6B1E

The structure of DPP4 in complex with Vildagliptin

PDB DOI: https://doi.org/10.2210/pdb6B1E/pdb

Classification: HYDROLASE/HYDROLASE Inhibitor
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): Yes

Deposited: 2017-09-18 Released: 2017-09-27
Deposition Author(s): Scapin, G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.77 Å
R-Value Free: 0.186
R-Value Work: 0.161
R-Value Observed: 0.162

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 3.0 of the entry. See complete history.

Literature

A comparative study of the binding properties, dipeptidyl peptidase-4 (DPP-4) inhibitory activity and glucose-lowering efficacy of the DPP-4 inhibitors alogliptin, linagliptin, saxagliptin, sitagliptin and vildagliptin in mice.

Berger, J.P., SinhaRoy, R., Pocai, A., Kelly, T.M., Scapin, G., Gao, Y.D., Pryor, K.A.D., Wu, J.K., Eiermann, G.J., Xu, S.S., Zhang, X., Tatosian, D.A., Weber, A.E., Thornberry, N.A., Carr, R.D.

(2018) Endocrinol Diabetes Metab 1: e00002-e00002

PubMed: 30815539 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1002/edm2.2
Primary Citation of Related Structures:
6B1E, 6B1O

PubMed Abstract:
Since 2006, DPP-4 inhibitors have become established therapy for the treatment of type 2 diabetes. Despite sharing a common mechanism of action, considerable chemical diversity exists amongst members of the DPP-4 inhibitor class, raising the question as to whether structural differences may result in differentiated enzyme inhibition and antihyperglycaemic activity.

Organizational Affiliation

Merck& Co., Inc. Kenilworth NJ USA.

Macromolecule Content

Total Structure Weight: 173.66 kDa
Atom Count: 14,219
Modelled Residue Count: 1,456
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	A, B	728	Homo sapiens	Mutation(s): 1 Gene Names: DPP4, ADCP2, CD26 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
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C, D, E, F, G C, D, E, F, G, H, I	2		N-Glycosylation	Interactions Focus chain C Focus chain D Focus chain E Focus chain F Focus chain G Focus chain H Focus chain I Interactions & Density Focus chain C Focus chain D Focus chain E Focus chain F Focus chain G Focus chain H Focus chain I
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LF7 Query on LF7 Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain O [auth B] MOL2 format, chain J [auth A] MOL2 format, chain O [auth B]	J [auth A], O [auth B]	2-{[(1r,3s,5R,7S)-3-hydroxytricyclo[3.3.1.1~3,7~]decan-1-yl]amino}-1-{(2S)-2-[(E)-iminomethyl]pyrrolidin-1-yl}ethan-1-o ne C₁₇ H₂₇ N₃ O₂ LUWVSODOPBYGON-FEZPVXCISA-N		Interactions Focus chain J [auth A] Focus chain O [auth B] Interactions & Density Focus chain J [auth A] Focus chain O [auth B]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain P [auth B] SDF format, chain M [auth A] SDF format, chain Q [auth B] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain P [auth B] MOL2 format, chain M [auth A] MOL2 format, chain Q [auth B]	K [auth A], L [auth A], M [auth A], P [auth B], Q [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain P [auth B] Focus chain Q [auth B] Interactions & Density Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain P [auth B] Focus chain Q [auth B]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain N [auth A] MOL2 format, chain N [auth A]	N [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain N [auth A] Interactions & Density Focus chain N [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
LF7	BindingDB: 6B1E	IC50: min: 3.5, max: 80.1 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.77 Å
R-Value Free: 0.186
R-Value Work: 0.161
R-Value Observed: 0.162
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.314	α = 90
b = 125.751	β = 90
c = 136.865	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
REFMAC	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2017-09-27

Deposition Author(s):

Scapin, G.

Revision History (Full details and data files)

Version 1.0: 2017-09-27
Type: Initial release
Version 2.0: 2018-02-07
Changes: Atomic model, Derived calculations, Non-polymer description, Structure summary
Version 2.1: 2018-12-12
Changes: Data collection, Database references
Version 2.2: 2019-03-13
Changes: Data collection, Database references
Version 3.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary