Structure of PDB 2i03 Chain B Binding Site BS01

Receptor Information

>2i03 Chain B (length=726) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

SRKTYTLTDYLKNTYRLKLYSLRWISDHEYLYKQENNILVFNAEYGNSSV
FLENSTFDEFGHSINDYSISPDGQFILLEYNYVKQWRHSYTASYDIYDLN
KRQLITEERIPNNTQWVTWSPVGHKLAYVWNNDIYVKIEPNLPSYRITWT
GKEDIIYNGITDWVYEEEVFSAYSALWWSPNGTFLAYAQFNDTEVPLIEY
SFYSDESLQYPKTVRVPYPKAGAVNPTVKFFVVNTDSLSSVTNATSIQIT
APASMLIGDHYLCDVTWATQERISLQWLRRIQNYSVMDICDYDESSGRWN
CLVARQHIEMSTTGWVGRFRPSEPHFTLDGNSFYKIISNEEGYRHICYFQ
IDKKDCTFITKGTWEVIGIEALTSDYLYYISNEYKGMPGGRNLYKIQLSD
YTKVTCLSCELNPERCQYYSVSFSKEAKYYQLRCSGPGLPLYTLHSSVND
KGLRVLEDNSALDKMLQNVQMPSKKLDFIILNETKFWYQMILPPHFDKSK
KYPLLLDVYAGPCSQKADTVFRLNWATYLASTENIIVASFDGRGSGYQGD
KIMHAINRRLGTFEVEDQIEAARQFSKMGFVDNKRIAIWGWSYGGYVTSM
VLGSGSGVFKCGIAVAPVSRWEYYDSVYTERYMGLPTPEDNLDHYRNSTV
MSRAENFKQVEYLLIHGTADDNVHFQQSAQISKALVDVGVDFQAMWYTDE
DHGIASSTAHQHIYTHMSHFIKQCFS

Ligand information

Ligand ID

AXD

InChI

InChI=1S/C21H29N5O3/c1-3-16-4-5-17(13-22)26(16)19(27)14-24-21(2)7-10-25(11-8-21)18-12-15(20(28)29)6-9-23-18/h1,6,9,12,16-17,24H,4-5,7-8,10-11,13-14,22H2,2H3,(H,28,29)/t16-,17-/m0/s1

InChIKey

SDLYKSXRUIHFDH-IRXDYDNUSA-N

SMILES

Software	SMILES
CACTVS 3.341	CC1(CCN(CC1)c2cc(ccn2)C(O)=O)NCC(=O)N3[CH](CN)CC[CH]3C#C
CACTVS 3.341	CC1(CCN(CC1)c2cc(ccn2)C(O)=O)NCC(=O)N3[C@H](CN)CC[C@@H]3C#C
ACDLabs 10.04	O=C(O)c1cc(ncc1)N3CCC(NCC(=O)N2C(C#C)CCC2CN)(CC3)C
OpenEye OEToolkits 1.5.0	CC1(CCN(CC1)c2cc(ccn2)C(=O)O)NCC(=O)N3[C@@H](CC[C@@H]3C#C)CN
OpenEye OEToolkits 1.5.0	CC1(CCN(CC1)c2cc(ccn2)C(=O)O)NCC(=O)N3C(CCC3C#C)CN

Formula

C21 H29 N5 O3

Name

2-[4-({2-[(2S,5R)-2-(AMINOMETHYL)-5-ETHYNYLPYRROLIDIN-1-YL]-2-OXOETHYL}AMINO)-4-METHYLPIPERIDIN-1-YL]ISONICOTINIC ACID

PDB chain

2i03 Chain B Residue 1630 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure

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Structure summary

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PDB	2i03 Discovery of 2-[4-{{2-(2S,5R)-2-cyano-5-ethynyl-1-pyrrolidinyl]-2-oxoethyl]amino]- 4-methyl-1-piperidinyl]-4-pyridinecarboxylic acid (ABT-279): a very potent, selective, effective, and well-tolerated inhibitor of dipeptidyl peptidase-IV, useful for the treatment of diabetes.
Resolution	2.4 Å
Binding residue (original residue number in PDB)	H126 E205 E206 Y547 S630 Y631 Y662 Y666 N710 V711
Binding residue (residue number reindexed from 1)	H88 E167 E168 Y509 S592 Y593 Y624 Y628 N672 V673
Annotation score	1
Binding affinity	PDBbind-CN: -logKd/Ki=9.00,Ki=1.0nM

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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External links

PDB	RCSB:2i03, PDBe:2i03, PDBj:2i03
PDBsum	2i03
PubMed	17034148
UniProt	P27487\|DPP4_HUMAN Dipeptidyl peptidase 4 (Gene Name=DPP4)

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