3WQH | pdb_00003wqh

Crystal Structure of human DPP-IV in complex with Anagliptin

PDB DOI: https://doi.org/10.2210/pdb3WQH/pdb

Classification: HYDROLASE/HYDROLASE INHIBITOR
Organism(s): Homo sapiens
Expression System: Bombyx mori
Mutation(s): No

Deposited: 2014-01-27 Released: 2015-07-15
Deposition Author(s): Watanabe, Y.S., Okada, S., Motoyama, T., Takahashi, R., Adachi, H., Oka, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.85 Å
R-Value Free:
0.288 (Depositor), 0.218 (DCC)
R-Value Work:
0.227 (Depositor), 0.220 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Anagliptin, a potent dipeptidyl peptidase IV inhibitor: its single-crystal structure and enzyme interactions.

Watanabe, Y.S., Yasuda, Y., Kojima, Y., Okada, S., Motoyama, T., Takahashi, R., Oka, M.

(2015) J Enzyme Inhib Med Chem 30: 981-988

PubMed: 26147347 Search on PubMed
DOI: https://doi.org/10.3109/14756366.2014.1002402
Primary Citation Related Structures:
3WQH

PubMed Abstract:
The single-crystal structure of anagliptin, N-[2-({2-[(2S)-2-cyanopyrrolidin-1-yl]-2-oxoethyl}amino)-2-methylpropyl]-2-methylpyrazolo[1,5-a]pyrimidine-6-carboxamide, was determined. Two independent molecules were held together by intermolecular hydrogen bonds, and the absolute configuration of the 2-cyanopyrrolidine ring delivered from l-prolinamide was confirmed to be S. The interactions of anagliptin with DPP-4 were clarified by the co-crystal structure solved at 2.85 Å resolution. Based on the structure determined by X-ray crystallography, the potency and selectivity of anagliptin were discussed, and an SAR study using anagliptin derivatives was performed.

Organizational Affiliation

a Mie Research Park, Sanwa Kagaku Kenkyusho Co., Ltd. , Mie , Japan .

Macromolecule Content

Total Structure Weight: 172.88 kDa
Atom Count: 12,269
Modeled Residue Count: 1,456
Deposited Residue Count: 1,460
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dipeptidyl peptidase 4	A, B	730	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P27487
Glycosylation
Glycosylation Sites: 6	Glycosylation Focus chain A Focus chain B	Go to GlyGen: P27487-1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SKK Query on SKK Download:Ideal Coordinates CCD File SDF format, chain Q [auth B] SDF format, chain J [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain J [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain J [auth A]	J [auth A], Q [auth B]	N-[2-({2-[(2S)-2-cyanopyrrolidin-1-yl]-2-oxoethyl}amino)-2-methylpropyl]-2-methylpyrazolo[1,5-a]pyrimidine-6-carboxamide C₁₉ H₂₅ N₇ O₂ LDXYBEHACFJIEL-HNNXBMFYSA-N		Interactions Focus chain J [auth A] Focus chain Q [auth B] Interactions & Density Focus chain J [auth A] Focus chain Q [auth B]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain N [auth B] SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain C [auth A]	C [auth A] D [auth A] E [auth A] F [auth A] G [auth A] C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], K [auth B], L [auth B], M [auth B], N [auth B], O [auth B], P [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
SKK	BindingDB: 3WQH	IC50: min: 3.3, max: 11.4 (nM) from 3 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.85 Å
R-Value Free: 0.288 (Depositor), 0.218 (DCC)
R-Value Work: 0.227 (Depositor), 0.220 (DCC)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.16	α = 90
b = 68.99	β = 90
c = 419.6	γ = 90

Software Package:

Software Name	Purpose
XDS	data scaling
MOLREP	phasing
PRIME-X	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2015-07-15

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2015-07-15
Type: Initial release
Version 1.1: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Database references, Derived calculations, Structure summary
Version 1.2: 2022-08-24
Changes: Database references, Refinement description, Structure summary
Version 1.3: 2023-11-08
Changes: Data collection, Refinement description
Version 1.4: 2024-10-16
Changes: Structure summary