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Structure of PDB 3d4l Chain A Binding Site BS01

Receptor Information >3d4l Chain A (length=728) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure] TRKTYTLTDYLKNTYRLKLYSLRWISDHEYLYKQENNILVFNAEYGNSSV FLENSTFDEFGHSINDYSISPDGQFILLEYNYVKQWRHSYTASYDIYDLN KRQLITEERIPNNTQWVTWSPVGHKLAYVWNNDIYVKIEPNLPSYRITWT GKEDIIYNGITDWVYEEEVFSAYSALWWSPNGTFLAYAQFNDTEVPLIEY SFYSDESLQYPKTVRVPYPKAGAVNPTVKFFVVNTDSLSSVTNATSIQIT APASMLIGDHYLCDVTWATQERISLQWLRRIQNYSVMDICDYDESSGRWN CLVARQHIEMSTTGWVGRFRPSEPHFTLDGNSFYKIISNEEGYRHICYFQ IDKKDCTFITKGTWEVIGIEALTSDYLYYISNEYKGMPGGRNLYKIQLSD YTKVTCLSCELNPERCQYYSVSFSKEAKYYQLRCSGPGLPLYTLHSSVND KGLRVLEDNSALDKMLQNVQMPSKKLDFIILNETKFWYQMILPPHFDKSK KYPLLLDVYAGPCSQKADTVFRLNWATYLASTENIIVASFDGRGSGYQGD KIMHAINRRLGTFEVEDQIEAARQFSKMGFVDNKRIAIWGWSYGGYVTSM VLGSGSGVFKCGIAVAPVSRWEYYDSVYTERYMGLPTPEDNLDHYRNSTV MSRAENFKQVEYLLIHGTADDNVHFQQSAQISKALVDVGVDFQAMWYTDE DHGIASSTAHQHIYTHMSHFIKQCFSLP

Ligand information Ligand ID 605 InChI InChI=1S/C21H18F2N2O/c22-18-8-9-19(23)17(11-18)12-20(24)14-6-4-13(5-7-14)15-2-1-3-16(10-15)21(25)26/h1-11,20H,12,24H2,(H2,25,26)/t20-/m1/s1 InChIKey JYKFWUXBFJJDTP-HXUWFJFHSA-N SMILES Software SMILES OpenEye OEToolkits 1.5.0 c1cc(cc(c1)C(=O)N)c2ccc(cc2)[C@@H](Cc3cc(ccc3F)F)N OpenEye OEToolkits 1.5.0 c1cc(cc(c1)C(=O)N)c2ccc(cc2)C(Cc3cc(ccc3F)F)N CACTVS 3.341 N[C@H](Cc1cc(F)ccc1F)c2ccc(cc2)c3cccc(c3)C(N)=O ACDLabs 10.04 Fc1ccc(F)cc1CC(c3ccc(c2cc(C(=O)N)ccc2)cc3)N CACTVS 3.341 N[CH](Cc1cc(F)ccc1F)c2ccc(cc2)c3cccc(c3)C(N)=O Formula C21 H18 F2 N2 O Name 4'-[(1R)-1-amino-2-(2,5-difluorophenyl)ethyl]biphenyl-3-carboxamide ChEMBL CHEMBL452289 DrugBank DB07181 ZINC ZINC000024981641 PDB chain 3d4l Chain A Residue 1521 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure Global view Local view Structure summary [Spin on] [Spin off] [Reset] [High quality] [Low quality] [White background] [Black background] [Spin on] [Spin off] [Reset] [High quality] [Low quality] [White background] [Black background] PDB 3d4l Discovery of new binding elements in DPP-4 inhibition and their applications in novel DPP-4 inhibitor design. Resolution 2.0 Å Binding residue (original residue number in PDB) E205 E206 S209 F357 R358 S630 Y662 Y666 N710 V711 Binding residue (residue number reindexed from 1) E167 E168 S171 F319 R320 S592 Y624 Y628 N672 V673 Annotation score 1 Binding affinity MOAD: ic50=32nM PDBbind-CN: -logKd/Ki=7.49,IC50=32nM BindingDB: IC50=32nM

Enzymatic activity Catalytic site (original residue number in PDB) Y547 S630 Y631 D708 H740 Catalytic site (residue number reindexed from 1) Y509 S592 Y593 D670 H702 Enzyme Commision number 3.4.14.5: dipeptidyl-peptidase IV.

Gene Ontology Molecular Function GO:0001618 virus receptor activity GO:0002020 protease binding GO:0004177 aminopeptidase activity GO:0004252 serine-type endopeptidase activity GO:0005102 signaling receptor binding GO:0005515 protein binding GO:0008236 serine-type peptidase activity GO:0008239 dipeptidyl-peptidase activity GO:0042802 identical protein binding GO:0042803 protein homodimerization activity GO:0045499 chemorepellent activity

	Biological Process
GO:0001662	behavioral fear response
GO:0001666	response to hypoxia
GO:0006508	proteolysis
GO:0007155	cell adhesion
GO:0008284	positive regulation of cell population proliferation
GO:0010716	negative regulation of extracellular matrix disassembly
GO:0016486	peptide hormone processing
GO:0019065	receptor-mediated endocytosis of virus by host cell
GO:0031295	T cell costimulation
GO:0033632	regulation of cell-cell adhesion mediated by integrin
GO:0035641	locomotory exploration behavior
GO:0036343	psychomotor behavior
GO:0042110	T cell activation
GO:0043542	endothelial cell migration
GO:0046718	symbiont entry into host cell
GO:0046813	receptor-mediated virion attachment to host cell
GO:0050919	negative chemotaxis
GO:0061025	membrane fusion
GO:0090024	negative regulation of neutrophil chemotaxis
GO:0120116	glucagon processing

	Cellular Component
GO:0005576	extracellular region
GO:0005765	lysosomal membrane
GO:0005886	plasma membrane
GO:0005925	focal adhesion
GO:0009986	cell surface
GO:0016020	membrane
GO:0016324	apical plasma membrane
GO:0030027	lamellipodium
GO:0030139	endocytic vesicle
GO:0031258	lamellipodium membrane
GO:0042995	cell projection
GO:0045121	membrane raft
GO:0046581	intercellular canaliculus
GO:0070062	extracellular exosome
GO:0070161	anchoring junction

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