3G0D

Crystal structure of dipeptidyl peptidase IV in complex with a pyrimidinedione inhibitor 2

PDB DOI: https://doi.org/10.2210/pdb3G0D/pdb

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

Deposited: 2009-01-27 Released: 2010-02-16
Deposition Author(s): Zhang, Z., Wallace, M.B., Feng, J., Stafford, J.A., Kaldor, S.W., Shi, L., Skene, R.J., Aertgeerts, K., Lee, B., Jennings, A., Xu, R., Kassel, D., Webb, D.R., Gwaltney, S.L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.39 Å
R-Value Free: 0.239
R-Value Work: 0.187
R-Value Observed: 0.189

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.2 of the entry. See complete history.

Literature

Design and Synthesis of Pyrimidinone and Pyrimidinedione Inhibitors of Dipeptidyl Peptidase IV.

Zhang, Z., Wallace, M.B., Feng, J., Stafford, J.A., Skene, R.J., Shi, L., Lee, B., Aertgeerts, K., Jennings, A., Xu, R., Kassel, D.B., Kaldor, S.W., Navre, M., Webb, D.R., Gwaltney, S.L.

(2011) J Med Chem 54: 510-524

PubMed: 21186796 Search on PubMed
DOI: https://doi.org/10.1021/jm101016w
Primary Citation of Related Structures:
3G0B, 3G0C, 3G0D, 3G0G

PubMed Abstract:
The discovery of two classes of heterocyclic dipeptidyl peptidase IV (DPP-4) inhibitors, pyrimidinones and pyrimidinediones, is described. After a single oral dose, these potent, selective, and noncovalent inhibitors provide sustained reduction of plasma DPP-4 activity and lowering of blood glucose in animal models of diabetes. Compounds 13a, 27b, and 27j were selected for development.

Organizational Affiliation

Takeda San Diego, Inc., 10410 Science Center Drive, San Diego, California 92121, United States.

Macromolecule Content

Total Structure Weight: 349.9 kDa
Atom Count: 25,530
Modelled Residue Count: 2,897
Deposited Residue Count: 2,960
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, C, D	740	Homo sapiens	Mutation(s): 0 Gene Names: ADCP2, CD26, DPP4 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
Glycosylation
Glycosylation Sites: 6	Glycosylation Focus chain A Focus chain B Focus chain C Focus chain D	Go to GlyGen: P27487-1
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	E, F, G, H, I	2		N-Glycosylation	Interactions Focus chain E Focus chain F Focus chain G Focus chain H Focus chain I Interactions & Density 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
XIH Query on XIH Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain O [auth B] SDF format, chain T [auth C] SDF format, chain Y [auth D] MOL2 format, chain J [auth A] MOL2 format, chain O [auth B] MOL2 format, chain T [auth C] MOL2 format, chain Y [auth D] mmCIF format, chain J [auth A] mmCIF format, chain O [auth B] mmCIF format, chain T [auth C] mmCIF format, chain Y [auth D]	J [auth A], O [auth B], T [auth C], Y [auth D]	2-({8-[(3R)-3-AMINOPIPERIDIN-1-YL]-1,3-DIMETHYL-2,6-DIOXO-1,2,3,6-TETRAHYDRO-7H-PURIN-7-YL}METHYL)BENZONITRILE C₂₀ H₂₃ N₇ O₂ XJNKUWDMCBZMTG-OAHLLOKOSA-N		Interactions Focus chain J [auth A] Focus chain O [auth B] Focus chain T [auth C] Focus chain Y [auth D] Interactions & Density Focus chain J [auth A] Focus chain O [auth B] Focus chain T [auth C] Focus chain Y [auth D]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain AA [auth D] 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 P [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain U [auth C] SDF format, chain V [auth C] SDF format, chain W [auth C] SDF format, chain X [auth C] SDF format, chain Z [auth D] MOL2 format, chain AA [auth D] 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 P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain U [auth C] MOL2 format, chain V [auth C] MOL2 format, chain W [auth C] MOL2 format, chain X [auth C] MOL2 format, chain Z [auth D] mmCIF format, chain AA [auth D] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain U [auth C] mmCIF format, chain V [auth C] mmCIF format, chain W [auth C] mmCIF format, chain X [auth C] mmCIF format, chain Z [auth D]	AA [auth D] K [auth A] L [auth A] M [auth A] N [auth A] AA [auth D], K [auth A], L [auth A], M [auth A], N [auth A], P [auth B], Q [auth B], R [auth B], S [auth B], U [auth C], V [auth C], W [auth C], X [auth C], Z [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth D] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth D] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Focus chain Z [auth D]

Binding Affinity Annotations
ID	Source	Binding Affinity
XIH	PDBBind: 3G0D	IC50: 5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.39 Å
R-Value Free: 0.239
R-Value Work: 0.187
R-Value Observed: 0.189
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 122.905	α = 90
b = 123.442	β = 114.69
c = 145.684	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2010-02-16

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2010-02-16
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-11-01
Changes: Refinement description
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary
Version 2.1: 2023-09-06
Changes: Data collection, Database references, Refinement description, Structure summary
Version 2.2: 2024-10-09
Changes: Structure summary

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Help and Resources

3G0D

Crystal structure of dipeptidyl peptidase IV in complex with a pyrimidinedione inhibitor 2

Design and Synthesis of Pyrimidinone and Pyrimidinedione Inhibitors of Dipeptidyl Peptidase IV.

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Glycosylation

Sequence Annotations

Expand

Entity ID: 2

Glycosylation Resources

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)