Structure of PDB 3ff3 Chain A Binding Site BS04

Receptor Information
>3ff3 Chain A (length=689) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SIRWKLVSEMKAENIKSFLRSFTKLPHLAGTEQNFLLAKKIQTQWKKFGL
DSAKLVHYDVLLSYPNETNANYISIVDEHETEIFKTSPPDGYENVTNIVP
PYNAFSAQGMPEGDLVYVNYARTEDFFKLEREMGINCTGKIVIARYGKIF
RGNKVKNAMLAGAIGIILYSDPADYFAPEVQPYPKGWNLPGTAAQRGNVL
NLNGAGDPLTPGYPAKEYTFRLDVEEGVGIPRIPVHPIGYNDAEILLRYL
GGIAPPDKSWKGALNVSYSIGPGFTGSSFRKVRMHVYNINKITRIYNVVG
TIRGSVEPDRYVILGGHRDSWVFGAIDPTSGVAVLQEIARSFGKLMSKGW
RPRRTIIFASWDAEEFGLLGSTEWAEENVKILQERSIAYINSDSSIEGNY
TLRVDCTPLLYQLVYKLTKEIPSPDDGFESKSLYESWLEKDPSPENKNLP
RINKLGSGSDFEAYFQRLGIASGRARYTKNKKTDKYSSYPVYHTIYETFE
LVEKFYDPTFKKQLSVAQLRGALVYELVDSKIIPFNIQDYAEALKNYAAS
IYNLSKKHDQQLTDHGVSFDSLFSAVKNFSEAASDFHKRLIQVDLNNPIA
VRMMNDQLMLLERAFIDPLGLPGKLFYRHIIFAPSSHNKYAGESFPGIYD
AIFDIENKANSRLAWKEVKKHISIAAFTIQAAAGTLKEV
Ligand information
Ligand IDGLU
InChIInChI=1S/C5H9NO4/c6-3(5(9)10)1-2-4(7)8/h3H,1-2,6H2,(H,7,8)(H,9,10)/t3-/m0/s1
InChIKeyWHUUTDBJXJRKMK-VKHMYHEASA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=C(O)C(N)CCC(=O)O
OpenEye OEToolkits 1.7.0C(CC(=O)O)C(C(=O)O)N
OpenEye OEToolkits 1.7.0C(CC(=O)O)[C@@H](C(=O)O)N
CACTVS 3.370N[C@@H](CCC(O)=O)C(O)=O
CACTVS 3.370N[CH](CCC(O)=O)C(O)=O
FormulaC5 H9 N O4
NameGLUTAMIC ACID
ChEMBLCHEMBL575060
DrugBankDB00142
ZINCZINC000001482113
PDB chain3ff3 Chain A Residue 1 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3ff3 Structural insight into the evolutionary and pharmacologic homology of glutamate carboxypeptidases II and III
Resolution1.37 Å
Binding residue
(original residue number in PDB)		R200 N247 E414 G508 Y542 H543 K689 Y690
Binding residue
(residue number reindexed from 1)		R151 N198 E364 G458 Y492 H493 K639 Y640
Annotation score5
Binding affinityPDBbind-CN: -logKd/Ki=3.57,Ki=270uM
Enzymatic activity
Catalytic site (original residue number in PDB) H367 D377 E414 E415
Catalytic site (residue number reindexed from 1) H317 D327 E364 E365
Enzyme Commision number 3.4.17.21: glutamate carboxypeptidase II.
Gene Ontology
Molecular Function
GO:0004180 carboxypeptidase activity
GO:0004181 metallocarboxypeptidase activity
GO:0005515 protein binding
GO:0008236 serine-type peptidase activity
GO:0008237 metallopeptidase activity
GO:0008239 dipeptidyl-peptidase activity
GO:0016805 dipeptidase activity
GO:0046872 metal ion binding
Biological Process
GO:0006508 proteolysis
Cellular Component
GO:0005886 plasma membrane
GO:0016020 membrane

View graph for
Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:3ff3, PDBe:3ff3, PDBj:3ff3
PDBsum3ff3
PubMed19678840
UniProtQ9Y3Q0|NALD2_HUMAN N-acetylated-alpha-linked acidic dipeptidase 2 (Gene Name=NAALAD2)

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