3Q8W | pdb_00003q8w

A b-aminoacyl containing thiazolidine derivative and DPPIV complex

PDB DOI: https://doi.org/10.2210/pdb3Q8W/pdb

Classification: HYDROLASE/HYDROLASE INHIBITOR
Organism(s): Homo sapiens
Expression System: Trichoplusia ni
Mutation(s): No

Deposited: 2011-01-07 Released: 2011-03-16
Deposition Author(s): Lee, J.O., Song, D.H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.64 Å
R-Value Free:
0.324 (Depositor)
R-Value Work:
0.282 (Depositor), 0.272 (DCC)
R-Value Observed:
0.282 (Depositor)

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Discovery of b-aminoacyl containing thiazolidine derivatives as potent and selective dipeptidyl peptidase IV inhibitors

Park, W.S., Kang, S.K., Jun, M.A., Shin, M.S., Kim, K.Y., Rhee, S.D., Bae, M.A., Kim, M.S., Kim, K.R., Kang, N.S., Yoo, S.E., Lee, J.O., Song, D.H., Silinski, P., Schneider, S.E., Ahn, J.H., Kim, S.S.

To be published.

Macromolecule Content

Total Structure Weight: 171.27 kDa
Atom Count: 11,972
Modeled Residue Count: 1,452
Deposited Residue Count: 1,464
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dipeptidyl peptidase 4	A, B	732	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
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AZV Query on AZV Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	N-(4-{[({(2R)-3-[(3R)-3-amino-4-(2,4,5-trifluorophenyl)butanoyl]-1,3-thiazolidin-2-yl}carbonyl)amino]methyl}phenyl)-D-valine C₂₆ H₃₁ F₃ N₄ O₄ S ZUNWVBNRQTWJFD-WQWSHVPRSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.64 Å
R-Value Free: 0.324 (Depositor)
R-Value Work: 0.282 (Depositor), 0.272 (DCC)
R-Value Observed: 0.282 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.412	α = 90
b = 124.501	β = 90
c = 133.119	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2011-03-16

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-03-16
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2024-10-30
Changes: Data collection, Database references, Derived calculations, Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.