3C45

Human dipeptidyl peptidase IV/CD26 in complex with a fluoroolefin inhibitor

PDB DOI: https://doi.org/10.2210/pdb3C45/pdb

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

Deposited: 2008-01-29 Released: 2008-04-22
Deposition Author(s): Scapin, G., Edmondson, S.D., Weber, A.E.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free: 0.218
R-Value Work: 0.191
R-Value Observed: 0.194

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 3.2 of the entry. See complete history.

Literature

Fluoroolefins as amide bond mimics in dipeptidyl peptidase IV inhibitors

Edmondson, S.D., Wei, L., Xu, J., Shang, J., Xu, S., Pang, J., Chaudhary, A., Dean, D.C., He, H., Leiting, B., Lyons, K.A., Patel, R.A., Patel, S.B., Scapin, G., Wu, J.K., Beconi, M.G., Thornberry, N.A., Weber, A.E.

(2008) Bioorg Med Chem Lett 18: 2409-2413

PubMed: 18331795 Search on PubMed
DOI: https://doi.org/10.1016/j.bmcl.2008.02.050
Primary Citation of Related Structures:
3C43, 3C45

PubMed Abstract:
The synthesis, selectivity, rat pharmacokinetic profile, and drug metabolism profiles of a series of potent fluoroolefin-derived DPP-4 inhibitors (4) are reported. A radiolabeled fluoroolefin 33 was shown to possess a high propensity to form reactive metabolites, thus revealing a potential liability for this class of DPP-4 inhibitors.

Organizational Affiliation

Department of Medicinal Chemistry, Merck & Co. Inc., PO Box 2000, Rahway, NJ 07065, USA. scott_edmondson@merck.com

Macromolecule Content

Total Structure Weight: 175.03 kDa
Atom Count: 13,342
Modelled Residue Count: 1,456
Deposited Residue Count: 1,456
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 soluble form	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
Glycosylation
Glycosylation Sites: 8	Glycosylation Focus chain A Focus chain B	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	C, D, E, F, G C, D, E, F, G, H, I, J, K	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 Focus chain J Focus chain K Interactions & Density Focus chain C Focus chain D Focus chain E Focus chain F Focus chain G Focus chain H Focus chain I Focus chain J Focus chain K
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
317 Query on 317 Download Ideal Coordinates CCD File SDF format, chain T [auth B] SDF format, chain P [auth A] MOL2 format, chain T [auth B] MOL2 format, chain P [auth A] mmCIF format, chain T [auth B] mmCIF format, chain P [auth A]	P [auth A], T [auth B]	(2S,3S)-3-{3-[2-chloro-4-(methylsulfonyl)phenyl]-1,2,4-oxadiazol-5-yl}-1-cyclopentylidene-4-cyclopropyl-1-fluorobutan-2-amine C₂₁ H₂₅ Cl F N₃ O₃ S XCCSSVMRGIQMGF-LPHOPBHVSA-N		Interactions Focus chain P [auth A] Focus chain T [auth B] Interactions & Density Focus chain P [auth A] Focus chain T [auth B]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B]	L [auth A] M [auth A] N [auth A] Q [auth B] R [auth B] L [auth A], M [auth A], N [auth A], Q [auth B], R [auth B], S [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Interactions & Density Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain O [auth A] MOL2 format, chain O [auth A] mmCIF format, chain O [auth A]	O [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain O [auth A] Interactions & Density Focus chain O [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
317	PDBBind: 3C45	IC50: 0.21 (nM) from 1 assay(s)
317	BindingDB: 3C45	IC50: min: 0.21, max: 12 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free: 0.218
R-Value Work: 0.191
R-Value Observed: 0.194
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.888	α = 90
b = 125.909	β = 90
c = 136.75	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
CNX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
CNX	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2008-04-22

Deposition Author(s):

Scapin, G.

Edmondson, S.D.

Weber, A.E.

Revision History (Full details and data files)

Version 1.0: 2008-04-22
Type: Initial release
Version 1.1: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
Version 3.0: 2021-10-20
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Source and taxonomy, Structure summary
Version 3.1: 2023-08-30
Changes: Data collection, Refinement description
Version 3.2: 2024-10-30
Changes: Structure summary