3EIO

Crystal Structure Analysis of DPPIV Inhibitor

PDB DOI: https://doi.org/10.2210/pdb3EIO/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Trichoplusia ni
Mutation(s): No

Deposited: 2008-09-17 Released: 2008-11-04
Deposition Author(s): Ahn, J.H., Lee, J.-O.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.272
R-Value Work: 0.239
R-Value Observed: 0.239

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.0 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 174.77 kDa
Atom Count: 12,596
Modelled Residue Count: 1,454
Deposited Residue Count: 1,456
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dipeptidyl peptidase 4 soluble form	A, B	728	Homo sapiens	Mutation(s): 0 EC: 3.4.14.5
UniProt & NIH Common Fund Data Resources
Find proteins for P27487 (Homo sapiens) Explore P27487 Go to UniProtKB: P27487
PHAROS: P27487 GTEx: ENSG00000197635
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P27487
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	3		N-Glycosylation	Interactions Focus chain C Interactions & Density Focus chain C
Glycosylation Resources
GlyTouCan: G62182OO GlyCosmos: G62182OO GlyGen: G62182OO

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D, E, F, G, H	2		N-Glycosylation	Interactions Focus chain D Focus chain E Focus chain F Focus chain G Focus chain H Interactions & Density Focus chain D Focus chain E Focus chain F Focus chain G Focus chain H
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AJH Query on AJH Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain P [auth B] MOL2 format, chain I [auth A] MOL2 format, chain P [auth B]	I [auth A], P [auth B]	4-({4-[(3R)-3-amino-4-(2,4,5-trifluorophenyl)butanoyl]-1,4-diazepan-1-yl}carbonyl)benzoic acid C₂₃ H₂₄ F₃ N₃ O₄ NXUBRAZWHJADLI-QGZVFWFLSA-N		Interactions Focus chain I [auth A] Focus chain P [auth B] Interactions & Density Focus chain I [auth A] Focus chain P [auth B]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain T [auth B] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B]	J [auth A] K [auth A] L [auth A] M [auth A] N [auth A] J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], Q [auth B], R [auth B], S [auth B], T [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Interactions & Density Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
AJH	Binding MOAD: 3EIO	IC50: 223 (nM) from 1 assay(s)
	PDBBind: 3EIO	IC50: 223 (nM) from 1 assay(s)
	BindingDB: 3EIO	IC50: 223 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.272
R-Value Work: 0.239
R-Value Observed: 0.239
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 119.368	α = 90
b = 123.387	β = 90
c = 133.185	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
HKL-2000	data reduction

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2008-11-04

Deposition Author(s):

Ahn, J.H.

Lee, J.-O.

Revision History (Full details and data files)

Version 1.0: 2008-11-04
Type: Initial release
Version 1.1: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.2: 2017-10-25
Changes: Refinement description
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary

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Deposit Data

Help and Resources

3EIO

Crystal Structure Analysis of DPPIV Inhibitor

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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Entity ID: 2

Glycosylation Resources