Structure of PDB 6y0f Chain D Binding Site BS01

Receptor Information
>6y0f Chain D (length=720) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TMRALTLKDILNGTFSYKTFFPNWISGQEYLHQSADNNIVLYNIETGQSY
TILSNRTMKSVNASNYGLSPDRQFVYLESDYSKLWRYSYTATYYIYDLSN
GEFVRGNELPRPIQYLCWSPVGSKLAYVYQNNIYLKQRPGDPPFQITFNG
RENKIFNGIPDWVYEEEMLATKYALWWSPNGKFLAYAEFNDTDIPVIAYS
YYGDEQYPRTINIPYPKAGAKNPVVRIFIIDTTYPAYVGPQEVPVPAMIA
SSDYYFSWLTWVTDERVCLQWLKRVQNVSVLSICDFREDWQTWDCPKTQE
HIEESRTGWAGGFFVSTPVFSYDAISYYKIFSDKDGYKHIHYIKDTVENA
IQITSGKWEAINIFRVTQDSLFYSSNEFEEYPGRRNIYRISIGSYPPSKK
CVTCHLRKERCQYYTASFSDYAKYYALVCYGPGIPISTLHDGRTDQEIKI
LEENKELENALKNIQLPKEEIKKLEVDEITLWYKMILPPQFDRSKKYPLL
IQVYGGPCSQSVRSVFAVNWISYLASKEGMVIALVDGRGTAFQGDKLLYA
VYRKLGVYEVEDQITAVRKFIEMGFIDEKRIAIWGWSYGGYVSSLALASG
TGLFKCGIAVAPVSSWEYYASVYTERFMGLPTKDDNLEHYKNSTVMARAE
YFRNVDYLLIHGTADDNVHFQNSAQIAKALVNAQVDFQAMWYSDQNHGLS
GLSTNHLYTHMTHFLKQCFS
Ligand information
Ligand ID356
InChIInChI=1S/C25H28N8O2/c1-4-5-13-32-21-22(29-24(32)31-12-8-9-17(26)14-31)30(3)25(35)33(23(21)34)15-20-27-16(2)18-10-6-7-11-19(18)28-20/h6-7,10-11,17H,8-9,12-15,26H2,1-3H3/t17-/m1/s1
InChIKeyLTXREWYXXSTFRX-QGZVFWFLSA-N
SMILES
SoftwareSMILES
CACTVS 3.341CC#CCn1c(nc2N(C)C(=O)N(Cc3nc(C)c4ccccc4n3)C(=O)c12)N5CCC[C@@H](N)C5
OpenEye OEToolkits 1.5.0CC#CCn1c2c(nc1N3CCCC(C3)N)N(C(=O)N(C2=O)Cc4nc(c5ccccc5n4)C)C
CACTVS 3.341CC#CCn1c(nc2N(C)C(=O)N(Cc3nc(C)c4ccccc4n3)C(=O)c12)N5CCC[CH](N)C5
OpenEye OEToolkits 1.5.0CC#CCn1c2c(nc1N3CCC[C@H](C3)N)N(C(=O)N(C2=O)Cc4nc(c5ccccc5n4)C)C
ACDLabs 10.04O=C2N(c1nc(n(c1C(=O)N2Cc4nc3ccccc3c(n4)C)CC#CC)N5CCCC(N)C5)C
FormulaC25 H28 N8 O2
Name8-[(3R)-3-Aminopiperidin-1-yl]-7-but-2-yn-1-yl-3-methyl-1-[(4-methylquinazolin-2-yl)methyl]-3,7-dihydro-1H-purine-2,6-d ione;
Linagliptin
ChEMBLCHEMBL237500
DrugBankDB08882
ZINCZINC000003820029
PDB chain6y0f Chain D Residue 808 [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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PDB6y0f Structure of human FAPalpha in complex with linagliptin
Resolution2.924 Å
Binding residue
(original residue number in PDB)		E203 E204 Y541 W623 S624 Y625 Y656 Y660
Binding residue
(residue number reindexed from 1)		E166 E167 Y504 W586 S587 Y588 Y619 Y623
Annotation score1
Binding affinityBindingDB: IC50=89nM
Enzymatic activity
Catalytic site (original residue number in PDB) Y541 S624 Y625 D702 H734
Catalytic site (residue number reindexed from 1) Y504 S587 Y588 D665 H697
Enzyme Commision number 3.4.14.5: dipeptidyl-peptidase IV.
3.4.21.-
3.4.21.26: prolyl oligopeptidase.
Gene Ontology
Molecular Function
GO:0002020 protease binding
GO:0004175 endopeptidase activity
GO:0004252 serine-type endopeptidase activity
GO:0005178 integrin binding
GO:0005515 protein binding
GO:0008233 peptidase activity
GO:0008236 serine-type peptidase activity
GO:0008239 dipeptidyl-peptidase activity
GO:0042802 identical protein binding
GO:0042803 protein homodimerization activity
Biological Process
GO:0001525 angiogenesis
GO:0006508 proteolysis
GO:0006915 apoptotic process
GO:0007155 cell adhesion
GO:0010710 regulation of collagen catabolic process
GO:0010716 negative regulation of extracellular matrix disassembly
GO:0043542 endothelial cell migration
GO:0051603 proteolysis involved in protein catabolic process
GO:0051726 regulation of cell cycle
GO:0051917 regulation of fibrinolysis
GO:0060244 negative regulation of cell proliferation involved in contact inhibition
GO:0097325 melanocyte proliferation
GO:1900119 positive regulation of execution phase of apoptosis
GO:1902362 melanocyte apoptotic process
GO:1903054 negative regulation of extracellular matrix organization
Cellular Component
GO:0005576 extracellular region
GO:0005615 extracellular space
GO:0005737 cytoplasm
GO:0005886 plasma membrane
GO:0005925 focal adhesion
GO:0009986 cell surface
GO:0016020 membrane
GO:0030027 lamellipodium
GO:0031258 lamellipodium membrane
GO:0032587 ruffle membrane
GO:0042995 cell projection
GO:0045177 apical part of cell
GO:0045178 basal part of cell
GO:0070161 anchoring junction
GO:1905368 peptidase complex

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6y0f, PDBe:6y0f, PDBj:6y0f
PDBsum6y0f
PubMed
UniProtQ12884|SEPR_HUMAN Prolyl endopeptidase FAP (Gene Name=FAP)

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