.5.0c1cc(ccc1CSCC(C(=O)O)NC(=O)NC(CCC(=O)O)C(=O)O)F
CACTVS 3.341OC(=O)CC[CH](NC(=O)N[CH](CSCc1ccc(F)cc1)C(O)=O)C(O)=O
ACDLabs 10.04Fc1ccc(cc1)CSCC(C(=O)O)NC(=O)NC(C(=O)O)CCC(=O)O
CACTVS 3.341OC(=O)CC[C@H](NC(=O)N[C@@H](CSCc1ccc(F)cc1)C(O)=O)C(O)=O
FormulaC16 H19 F N2 O7 S
NameN-({(1R)-1-carboxy-2-[(4-fluorobenzyl)sulfanyl]ethyl}carbamoyl)-L-glutamic acid;
(S)-2-(3-((R)-1-carboxy-2-(4-fluorobenzylthio)ethyl)ureido)pentanedioic acid
ChEMBLCHEMBL1232667
DrugBankDB07754
ZINCZINC000039111997
PDB chain3d7d 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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PDB3d7d Interactions between Human Glutamate Carboxypeptidase II and Urea-Based Inhibitors: Structural Characterization
Resolution1.69 Å
Binding residue
(original residue number in PDB)		R210 N257 E424 L428 E457 R463 G518 N519 R534 R536 Y552 H553 K699 Y700
Binding residue
(residue number reindexed from 1)		R156 N203 E370 L374 E403 R409 G464 N465 R480 R482 Y498 H499 K643 Y644
Annotation score1
Binding affinityMOAD: ic50=14nM
PDBbind-CN: -logKd/Ki=7.85,IC50=14nM
BindingDB: Ki=50.0nM
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

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Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:3d7d, PDBe:3d7d, PDBj:3d7d
PDBsum3d7d
PubMed19053759
UniProtQ04609|FOLH1_HUMAN Glutamate carboxypeptidase 2 (Gene Name=FOLH1)

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