2BUB

Crystal Structure Of Human Dipeptidyl Peptidase IV (CD26) in Complex with a Reversed Amide Inhibitor

PDB DOI: https://doi.org/10.2210/pdb2BUB/pdb

Classification: HYDROLASE/INHIBITOR
Organism(s): Homo sapiens
Expression System: Ogataea methanolica
Mutation(s): No

Deposited: 2005-06-09 Released: 2006-01-23
Deposition Author(s): Nordhoff, S., Cerezo-Galvez, S., Feurer, A., Hill, O., Matassa, V.G., Metz, G., Rummey, C., Thiemann, M., Edwards, P.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.66 Å
R-Value Free: 0.329
R-Value Work: 0.258
R-Value Observed: 0.260

wwPDB Validation 3D Report Full Report

This is version 2.4 of the entry. See complete history.

Literature

The reversed binding of beta-phenethylamine inhibitors of DPP-IV: X-ray structures and properties of novel fragment and elaborated inhibitors.

Nordhoff, S., Cerezo-Galvez, S., Feurer, A., Hill, O., Matassa, V.G., Metz, G., Rummey, C., Thiemann, M., Edwards, P.J.

(2006) Bioorg Med Chem Lett 16: 1744-1748

PubMed: 16376544 Search on PubMed
DOI: https://doi.org/10.1016/j.bmcl.2005.11.103
Primary Citation of Related Structures:
2BUA, 2BUB, 2BUC

PubMed Abstract:
The co-crystal structure of beta-phenethylamine fragment inhibitor 5 bound to DPP-IV revealed that the phenyl ring occupied the proline pocket of the enzyme. This finding provided the basis for a general hypothesis of a reverse binding mode for beta-phenethylamine-based DPP-IV inhibitors. Novel inhibitor design concepts that obviate substrate-like structure-activity relationships (SAR) were thereby enabled, and novel, potent inhibitors were discovered.

Organizational Affiliation

Medicinal Chemistry, Santhera Pharmaceuticals, Im Neuenheimer Feld 518-519, D-69120 Heidelberg, Germany. sonja.nordhoff@santhera.com

Macromolecule Content

Total Structure Weight: 171.46 kDa
Atom Count: 12,414
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	A, B	728	Homo sapiens	Mutation(s): 0 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: 4	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
FPB Query on FPB Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain L [auth B] MOL2 format, chain G [auth A] MOL2 format, chain L [auth B]	G [auth A], L [auth B]	N-({(2S)-1-[(3R)-3-AMINO-4-(2-FLUOROPHENYL)BUTANOYL]PYRROLIDIN-2-YL}METHYL)BENZAMIDE C₂₂ H₂₆ F N₃ O₂ ANQHSFFUNMTTRS-MOPGFXCFSA-N		Interactions Focus chain G [auth A] Focus chain L [auth B]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain J [auth B] SDF format, chain K [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B]	C [auth A] D [auth A] E [auth A] F [auth A] H [auth B] C [auth A], D [auth A], E [auth A], F [auth A], H [auth B], I [auth B], J [auth B], K [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 H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
FPB	BindingDB: 2BUB	IC50: min: 90, max: 410 (nM) from 2 assay(s)
FPB	PDBBind: 2BUB	IC50: 90 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.66 Å
R-Value Free: 0.329
R-Value Work: 0.258
R-Value Observed: 0.260
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.486	α = 90
b = 66.773	β = 90
c = 425.407	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2006-01-23

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2006-01-23
Type: Initial release
Version 1.1: 2011-05-08
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 2.0: 2018-08-22
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
Version 2.1: 2019-07-10
Changes: Data collection, Derived calculations
Version 2.2: 2019-07-24
Changes: Data collection
Version 2.3: 2019-09-04
Changes: Data collection
Version 2.4: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary