3W2T

Crystal structure of human depiptidyl peptidase IV (DPP-4) in complex with vildagliptin

PDB DOI: https://doi.org/10.2210/pdb3W2T/pdb

Classification: HYDROLASE/HYDROLASE INHIBITOR
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2012-12-04 Released: 2013-05-15
Deposition Author(s): Kishida, H., Nabeno, M., Miyaguchi, I., Tanaka, Y., Katou, R., Akahoshi, F.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.36 Å
R-Value Free: 0.231
R-Value Work: 0.180
R-Value Observed: 0.183

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 3.1 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 176.94 kDa
Atom Count: 13,311
Modelled Residue Count: 1,458
Deposited Residue Count: 1,480
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	740	Homo sapiens	Mutation(s): 0 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
beta-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose	C, G	2		N-Glycosylation	Interactions Focus chain C Focus chain G Interactions & Density Focus chain C Focus chain G
Glycosylation Resources
GlyTouCan: G61843VN GlyCosmos: G61843VN GlyGen: G61843VN

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, H, I D, E, F, H, I, J	2		N-Glycosylation	Interactions Focus chain D Focus chain E Focus chain F Focus chain H Focus chain I Focus chain J Interactions & Density Focus chain D Focus chain E Focus chain F Focus chain H Focus chain I Focus chain J
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 K [auth A] SDF format, chain P [auth B] MOL2 format, chain K [auth A] MOL2 format, chain P [auth B]	K [auth A], P [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 K [auth A] Focus chain P [auth B] Interactions & Density Focus chain K [auth A] Focus chain P [auth B]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain R [auth B] SDF format, chain S [auth B] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B]	M [auth A], N [auth A], O [auth A], R [auth B], S [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain R [auth B] Focus chain S [auth B] Interactions & Density Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain R [auth B] Focus chain S [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain Q [auth B] MOL2 format, chain L [auth A] MOL2 format, chain Q [auth B]	L [auth A], Q [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Focus chain Q [auth B] Interactions & Density Focus chain L [auth A] Focus chain Q [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
LF7	BindingDB: 3W2T	IC50: min: 3.5, max: 80.1 (nM) from 2 assay(s)
LF7	PDBBind: 3W2T	IC50: 29.2 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.36 Å
R-Value Free: 0.231
R-Value Work: 0.180
R-Value Observed: 0.183
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.216	α = 90
b = 126.237	β = 90
c = 137.089	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2013-05-15

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-05-15
Type: Initial release
Version 2.0: 2018-02-14
Changes: Non-polymer description, Structure summary
Version 3.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
Version 3.1: 2023-11-08
Changes: Data collection, Database references, Refinement description, Structure summary

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Help and Resources

3W2T

Crystal structure of human depiptidyl peptidase IV (DPP-4) in complex with vildagliptin

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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Entity ID: 2

Glycosylation Resources