3F8S

Crystal structure of dipeptidyl peptidase IV in complex with inhibitor

PDB DOI: https://doi.org/10.2210/pdb3F8S/pdb

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

Deposited: 2008-11-13 Released: 2009-06-23
Deposition Author(s): Ammirati, M.J., Liu, S., Piotrowski, D.W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.43 Å
R-Value Free: 0.295
R-Value Work: 0.243
R-Value Observed: 0.246

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

(3,3-Difluoro-pyrrolidin-1-yl)-[(2S,4S)-(4-(4-pyrimidin-2-yl-piperazin-1-yl)-pyrrolidin-2-yl]-methanone: a potent, selective, orally active dipeptidyl peptidase IV inhibitor.

Ammirati, M.J., Andrews, K.M., Boyer, D.D., Brodeur, A.M., Danley, D.E., Doran, S.D., Hulin, B., Liu, S., McPherson, R.K., Orena, S.J., Parker, J.C., Polivkova, J., Qiu, X., Soglia, C.B., Treadway, J.L., VanVolkenburg, M.A., Wilder, D.C., Piotrowski, D.W.

(2009) Bioorg Med Chem Lett 19: 1991-1995

PubMed: 19275964 Search on PubMed
DOI: https://doi.org/10.1016/j.bmcl.2009.02.041
Primary Citation of Related Structures:
3F8S

PubMed Abstract:
A series of 4-substituted proline amides was synthesized and evaluated as inhibitors of dipeptidyl pepdidase IV for the treatment of type 2 diabetes. (3,3-Difluoro-pyrrolidin-1-yl)-[(2S,4S)-(4-(4-pyrimidin-2-yl-piperazin-1-yl)-pyrrolidin-2-yl]-methanone (5) emerged as a potent (IC(50) = 13 nM) and selective compound, with high oral bioavailability in preclinical species and low plasma protein binding. Compound 5, PF-00734200, was selected for development as a potential new treatment for type 2 diabetes.

Organizational Affiliation

Pfizer Global Research & Development, Groton/New London Laboratories, Pfizer Inc, Groton, CT 06340, United States.

Macromolecule Content

Total Structure Weight: 176.39 kDa
Atom Count: 12,132
Modelled Residue Count: 1,456
Deposited Residue Count: 1,496
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dipeptidyl peptidase 4	A, B	748	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
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain A Focus chain B	Go to GlyGen: P27487-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

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	2		N-Glycosylation	Interactions Focus chain C Focus chain D Focus chain E Focus chain F Interactions & Density Focus chain C Focus chain D Focus chain E Focus chain F
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PF2 Query on PF2 Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain K [auth B] MOL2 format, chain H [auth A] MOL2 format, chain K [auth B] mmCIF format, chain H [auth A] mmCIF format, chain K [auth B]	H [auth A], K [auth B]	2-(4-{(3S,5S)-5-[(3,3-difluoropyrrolidin-1-yl)carbonyl]pyrrolidin-3-yl}piperazin-1-yl)pyrimidine C₁₇ H₂₄ F₂ N₆ O QWEWGXUTRTXFRF-KBPBESRZSA-N		Interactions Focus chain H [auth A] Focus chain K [auth B] Interactions & Density Focus chain H [auth A] Focus chain K [auth B]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] MOL2 format, chain G [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] mmCIF format, chain G [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B]	G [auth A], I [auth B], J [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Interactions & Density Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
PF2	PDBBind: 3F8S	IC50: 13 (nM) from 1 assay(s)
PF2	BindingDB: 3F8S	IC50: min: 11, max: 13 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.43 Å
R-Value Free: 0.295
R-Value Work: 0.243
R-Value Observed: 0.246
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.429	α = 90
b = 67.141	β = 90
c = 421.529	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2009-06-23

Deposition Author(s):

Ammirati, M.J.

Liu, S.

Piotrowski, D.W.

Revision History (Full details and data files)

Version 1.0: 2009-06-23
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
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: 2024-10-16
Changes: Structure summary